Administrative Appointments


  • Director, Morrison Institute for Population Biology and Resource Studies (1986 - Present)
  • Co-Director, Center for Computational, Evolutionary and Human Genetics (2012 - Present)

Program Affiliations


  • Center for East Asian Studies

Current Research and Scholarly Interests


Human genetic and cultural evolution, mathematical biology, demography of China

Projects


  • China Population Collaboration, Stanford univrsity and Xi'an Jiaotong University (June 10, 1991 - Present)

    We work on such issues as the male-biased sex ratio and its consequences for Chinese demography, the social and demographic ramifications of the massive rural-to urban migration, and the rapid aging of China's population

    Location

    China

  • Behavioral Ecology and Evolution, Stanford University and Tel Aviv University (May 6, 2004 - Present)

    Studies of data and mathematical modeld of foraging behavior

    Location

    Israel

  • Replacement of Neaderthals by Modern Humans, Stanford University and Meiji University (6/5/1986 - Present)

    Mathematical models of the competition between Modern Humans and Neanderthals in Europe through cultural Inheritance

    Location

    Japan

2023-24 Courses


Stanford Advisees


Graduate and Fellowship Programs


  • Biology (School of Humanities and Sciences) (Phd Program)

All Publications


  • Drowning in shallow causality. The Behavioral and brain sciences Shen, H., Feldman, M. W. 2023; 46: e199

    Abstract

    It has been known for decades that inference concerning genetic causes of human behavioral phenotypes cannot be legitimately made from correlations among relatives. We claim that these inferential difficulties cannot be overcome by assigning different names to causes inferred from within-family and population-level genome-wide association studies (GWASs). For educational attainment, for example, unraveling gene-environment interactions requires more than new names for causes.

    View details for DOI 10.1017/S0140525X22002278

    View details for PubMedID 37694932

  • Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics. PLoS computational biology Arthur, R. F., Levin, M., Labrogere, A., Feldman, M. W. 2023; 19 (9): e1011217

    Abstract

    Heterogeneity in contact patterns, mortality rates, and transmissibility among and between different age classes can have significant effects on epidemic outcomes. Adaptive behavior in response to the spread of an infectious pathogen may give rise to complex epidemiological dynamics. Here we model an infectious disease in which adaptive behavior incentives, and mortality rates, can vary between two and three age classes. The model indicates that age-dependent variability in infection aversion can produce more complex epidemic dynamics at lower levels of pathogen transmissibility and that those at less risk of infection can still drive complexity in the dynamics of those at higher risk of infection. Policymakers should consider the interdependence of such heterogeneous groups when making decisions.

    View details for DOI 10.1371/journal.pcbi.1011217

    View details for PubMedID 37669282

  • Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia. Proceedings. Biological sciences Aoki, K., Takahata, N., Oota, H., Wakano, J. Y., Feldman, M. W. 2023; 290 (2005): 20231262

    Abstract

    An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.

    View details for DOI 10.1098/rspb.2023.1262

    View details for PubMedID 37644833

  • Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis. Communications biology Lewin-Epstein, O., Jaques, Y., Feldman, M. W., Kaufer, D., Hadany, L. 2023; 6 (1): 782

    Abstract

    Recent studies revealed mechanisms by which the microbiome affects its host's brain, behavior and wellbeing, and that dysbiosis - persistent microbiome-imbalance - is associated with the onset and progress of various chronic diseases, including addictive behaviors. Yet, understanding of the ecological and evolutionary processes that shape the host-microbiome ecosystem and affect the host state, is still limited. Here we propose that competition dynamics within the microbiome, associated with host-microbiome mutual regulation, may promote dysbiosis and aggravate addictive behaviors. We construct a mathematical framework, modeling the dynamics of the host-microbiome ecosystem in response to alterations. We find that when this ecosystem is exposed to substantial perturbations, the microbiome may shift towards a composition that reinforces the new host state. Such a positive feedback loop augments post-perturbation imbalances, hindering attempts to return to the initial equilibrium, promoting relapse episodes and prolonging addictions. We show that the initial microbiome composition is a key factor: a diverse microbiome enhances the ecosystem's resilience, whereas lower microbiome diversity is more prone to lead to dysbiosis, exacerbating addictions. This framework provides evolutionary and ecological perspectives on host-microbiome interactions and their implications for host behavior and health, while offering verifiable predictions with potential relevance to clinical treatments.

    View details for DOI 10.1038/s42003-023-05099-0

    View details for PubMedID 37495841

  • Cultural niche construction with application to fertility control: A model for education and social transmission of contraceptive use. Theoretical population biology Denton, K. K., Kendal, J. R., Ihara, Y., Feldman, M. W. 2023

    Abstract

    The evolution of a cultural trait may be affected by niche construction, or changes in the selective environment of that trait due to the inheritance of other cultural traits that make up a cultural background. This study investigates the evolution of a cultural trait, such as the acceptance of the idea of contraception, that is both vertically and horizontally transmitted within a homogeneous social network. Individuals may conform to the norm, and adopters of the trait have fewer progeny than others. In addition, adoption of this trait is affected by a vertically transmitted aspect of the cultural background, such as the preference for high or low levels of education. Our model shows that such cultural niche construction can facilitate the spread of traits with low Darwinian fitness while providing an environment that counteracts conformity to norms. In addition, niche construction can facilitate the 'demographic transition' by making reduced fertility socially accepted.

    View details for DOI 10.1016/j.tpb.2023.06.001

    View details for PubMedID 37321354

  • Conditions that favour cumulative cultural evolution. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Denton, K. K., Ram, Y., Feldman, M. W. 2023; 378 (1872): 20210400

    Abstract

    The emergence of human societies with complex language and cumulative culture is considered a major evolutionary transition. Why such a high degree of cumulative culture is unique to humans is perplexing given the potential fitness advantages of cultural accumulation. Here, Boyd & Richerson's (1996 Why culture is common, but cultural evolution is rare. Proc. Br. Acad. 88, 77-93) discrete-cultural-trait model is extended to incorporate arbitrarily strong selection; conformist, anti-conformist and unbiased frequency-dependent transmission; random and periodic environmental variation; finite population size; and multiple 'skill levels.' From their infinite-population-size model with success bias and a single skill level, Boyd and Richerson concluded that social learning is favoured over individual learning under a wider range of conditions when social learning is initially common than initially rare. We find that this holds only if the number n of individuals observed by a social learner is sufficiently small, but with a finite population and/or a combination of success-biased and conformist or unbiased transmission, this result holds with larger n. Assuming social learning has reached fixation, the increase in a population's mean skill level is lower if cumulative culture is initially absent than initially present, if population size is finite, or if cultural transmission has a frequency-dependent component. Hence, multiple barriers to cultural accumulation may explain its rarity. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.

    View details for DOI 10.1098/rstb.2021.0400

    View details for PubMedID 36688392

  • Conformity and anti-conformity in a finite population. Journal of theoretical biology Lappo, E., Denton, K. K., Feldman, M. W. 2023: 111429

    Abstract

    Conformist and anti-conformist cultural transmission have been studied both empirically, in several species, and theoretically, with population genetic models. Building upon standard, infinite-population models (IPMs) of conformity, we introduce finite-population models (FPMs) and study them via simulation and a diffusion approximation. In previous IPMs of conformity, offspring observe the variants of n adult role models, where n is often three. Numerical simulations show that while the short-term behavior of the FPM with n=3 role models is well approximated by the IPM, stable polymorphic equilibria of the IPM become effective equilibria of the FPM at which the variation persists prior to fixation or loss, and which produce plateaus in curves for fixation probabilities and expected times to absorption. In the FPM with n=5 role models, the population may switch between two effective equilibria, which is not possible in the IPM, or may cycle between frequencies that are not effective equilibria, which is possible in the IPM. In all observed cases of 'equilibrium switching' and 'cycling' in the FPM, model parameters exceed O(1/N), required for the diffusion approximation, resulting in an over-estimation of the actual times to absorption. However, in those cases with n=5 role models that have one effective equilibrium and stable fixation states, even if conformity coefficients exceed O(1/N), the diffusion approximation matches closely the numerical simulations of the FPM. This suggests that the robustness of the diffusion approximation depends not only on the magnitudes of coefficients, but also on the qualitative behavior of the conformity model.

    View details for DOI 10.1016/j.jtbi.2023.111429

    View details for PubMedID 36746297

  • A memetic algorithm for finding multiple subgraphs that optimally cover an input network. PloS one He, X., Wang, Y., Du, H., Feldman, M. W. 2023; 18 (1): e0280506

    Abstract

    Finding dense subgraphs is a central problem in graph mining, with a variety of real-world application domains including biological analysis, financial market evaluation, and sociological surveys. While a series of studies have been devoted to finding subgraphs with maximum density, the problem of finding multiple subgraphs that best cover an input network has not been systematically explored. The present study discusses a variant of the densest subgraph problem and presents a mathematical model for optimizing the total coverage of an input network by extracting multiple subgraphs. A memetic algorithm that maximizes coverage is proposed and shown to be both effective and efficient. The method is applied to real-world networks. The empirical meaning of the optimal sampling method is discussed.

    View details for DOI 10.1371/journal.pone.0280506

    View details for PubMedID 36662749

  • Care-receivers' expected intergenerational support in aging rural China: A perspective of sustainable livelihoods and the sandwich effect SOCIAL SCIENCE JOURNAL Yang, B., Feldman, M. W., Li, S. 2022
  • Livelihood adaptive capacities and adaptation strategies of relocated households in rural China FRONTIERS IN SUSTAINABLE FOOD SYSTEMS Liu, W., Cheng, Y., Li, J., Feldman, M. 2022; 6
  • How Family Living Arrangements and Migration Distances Shape the Settlement Intentions of Rural Migrant Workers in China. International journal of environmental research and public health Che, L., Du, H., Jin, X., Feldman, M. W. 2022; 19 (23)

    Abstract

    Rural migrant workers and their families will decide the future of China's urbanization. Using data from the "China Migrants Dynamic Survey and Hundreds of Villages Investigation" carried out in 2018, we examine whether and how family living arrangements and migration distances shape rural migrant workers' settlement intentions in urban areas. In general, rural migrant workers' settlement intention is shown to be weak. However, individuals with children are more likely to have a stronger intention to settle permanently in urban areas. Among geographical factors, geospatial distance exerts a negative influence on migrant parents' settlement intention when the interaction effect of family living arrangements and migration distances is considered. Migrant families are increasingly concentrated in cities near their hometowns with a low entry barrier that allows them to gain access to better amenities. Socio-economic factors, especially disposable income, human resources, and housing conditions, play significant roles in migrant parents' settlement intention. The age and hometown region of migrant parents are also closely related to their intentions to settle in urban areas. Potential channels for the management of urbanization policy are also explored.

    View details for DOI 10.3390/ijerph192316308

    View details for PubMedID 36498381

    View details for PubMedCentralID PMC9741260

  • Polychotomous traits and evolution under conformity. Proceedings of the National Academy of Sciences of the United States of America Denton, K. K., Liberman, U., Feldman, M. W. 2022; 119 (39): e2205914119

    Abstract

    Conformist and anticonformist transmission of dichotomous cultural traits (i.e., traits with two variants) have been studied both experimentally, in many species, and theoretically, with mathematical models. Signatures of types of conformity to polychotomous traits (with more than two variants; e.g., baby names and syllables in bird song) have been inferred from population-level data, but there are few models that include individual-level biases among more than two discrete variants. We generalize the standard dichotomous trait conformity model by Boyd and Richerson to incorporate [Formula: see text] role models and [Formula: see text] variants. Our analysis shows that in the case of [Formula: see text] role models, under anticonformity, the central polymorphic equilibrium [Formula: see text] is globally stable, whereas under conformity, if initially the frequencies of [Formula: see text] variants are all equal to the maximum variant frequency in the population, there is global convergence to an equilibrium in which the frequencies of these variants are all [Formula: see text] and all other variants are absent. With a general number n of role models, the same result holds with conformity, whereas under anticonformity, global convergence is not guaranteed, and there may be stable frequency cycles or chaos. If both conformity and anticonformity occur for different configurations of variants among the n role models, a variety of novel polymorphic equilibria may exist and be stable. Future empirical studies may use this formulation to directly quantify an individual's level of (anti)conformist bias to a polychotomous trait.

    View details for DOI 10.1073/pnas.2205914119

    View details for PubMedID 36122242

  • How Does Migration Affect HIV Sexual Risk Behaviors Among Involuntary Bachelors? The Mediating Roles of Neighborhoods and Social Networks. Archives of sexual behavior Gou, H., Liu, H., Feldman, M. W. 2022

    Abstract

    The sex ratio imbalance in China since the 1980s has resulted in a large number of involuntary bachelors in rural China. Previous studies have found an association between migration and HIV sexual risk behaviors among involuntary bachelors, but how migration affects these bachelors' HIV sexual risk behaviors remain poorly understood. Using data from a cross-sectional survey in 2017 (a sample of 740 male respondents who had rural household registration, had never been married, and were aged 28-49 years), we investigated the relationship between migration and HIV sexual risk behaviors. Logistic regressions show that migration, neighborhood characteristics, and social networks were significantly associated with commercial sex and multiple sex partners, whereas only neighborhood characteristics and social networks were positively correlated with sexual partnership concurrency. Neighborhood characteristics and social networks mediated the relationships of migration with commercial sex and migration with multiple sex partners. Social networks mediated the association between neighborhood characteristics and concurrency. Multiple-step mediation analysis showed that the indirect effect of migration on commercial sex and multiple sexual partners through neighborhood characteristics and social networks was significant. Our findings suggest that further interventions should address neighborhood characteristics and social networks together.

    View details for DOI 10.1007/s10508-022-02391-8

    View details for PubMedID 36044127

  • Short-Term Dairy Product Elimination and Reintroduction Minimally Perturbs the Gut Microbiota in Self-Reported Lactose-Intolerant Adults. mBio Smith, C. J., Dethlefsen, L., Gardner, C., Nguyen, L., Feldman, M., Costello, E. K., Kolodny, O., Relman, D. A. 2022: e0105122

    Abstract

    An outstanding question regarding the human gut microbiota is whether and how microbiota-directed interventions influence host phenotypic traits. Here, we employed a dietary intervention to probe this question in the context of lactose intolerance. To assess the effects of dietary dairy product elimination and (re)introduction on the microbiota and host phenotype, we studied 12 self-reported mildly lactose-intolerant adults with triweekly collection of fecal samples over a 12-week study period: 2weeks of baseline diet, 4weeks of dairy product elimination, and 6weeks of gradual whole cow milk (re)introduction. Of the 12 subjects, 6 reported either no dairy or only lactose-free dairy product consumption. A clinical assay for lactose intolerance, the hydrogen breath test, was performed before and after each of these three study phases, and 16S rRNA gene amplicon sequencing was performed on all fecal samples. We found that none of the subjects showed change in a clinically defined measure of lactose tolerance. Similarly, fecal microbiota structure resisted modification. Although the mean fraction of the genus Bifidobacterium, a group known to metabolize lactose, increased slightly with milk (re)introduction (from 0.0125 to 0.0206; Wilcoxon P=0.068), the overall structure of each subject's gut microbiota remained highly individualized and largely stable in the face of diet manipulation. IMPORTANCE Lactose intolerance is a gastrointestinal disorder diagnosed with a lactose hydrogen breath test. Lifestyle changes such as diet interventions can impact the gut microbiome; however, the role of the microbiome in lactose intolerance is unclear. Our study assessed the effects of a 12-week dietary dairy product elimination and (re)introduction on the microbiome and clinical lactose intolerance status in 12 adult self-reported lactose-intolerant individuals. We found each subject's gut microbiome remained highly individualized and largely stable in the face of this diet manipulation. We also report that none of the subjects showed change in a clinically defined measure of lactose tolerance.

    View details for DOI 10.1128/mbio.01051-22

    View details for PubMedID 35695459

  • Success-biased social learning in a one-consumer, two-resource model. Theoretical population biology Borofsky, T., Feldman, M. W. 2022

    Abstract

    Previous analyses have predicted that social learning should not evolve in a predator-prey system. Here we examine whether success-biased social learning, by which social learners copy successful demonstrators, allows social learning by foragers to evolve. We construct a one-predator, two-prey system in which foragers must learn how to feed on depletable prey populations in an environment where foraging information can be difficult to obtain individually. We analyze two models in which social learning is success-biased: in the first, individual learning does not depend on the resource dynamics, and in the second model it depends on the relative frequency of the resource. Unlike previous results, we find that social learning does not cause predators to over-harvest one type of prey over the other. Furthermore, increasing the probability of social learning increases the probability of learning a successful foraging behavior, especially when individually learned information tends to be inaccurate. Whereas social learning does not evolve among individual learners in the first model, the assumption of resource-dependent learning in the second model allows a mutant with an increased probability of social learning to spread through the forager population.

    View details for DOI 10.1016/j.tpb.2022.05.004

    View details for PubMedID 35709950

  • Diversity and its causes: Lewontin on racism, biological determinism and the adaptationist programme. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Shen, H., Feldman, M. W. 2022; 377 (1852): 20200417

    Abstract

    Lewontin's 1972 paper (RC Lewontin, 1972 The apportionment of human diversity, in Evolutionary biology, vol. 6 (eds T Dobzhansky, MK Hecht, WC Steere), pp. 381-398) can be viewed as one foray in his battle against biological determinism. Our paper shows where Lewontin, The apportionment of human diversity, fits in the debate over human classification that it stimulated. We outline three assumptions inherent in the biological deterministic view of human phenotypic diversity and show how the 1972 paper, as well as Lewontin's papers in 1970 and 1974 on the problems with the heritability statistic and his 1979 criticism of naive pan-selectionism, invalidate these assumptions. These papers were crucial components of his campaign against biological determinism and the racism with which it was associated. In the current climate of widespread racism and the rise of sociogenomics, it is important to revisit Lewontin's writings and to disseminate the messages they contain. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

    View details for DOI 10.1098/rstb.2020.0417

    View details for PubMedID 35430891

  • Disaster Resettlement and Adaptive Capacity among Rural Households in China SOCIETY & NATURAL RESOURCES Xu, J., Liu, W., Li, J., Li, C., Feldman, M. 2022
  • Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa. Current biology : CB Gopalan, S., Berl, R. E., Myrick, J. W., Garfield, Z. H., Reynolds, A. W., Bafens, B. K., Belbin, G., Mastoras, M., Williams, C., Daya, M., Negash, A. N., Feldman, M. W., Hewlett, B. S., Henn, B. M. 2022

    Abstract

    The fate of hunting and gathering populations following the rise of agriculture and pastoralism remains a topic of debate in the study of human prehistory. Studies of ancient and modern genomes have found that autochthonous groups were largely replaced by expanding farmer populations with varying levels of gene flow, a characterization that is influenced by the almost universal focus on the European Neolithic.1-5 We sought to understand the demographic impact of an ongoing cultural transition to farming in Southwest Ethiopia, one of the last regions in Africa to experience such shifts.6 Importantly, Southwest Ethiopia is home to several of the world's remaining hunter-gatherer groups, including the Chabu people, who are currently transitioning away from their traditional mode of subsistence.7 We generated genome-wide data from the Chabu and four neighboring populations, the Majang, Shekkacho, Bench, and Sheko, to characterize their genetic ancestry and estimate their effective population sizes over the last 60 generations. We show that the Chabu are a distinct population closely related to ancient people who occupied Southwest Ethiopia >4,500 years ago. Furthermore, the Chabu are undergoing a severe population bottleneck, which began approximately 1,400 years ago. By analyzing eleven Eastern African populations, we find evidence for divergent demographic trajectories among hunter-gatherer-descendant groups. Our results illustrate that although foragers respond to encroaching agriculture and pastoralism with multiple strategies, including cultural adoption of agropastoralism, gene flow, and economic specialization, they often face population decline.

    View details for DOI 10.1016/j.cub.2022.02.050

    View details for PubMedID 35271793

  • Differential application of cultural practices at the family and individual levels may alter heritability estimates. The Behavioral and brain sciences Kolodny, O., Feldman, M. W., Lotem, A., Ram, Y. 2022; 45: e167

    Abstract

    Uchiyama et al. emphasize that culture evolves directionally and differentially as a function of selective pressures in different populations. Extending these principles to the level of families, lineages, and individuals exposes additional challenges to estimating heritability. Cultural traits expressed differentially as a function of the genetics whose influence they mask or unmask render inseparable the influences of culture and genetics.

    View details for DOI 10.1017/S0140525X21001576

    View details for PubMedID 36098428

  • Static environments with limited resources select for multiple foraging strategies rather than conformity ECOLOGICAL MONOGRAPHS Borofsky, T. M., Feldman, M. W. 2021

    View details for DOI 10.1002/ecm.1483

    View details for Web of Science ID 000728706800001

  • Advantages of being bicultural: Acculturation and mental health among rural-urban migrants in China CITIES Yue, Z., Wang, B., Li, S., Fong, E., Feldman, M. W. 2021; 119
  • Conformity and content-biased cultural transmission in the evolution of altruism. Theoretical population biology Denton, K. K., Ram, Y., Feldman, M. W. 2021

    Abstract

    The evolution of altruism has been extensively modeled under the assumption of genetic transmission, whereas the dynamics under cultural transmission are less well understood. Previous research has shown that cultural transmission can facilitate the evolution of altruism by increasing 1) the probability of adopting the altruistic phenotype, and 2) assortment between altruists. We incorporate vertical and oblique transmission, which can be conformist or anti-conformist, into models of parental care, sibling altruism, and altruism between individuals that meet assortatively. If oblique transmission is conformist, it becomes easier for altruism to invade a population of non-altruists as the probability of vertical transmission increases. If oblique transmission is anti-conformist, decreasing vertical transmission facilitates invasion by altruism in the assortative meeting model, whereas in other models, there is a trade-off: greater vertical transmission produces greater assortment among genetically related altruists, but lowers the probability of adopting altruism via anti-conformity. Compared to conditions for invasion under genetic transmission, e.g., Hamilton's rule, we show that invasion can be easier with sufficiently strong anti-conformity, and in some models, with sufficiently high assortment even if oblique transmission is conformist. We also explore invasion by an allele A that increases individuals' content bias for altruism, in the absence of other forms of cultural transmission. If costs and benefits combine additively, A invades under previously known conditions. If costs and benefits combine multiplicatively, invasion by A and by altruism become more difficult than in the corresponding additive models.

    View details for DOI 10.1016/j.tpb.2021.10.004

    View details for PubMedID 34793823

  • Socioeconomic Status, Institutional Power, and Body Mass Index among Chinese Adults. International journal of environmental research and public health Li, W., Li, S., Feldman, M. W. 2021; 18 (20)

    Abstract

    Despite the vast literature on the socioeconomic status (SES) gradient of obesity among adult people, no study has investigated the relationship between institutional power and body mass index. Using national survey data from the "China Labor-force Dynamics Survey 2016" (CLDS 2016), multistage cluster-stratified probability proportional to size (PPS) sampling was employed to select cases from 29 provinces, cities, and autonomous regions in China. This study adopts an institutional approach to explore the influences of SES and institutional power on the state of being overweight or severely overweight (obese) among Chinese adults. It is shown that SES has a non-linear influence on being overweight or obese, higher education has a negative effect on being overweight or obese, income has an inverted U-shaped effect on being overweight or obese, and having a managerial or administrative job has a positive effect on being overweight but less so on obesity. These findings reveal that disparities in health outcome and risks are due to inequality in SES. The work unit is a stronger predictor of adults being overweight or obese than occupation. Working in the public sector has a positive effect on being overweight relative to working in the private sector, and only state institutions and government departments have a positive association with obesity. Our results indicate that institutional structure still has effects on individuals' life chances in the era of China's market transition.

    View details for DOI 10.3390/ijerph182010620

    View details for PubMedID 34682366

  • The Risk of HIV/STDs Infection and Transmission Among Never-Married Male Migrants in China: Is Risk Attributable to Bachelorhood or Migration? Archives of sexual behavior Liu, H., Wang, H., Feldman, M. 2021

    Abstract

    In the context of sex-ratio imbalance and rural-to-urban migration in China, never-married male migrants may become a vulnerable group as well as a bridge population that facilitates HIV/STDs transmission. It is still not clear, however, whether increased HIV/STDs transmission risk can be attributed to bachelorhood, migration, or both. This study identified the contributions of bachelorhood and migration to an increased risk of HIV/STDs infection, as well as the risk of HIV/STDs transmission across populations and regions. Data were from a cross-sectional questionnaire survey, in which 180 never-married non-migrant males in rural areas, 558 never-married male migrants, and 302 married male migrants in urban areas of China were interviewed in 2017. Results showed that never-married male migrants are more likely to engage in commercial sex and unsafe sex than never-married non-migrant males, and their likelihood of engaging in unsafe sex was also higher than married male migrants. Although never-married male migrants were less likely to have multiple sex partners than married male migrants, they were more likely to have multiple sex partners and sex partners from different regions than never-married non-migrant males. These findings indicate that both migration and bachelorhood increase the risk of HIV/STDs infection for never-married male migrants, and migration also increases the risk of HIV/STDs transmission across populations and regions.

    View details for DOI 10.1007/s10508-021-02015-7

    View details for PubMedID 34606023

  • Poverty and income inequality effects of the relocation program in Shaanxi, China ASIAN-PACIFIC ECONOMIC LITERATURE Li, C., Wang, L., Feldman, M. W., Li, S. 2021

    View details for DOI 10.1111/apel.12336

    View details for Web of Science ID 000698506000001

  • On randomly changing conformity bias in cultural transmission. Proceedings of the National Academy of Sciences of the United States of America Denton, K. K., Liberman, U., Feldman, M. W. 2021; 118 (34)

    Abstract

    Humans and nonhuman animals display conformist as well as anticonformist biases in cultural transmission. Whereas many previous mathematical models have incorporated constant conformity coefficients, empirical research suggests that the extent of (anti)conformity in populations can change over time. We incorporate stochastic time-varying conformity coefficients into a widely used conformity model, which assumes a fixed number n of "role models" sampled by each individual. We also allow the number of role models to vary over time ([Formula: see text]). Under anticonformity, nonconvergence can occur in deterministic and stochastic models with different parameter values. Even if strong anticonformity may occur, if conformity or random copying (i.e., neither conformity nor anticonformity) is expected, there is convergence to one of the three equilibria seen in previous deterministic models of conformity. Moreover, this result is robust to stochastic variation in [Formula: see text] However, dynamic properties of these equilibria may be different from those in deterministic models. For example, with random conformity coefficients, all equilibria can be stochastically locally stable simultaneously. Finally, we study the effect of randomly changing weak selection. Allowing the level of conformity, the number of role models, and selection to vary stochastically may produce a more realistic representation of the wide range of group-level properties that can emerge under (anti)conformist biases. This promises to make interpretation of the effect of conformity on differences between populations, for example those connected by migration, rather difficult. Future research incorporating finite population sizes and migration would contribute added realism to these models.

    View details for DOI 10.1073/pnas.2107204118

    View details for PubMedID 34417299

  • Effects of cultural transmission of surnaming decisions on the sex ratio at birth. Theoretical population biology Liu, X., Feldman, M. W. 2021

    Abstract

    The patriarchal tradition of surnaming a child after its father in Han Chinese families may contribute to their preference for sons, a major cause of the abnormally high SRB (sex ratio at birth) in China. This high SRB can subsequently contribute to the marriage squeeze on males of marriageable age. Encouraging matrilineal surnaming has been proposed as a strategy that could potentially reduce son preference and help to adjust the imbalance in SRB. Here, we model factors that are likely to influence surnaming decisions, including cultural transmission of parents' surnaming decisions, the cultural value of a daughter, reward given to matrilineal surnaming, and awareness of current imbalance in SRB. Mathematical and computational analyses suggest that offering a significant reward and raising public awareness of the problems inherent in an excess of marriage-age males may overcome the son preference and reduce the male-biased SRB.

    View details for DOI 10.1016/j.tpb.2021.07.001

    View details for PubMedID 34358559

  • Public Participation and Governance Performance in Gender-Imbalanced Central Rural China: The Roles of Trust and Risk Perception SOCIAL SCIENCES-BASEL Song, R., Li, S., Feldman, M. W. 2021; 10 (7)
  • Sexual network and condom use among male migrants in the context of China's gender imbalance. AIDS care Zhao, M., Liu, H., Chen, X., Feldman, M. W. 2021: 1-5

    Abstract

    In the context of China's gender imbalance, this study addresses the characteristics of sexual networks and their association with condom use in a sample of 713 male migrants (aged 28-64) who have rural hukou (household registration) in China. Descriptive statistics, univariate analyses, and multilevel random intercept models were used to investigate the characteristics of sexual networks and their associations with condom use. We found that age, marital status, type of sex partners, support (the main help given to each sex partner by the participant), type of sexual intercourse, and stability of sexual relationships were associated with condom use. The sexual networks were mainly composed of sex partners of similar age (58.46%), unmarried people (50.53%), and regular partners (49.38%). Married male migrants were more likely to use condoms with casual partners; unmarried male migrants were less likely to use condoms in emotional and stable relationships. Variation in individual factors, sex partners, and sexual relationship characteristics contribute to participation in condomless sex by male migrants. HIV prevention strategies should target unmarried male migrants and their casual sex partners by increasing their awareness of the risk of HIV transmission and the availability of free condoms.

    View details for DOI 10.1080/09540121.2021.1938965

    View details for PubMedID 34115571

  • Non-vertical cultural transmission, assortment and the evolution of cooperation. Proceedings. Biological sciences Cohen, D., Lewin-Epstein, O., Feldman, M. W., Ram, Y. 2021; 288 (1951): 20203162

    Abstract

    Cultural evolution of cooperation under vertical and non-vertical cultural transmission is studied, and conditions are found for fixation and coexistence of cooperation and defection. The evolution of cooperation is facilitated by its horizontal transmission and by an association between social interactions and horizontal transmission. The effect of oblique transmission depends on the horizontal transmission bias. Stable polymorphism of cooperation and defection can occur, and when it does, reduced association between social interactions and horizontal transmission evolves, which leads to a decreased frequency of cooperation and lower population mean fitness. The deterministic conditions are compared to outcomes of stochastic simulations of structured populations. Parallels are drawn with Hamilton's rule incorporating relatedness and assortment.

    View details for DOI 10.1098/rspb.2020.3162

    View details for PubMedID 34034521

  • Marriage, Health, and Old-Age Support: Risk to Rural Involuntary Bachelors' Family Development in Contemporary China. Asian bioethics review Meng, Y., Yang, B., Li, S., Feldman, M. W. 2021; 13 (1): 77-89

    Abstract

    In the traditional system of Chinese families, individuals are embedded in the institution of the family with defined obligations to enhance family development. As a consequence of the male-biased sex ratio at birth in China since the 1980s, an increasing number of surplus rural males have been affected by a marriage squeeze becoming involuntary bachelors. Under China's universal heterosexual marriage tradition, family development of rural involuntary bachelors has largely been ignored, but in China's gender-imbalanced society, it is necessary to adopt a family-based approach to identify and study the plight of rural involuntary bachelors. Studies on gender imbalance indicate that these men face multiple risks from the perspectives of their life course, the family life cycle, and the family ethic. To a certain extent, these risks are caused by a conflict between the individual's family life and family ethics and are mainly reflected in problems concerning marriage, health, and old-age support. Not only do these vulnerabilities affect the individual and family development across the whole life cycle but also pose major risks to social development in the face of strong gender imbalance. In order to deal with risks faced by rural involuntary bachelors, core ethical principles, including autonomy, beneficence, and justice, need to be adopted. Through adjustments to informal support provided by the family and formal support provided by policy-makers, risk of uncertainty in family development faced by rural involuntary bachelors could be reduced.

    View details for DOI 10.1007/s41649-020-00163-x

    View details for PubMedID 33717348

    View details for PubMedCentralID PMC7813918

  • Ethical considerations and community engagement experiences of the Afromexico Genomics Project Avila Arcos, M. C., Sanchez Romero, G., Moreno-Estrada, A., Bustamante, C. D., Feldman, M. W. WILEY. 2021: 6–7
  • Designing gene drives to limit spillover to non-target populations. PLoS genetics Greenbaum, G., Feldman, M. W., Rosenberg, N. A., Kim, J. 2021; 17 (2): e1009278

    Abstract

    The prospect of utilizing CRISPR-based gene-drive technology for controlling populations has generated much excitement. However, the potential for spillovers of gene-drive alleles from the target population to non-target populations has raised concerns. Here, using mathematical models, we investigate the possibility of limiting spillovers to non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene-drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene drive parameters, but, in most cases, only under relatively low migration rates between populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. We apply our model to two potential applications of gene drives-field trials for malaria-vector gene drives and control of invasive species on islands. We discuss theoretical predictions of key requirements for differential targeting and their practical implications.

    View details for DOI 10.1371/journal.pgen.1009278

    View details for PubMedID 33630838

  • Adaptive social contact rates induce complex dynamics during epidemics. PLoS computational biology Arthur, R. F., Jones, J. H., Bonds, M. H., Ram, Y., Feldman, M. W. 2021; 17 (2): e1008639

    Abstract

    Epidemics may pose a significant dilemma for governments and individuals. The personal or public health consequences of inaction may be catastrophic; but the economic consequences of drastic response may likewise be catastrophic. In the face of these trade-offs, governments and individuals must therefore strike a balance between the economic and personal health costs of reducing social contacts and the public health costs of neglecting to do so. As risk of infection increases, potentially infectious contact between people is deliberately reduced either individually or by decree. This must be balanced against the social and economic costs of having fewer people in contact, and therefore active in the labor force or enrolled in school. Although the importance of adaptive social contact on epidemic outcomes has become increasingly recognized, the most important properties of coupled human-natural epidemic systems are still not well understood. We develop a theoretical model for adaptive, optimal control of the effective social contact rate using traditional epidemic modeling tools and a utility function with delayed information. This utility function trades off the population-wide contact rate with the expected cost and risk of increasing infections. Our analytical and computational analysis of this simple discrete-time deterministic strategic model reveals the existence of an endemic equilibrium, oscillatory dynamics around this equilibrium under some parametric conditions, and complex dynamic regimes that shift under small parameter perturbations. These results support the supposition that infectious disease dynamics under adaptive behavior change may have an indifference point, may produce oscillatory dynamics without other forcing, and constitute complex adaptive systems with associated dynamics. Implications for any epidemic in which adaptive behavior influences infectious disease dynamics include an expectation of fluctuations, for a considerable time, around a quasi-equilibrium that balances public health and economic priorities, that shows multiple peaks and surges in some scenarios, and that implies a high degree of uncertainty in mathematical projections.

    View details for DOI 10.1371/journal.pcbi.1008639

    View details for PubMedID 33566839

  • Marriage, Health, and Old-Age Support: Risk to Rural Involuntary Bachelors' Family Development in Contemporary China ASIAN BIOETHICS REVIEW Meng, Y., Yang, B., Li, S., Feldman, M. W. 2021
  • Jaw Epidemic: A Reply to Singh BIOSCIENCE Kahn, S., Ehrlich, P., Feldman, M., Sapolsky, R., Wong, S. 2020; 70 (12): 1044
  • The status of perceived community resilience in transitional rural society: An empirical study from central China JOURNAL OF RURAL STUDIES Yang, B., Feldman, M. W., Li, S. 2020; 80: 427–38
  • The power of randomization by sex in multilocus genetic evolution. Biology direct Vasylenko, L., Feldman, M. W., Livnat, A. 2020; 15 (1): 26

    Abstract

    BACKGROUND: Many hypotheses have been proposed for how sexual reproduction may facilitate an increase in the population mean fitness, such as the Fisher-Muller theory, Muller's ratchet and others. According to the recently proposed mixability theory, however, sexual recombination shifts the focus of natural selection away from favoring particular genetic combinations of high fitness towards favoring alleles that perform well across different genetic combinations. Mixability theory shows that, in finite populations, because sex essentially randomizes genetic combinations, if one allele performs better than another across the existing combinations of alleles, that allele will likely also perform better overall across a vast space of untested potential genotypes. However, this superiority has been established only for a single-locus diploid model.RESULTS: We show that, in both haploids and diploids, the power of randomization by sex extends to the multilocus case, and becomes substantially stronger with increasing numbers of loci. In addition, we make an explicit comparison between the sexual and asexual cases, showing that sexual recombination is the cause of the randomization effect.CONCLUSIONS: That the randomization effect applies to the multilocus case and becomes stronger with increasing numbers of loci suggests that it holds under realistic conditions. One may expect, therefore, that in nature the ability of an allele to perform well in interaction with existing genetic combinations is indicative of how well it will perform in a far larger space of potential combinations that have not yet materialized and been tested. Randomization plays a similar role in a statistical test, where it allows one to draw an inference from the outcome of the test in a small sample about its expected outcome in a larger space of possibilities-i.e., to generalize. Our results are relevant to recent theories examining evolution as a learning process.REVIEWERS: This article was reviewed by David Ardell and Brian Golding.

    View details for DOI 10.1186/s13062-020-00277-0

    View details for PubMedID 33225949

  • Loss of genetic variation in the two-locus multiallelic haploid model. Theoretical population biology Pontz, M., Feldman, M. W. 2020

    Abstract

    In the evolutionary biology literature, it is generally assumed that for deterministic frequency-independent haploid selection models, no polymorphic equilibrium can be stable in the absence of variation-generating mechanisms such as mutation. However, mathematical analyses that corroborate this claim are scarce and almost always depend upon additional assumptions. Using ideas from game theory, we show that a monomorphism is a global attractor if one of its alleles dominates all other alleles at its locus. Further, we show that no isolated equilibrium exists, at which an unequal number of alleles from two loci is present. Under the assumption of convergence of trajectories to equilibrium points, we resolve the two-locus three-allele case for a fitness scheme formally equivalent to the classical symmetric viability model. We also provide an alternative proof for the two-locus two-allele case.

    View details for DOI 10.1016/j.tpb.2020.10.001

    View details for PubMedID 33221333

  • The Status of Family Resilience: Effects of Sustainable Livelihoods in Rural China SOCIAL INDICATORS RESEARCH Yang, B., Feldman, M. W., Li, S. 2020
  • Evolution of transmission modifiers under frequency-dependent selection and transmission in constant or fluctuating environments. Theoretical population biology Shen, H., Liberman, U., Feldman, M. 2020

    Abstract

    Although the Reduction Principle for rates of mutation, migration, and recombination has been proved for large populations under constant selection, the fate of modifiers of these evolutionary forces under frequency-dependent or fluctuating selection is, in general, less well understood. Here we study modifiers of transmission, which include modifiers of mutation and oblique cultural transmission, under frequency-dependent and cyclically fluctuating selection, and develop models for which the Reduction Principle fails. We show that whether increased rates of transmission can evolve from an equilibrium at which there is zero transmission (for example, no mutation) depends on the number of alleles among which transmission is occurring. In addition, properties of the zero-transmission state are clarified.

    View details for DOI 10.1016/j.tpb.2020.09.001

    View details for PubMedID 32926905

  • The Jaw Epidemic: Recognition, Origins, Cures, and Prevention BIOSCIENCE Kahn, S., Ehrlich, P., Feldman, M., Sapolsky, R., Wong, S. 2020; 70 (9): 759–71

    Abstract

    Contemporary humans are living very different lives from those of their ancestors, and some of the changes have had serious consequences for health. Multiple chronic "diseases of civilization," such as cardiovascular problems, cancers, ADHD, and dementias are prevalent, increasing morbidity rates. Stress, including the disruption of traditional sleep patterns by modern lifestyles, plays a prominent role in the etiology of these diseases, including obstructive sleep apnea. Surprisingly, jaw shrinkage since the agricultural revolution, leading to an epidemic of crooked teeth, a lack of adequate space for the last molars (wisdom teeth), and constricted airways, is a major cause of sleep-related stress. Despite claims that the cause of this jaw epidemic is somehow genetic, the speed with which human jaws have changed, especially in the last few centuries, is much too fast to be evolutionary. Correlation in time and space strongly suggests the symptoms are phenotypic responses to a vast natural experiment-rapid and dramatic modifications of human physical and cultural environments. The agricultural and industrial revolutions have produced smaller jaws and less-toned muscles of the face and oropharynx, which contribute to the serious health problems mentioned above. The mechanism of change, research and clinical trials suggest, lies in orofacial posture, the way people now hold their jaws when not voluntarily moving them in speaking or eating and especially when sleeping. The critical resting oral posture has been disrupted in societies no longer hunting and gathering. Virtually all aspects of how modern people function and rest are radically different from those of our ancestors. We also briefly discuss treatment of jaw symptoms and possible clinical cures for individuals, as well as changes in society that might lead to better care and, ultimately, prevention.

    View details for DOI 10.1093/biosci/biaa073

    View details for Web of Science ID 000580986300005

    View details for PubMedID 32973408

    View details for PubMedCentralID PMC7498344

  • Widowhood and mortality risk of older people in rural China: do gender and living arrangement make a difference? AGEING & SOCIETY Liu, H., Jiang, Q., Feldman, M. W. 2020; 40 (9): 1939–55
  • A new perspective for mitigation of SARS-CoV-2 infection: priming the innate immune system for viral attack OPEN BIOLOGY Kolodny, O., Berger, M., Feldman, M. W., Ram, Y. 2020; 10 (7)
  • A new perspective for mitigation of SARS-CoV-2 infection: priming the innate immune system for viral attack. Open biology Kolodny, O., Berger, M., Feldman, M. W., Ram, Y. 2020; 10 (7): 200138

    Abstract

    The course of infection by SARS-CoV-2 frequently includes a long asymptomatic period, followed in some individuals by an immune dysregulation period that may lead to complications and immunopathology-induced death. This course of disease suggests that the virus often evades detection by the innate immune system. We suggest a novel therapeutic approach to mitigate the infection's severity, probability of complications and duration. We propose that priming an individual's innate immune system for viral attack shortly before it is expected to occur may allow pre-activation of the preferable trajectory of immune response, leading to early detection of the virus. Priming can be carried out, for example, by administering a standard vaccine or another reagent that elicits a broad anti-viral innate immune response. By the time that the expected SARS-CoV-2 infection occurs, activation cascades will have been put in motion and levels of immune factors needed to combat the infection will have been elevated. The infection would thus be cleared faster and with less complication than otherwise, alleviating adverse clinical outcomes at the individual level. Moreover, priming may also mitigate population-level risk by reducing need for hospitalizations and decreasing the infectious period of individuals, thus slowing the spread and reducing the impact of the epidemic. In view of the latter consideration, our proposal may have a significant epidemiological impact even if applied primarily to low-risk individuals, such as young adults, who often show mild symptoms or none, by shortening the period during which they unknowingly infect others. The proposed view is, at this time, an unproven hypothesis. Although supported by robust bio-medical reasoning and multiple lines of evidence, carefully designed clinical trials are necessary.

    View details for DOI 10.1098/rsob.200138

    View details for PubMedID 36416599

  • L. Luca Cavalli-Sforza: A Renaissance Scientist THEORETICAL POPULATION BIOLOGY Feldman, M. W. 2020; 133: 75–79
  • Is change of natural capital essential for assessing relocation policies? A case from Baihe county in western China IMPACT ASSESSMENT AND PROJECT APPRAISAL Xiao, Q., Liu, H., Feldman, M. W. 2020
  • The Impact of the Anti-Poverty Relocation and Settlement Program on Rural Households' Well-Being and Ecosystem Dependence: Evidence from Western China SOCIETY & NATURAL RESOURCES Li, C., Guo, M., Li, S., Feldman, M. 2020
  • The sexual networks of female sex workers and potential HIV transmission risk: an entertainment venue-based study in Shaanxi, China. International journal of STD & AIDS Liu, H. n., Zhao, M. n., Wang, Y. n., Feldman, M. W., Xiao, Q. n. 2020: 956462419886780

    View details for DOI 10.1177/0956462419886780

    View details for PubMedID 32192372

  • High-resolution inference of genetic relationships among Jewish populations. European journal of human genetics : EJHG Kopelman, N. M., Stone, L. n., Hernandez, D. G., Gefel, D. n., Singleton, A. B., Heyer, E. n., Feldman, M. W., Hillel, J. n., Rosenberg, N. A. 2020

    Abstract

    Recent studies have used genome-wide single-nucleotide polymorphisms (SNPs) to investigate relationships among various Jewish populations and their non-Jewish historical neighbors, often focusing on small subsets of populations from a limited geographic range or relatively small samples within populations. Here, building on the significant progress that has emerged from genomic SNP studies in the placement of Jewish populations in relation to non-Jewish populations, we focus on population structure among Jewish populations. In particular, we examine Jewish population-genetic structure in samples that span much of the historical range of Jewish populations in Europe, the Middle East, North Africa, and South Asia. Combining 429 newly genotyped samples from 29 Jewish and 3 non-Jewish populations with previously reported genotypes on Jewish and non-Jewish populations, we investigate variation in 2789 individuals from 114 populations at 486,592 genome-wide autosomal SNPs. Using multidimensional scaling analysis, unsupervised model-based clustering, and population trees, we find that, genetically, most Jewish samples fall into four major clusters that largely represent four culturally defined groupings, namely the Ashkenazi, Mizrahi, North African, and Sephardi subdivisions of the Jewish population. We detect high-resolution population structure, including separation of the Ashkenazi and Sephardi groups and distinctions among populations within the Mizrahi and North African groups. Our results refine knowledge of Jewish population-genetic structure and contribute to a growing understanding of the distinctive genetic ancestry evident in closely related but historically separate Jewish communities.

    View details for DOI 10.1038/s41431-019-0542-y

    View details for PubMedID 31919450

  • Genetic nurturing, missing heritability, and causal analysis in genetic statistics. Proceedings of the National Academy of Sciences of the United States of America Shen, H. n., Feldman, M. W. 2020

    Abstract

    Genetic nurturing, the effect of parents' genotypes on offspring phenotypes through parental phenotypic transmission, can be modeled in terms of gene-culture interactions. This paper first uses a simple one-locus, two-phenotype gene-culture cotransmission model to compute the effect of genetic nurturing in terms of regression of children's phenotypes on transmitted and nontransmitted alleles. With genetic nurturing, interpreting heritability and hence the meaning of "missing heritability" becomes problematic. Other factors, for example, population subdivision and assortative mating, generate similar signals to those of genetic nurturing, namely, correlation between parents' nontransmitted alleles and children's phenotypes. Corrections must be made for these to isolate the signal of genetic nurturing. Finally, a unified causal framework is constructed for genetic nurturing, population subdivision, and assortative mating. Causal and noncausal paths from transmitted and nontransmitted alleles to children's phenotypes are identified and investigated in the presence of genetic nurturing, population subdivision, and assortative mating. Using causal analysis, assumptions made in inferring direct and indirect effects are then clarified and evaluated in a broader causal context.

    View details for DOI 10.1073/pnas.2015869117

    View details for PubMedID 32989124

  • Migration, Social Networks, and HIV Sexual Risk Behaviors Among Involuntary Bachelors in Rural China. AIDS and behavior Gou, H. n., Liu, H. n., Wang, Y. n., Li, X. n., Feldman, M. W. 2020

    Abstract

    In rural China there is an abnormally high male-biased sex ratio. The result is a large number of involuntary bachelors. This study examines how migration and social networks relate to bachelors' sexual risk behaviors. Data are from a cross-sectional questionnaire survey in which 740 male respondents who had rural household registration, had never married, and were aged 28 or older were interviewed in 2017. Logistic regression reveals that both migration and social networks place the bachelors at an especially high risk of HIV transmission by increasing the chance that they engage in commercial sex, whereas only social networks are significantly associated with sexual partnership concurrency. Additionally, social networks mediate the association between migration and commercial sex. This suggests that social networks play an important role in bachelors' risk of HIV transmission and that further intervention should address their social networks.

    View details for DOI 10.1007/s10461-020-03052-4

    View details for PubMedID 32990878

  • Cultural evolution of conformity and anticonformity. Proceedings of the National Academy of Sciences of the United States of America Denton, K. K., Ram, Y. n., Liberman, U. n., Feldman, M. W. 2020

    Abstract

    Conformist bias occurs when the probability of adopting a more common cultural variant in a population exceeds its frequency, and anticonformist bias occurs when the reverse is true. Conformist and anticonformist bias have been widely documented in humans, and conformist bias has also been observed in many nonhuman animals. Boyd and Richerson used models of conformist and anticonformist bias to explain the evolution of large-scale cooperation, and subsequent research has extended these models. We revisit Boyd and Richerson's original analysis and show that, with conformity based on more than three role models, the evolutionary dynamics can be more complex than previously assumed. For example, we show the presence of stable cycles and chaos under strong anticonformity and the presence of new equilibria when both conformity and anticonformity act at different variant frequencies, with and without selection. We also investigate the case of population subdivision with migration and find that the common claim that conformity can maintain between-group differences is not always true. Therefore, the effect of conformity on the evolution of cooperation by group selection may be more complicated than previously stated. Finally, using Feldman and Liberman's modifier approach, we investigate the conditions under which a rare modifier of the extent of conformity or the number of role models can invade a population. Understanding the dynamics of conformist- and anticonformist-biased transmission may have implications for research on human and nonhuman animal behavior, the evolution of cooperation, and frequency-dependent transmission in general.

    View details for DOI 10.1073/pnas.2004102117

    View details for PubMedID 32461360

  • Reply to Balsa-Canto et al.: Growth models are applicable to growth data, not to stationary-phase data. Proceedings of the National Academy of Sciences of the United States of America Ram, Y., Obolski, U., Feldman, M. W., Berman, J., Hadany, L. 2019

    View details for DOI 10.1073/pnas.1917758117

    View details for PubMedID 31874931

  • The evolution of frequency-dependent cultural transmission. Theoretical population biology Liberman, U., Ram, Y., Altenberg, L., Feldman, M. W. 2019

    Abstract

    In a model of vertical and oblique cultural transmission of a dichotomous trait, the rates of transmission of each form of the trait are functions of the trait frequency in the population. Sufficient conditions on these functions are derived for a stable trait polymorphism to exist. If the vertical transmission rates are monotone decreasing functions of the trait frequency, a complete global stability analysis is presented. It is also shown that a unique protected polymorphism can be globally stable even though the sufficient conditions are not met. The evolution of frequency-dependent transmission is modeled using modifier theory, and exact conditions are derived for a transmission modifier to invade a population at a stable polymorphism. Finally, the interaction between frequency-dependent selection and frequency-dependent transmission is explored.

    View details for DOI 10.1016/j.tpb.2019.12.004

    View details for PubMedID 31866423

  • Acculturation of rural-urban migrants in urbanising China: a multidimensional and bicultural framework POPULATION SPACE AND PLACE Yue, Z., Fong, E., Li, S., Feldman, M. W. 2019

    View details for DOI 10.1002/psp.2278

    View details for Web of Science ID 000496872200001

  • Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nature communications Greenbaum, G., Getz, W. M., Rosenberg, N. A., Feldman, M. W., Hovers, E., Kolodny, O. 2019; 10 (1): 5003

    Abstract

    Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-basedtransmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated 'pathogen packages' could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.

    View details for DOI 10.1038/s41467-019-12862-7

    View details for PubMedID 31676766

  • Sex: The power of randomization Vasylenko, L., Feldman, M. W., Papadimitriou, C., Livnat, A. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2019: 41–53
  • Family Structure and Competing Demands From Aging Parents and Adult Children Among Middle-Aged People in China JOURNAL OF FAMILY ISSUES Liu, H., Feng, Z., Jiang, Q., Feldman, M. 2019
  • Process of Decline in Activities of Daily Living of Older Chinese People Prior to Death: Evidence From Three Cohorts RESEARCH ON AGING Zhang, W., Feldman, M. W., Du, P. 2019; 41 (8): 727–50
  • Was inter-population connectivity of Neanderthals and modern humans the driver of the Upper Paleolithic transition rather than its product? QUATERNARY SCIENCE REVIEWS Greenbaum, G., Friesem, D. E., Hovers, E., Feldman, M. W., Kolodny, O. 2019; 217: 316–29
  • Sex with partners met online: risky sexual behavior among bachelors in rural China. AIDS care Wang, Y., Liu, H., Zhao, M., Feldman, M. W., Williams, A. B. 2019: 1–5

    Abstract

    In the context of gender imbalance and marriage squeeze in China, this study identifies socio-demographic characteristics of bachelors who reported having sex with partners whom they met online and examines associations between having sex with such partners and other risky sexual behaviors. Data are from a cross-sectional survey conducted in 2017. 735 men who have rural household registration (hukou, in Chinese), and who were at least 28 years old and unmarried were interviewed. 16.5% of the sample had experienced sexual intercourse with a partner met online. After adjustment for socio-demographic characteristics, having sex with such partners was associated with a range of risky sexual behaviors: unsafe sexual intercourse (such as anal sex, group sex, not using a condom) (adjusted OR (aOR)=5.11, 3.14-8.33, p<0.001); commercial sex (aOR=4.42, 2.78-7.02, p<0.001); having sex in public places (aOR=3.11, 1.97-4.91, p<0.001); and multiple sexual partners (>=6 partners) (aOR=12.57, 6.55-24.12, p<0.001). This suggests that bachelors who had sexual intercourse with partners whom they met online are at higher risk for HIV or other STD infections. Future interventions targeted at this population will improve the efficiency of China's HIV/STD prevention.

    View details for DOI 10.1080/09540121.2019.1640849

    View details for PubMedID 31293175

  • Evolution of hierarchy in bacterial metabolic networks BIOSYSTEMS Goodman, A. J., Feldman, M. W. 2019; 180: 71–78
  • The great human expansion RESONANCE-JOURNAL OF SCIENCE EDUCATION Henn, B. M., Cavalli-Sforza, L. L., Feldman, M. W. 2019; 24 (6): 711–18
  • Marriage Aspiration, Perceived Marriage Squeeze, and Anomie Among Unmarried Rural Male Migrant Workers in China. American journal of men's health Li, W., Li, S., Feldman, M. W. 2019; 13 (3): 1557988319856170

    Abstract

    Using data from a survey of rural-urban migrants conducted in Xiamen City, China, during 2009, this study explores determinants of anomie among unmarried rural male migrant workers in the context of China's gender imbalance. Results indicate that the perceived marriage squeeze has exerted direct effects on anomie, and marriage aspiration has indirect effects on anomie among rural male migrant workers. The perceived marriage squeeze also has a mediating effect between marriage aspiration and anomie among unmarried rural male migrant workers. Social integration in the destination city is also a determinant of anomie among these unmarried migrant workers.

    View details for DOI 10.1177/1557988319856170

    View details for PubMedID 31177897

  • Process of Decline in Activities of Daily Living of Older Chinese People Prior to Death: Evidence From Three Cohorts. Research on aging Zhang, W., Feldman, M. W., Du, P. 2019: 164027519841016

    Abstract

    OBJECTIVE:: The study analyzes the decline in activities of daily living (ADL) prior to death among three cohorts of older Chinese.METHOD:: With data from the Chinese Longitudinal Healthy Longevity Survey, the process of decline in ADL in older people born during the periods 1899-1908, 1909-1918, and 1919-1928 is analyzed using the hierarchical linear model with mixed effects.RESULTS:: The remaining survival time has a stronger effect on changes in ADL than chronological age, and there is significant heterogeneity among the older adults in ADL.CONCLUSION:: Decline in ADL is delayed by extending life span. Older people with healthy behaviors, good living conditions in childhood, and age-friendly living environment have long-lasting good ADL during their remaining life span; socioeconomic resources help the older adults with ADL disabilities to survive. Selective effects of mortality and protective effects of socioeconomic resources explain the heterogeneity in ADL and its changes over time.

    View details for PubMedID 30943869

  • The life history of learning: Demographic structure changes cultural outcomes PLOS COMPUTATIONAL BIOLOGY Fogarty, L., Creanza, N., Feldman, M. W. 2019; 15 (4)
  • Evolution of Hierarchy in Bacterial Metabolic Networks. Bio Systems Goodman, A., Feldman, M. 2019

    Abstract

    Flow hierarchy is a useful way to characterize the movement of information and matter throughout a network. Hierarchical network organizations are shown to arise when there is a cost of maintaining links in the network. A similar constraint exists in metabolic networks, where costs come from reduced efficiency of nonspecific enzymes or from producing unnecessary enzymes. Previous analyses of bacterial metabolic networks have been used to predict the minimal nutrients that a bacterium needs to grow, its mutualistic relationships with other bacteria, and its major ecological niche. We use metabolic network inference to obtain metabolite flow graphs of 2,935 bacterial metabolic networks and find that flow hierarchy evolves independently of modularity and other network properties. By inferring the ancestral metabolic networks and estimating the hierarchical character of the inferred network, we show that hierarchical structure first increased and later decreased over evolutionary history. Furthermore, hierarchical structure in the network is associated with slower growth rates; bacteria with hierarchy scores above the median grow on average 2.25 times faster than those with hierarchy scores below the median.

    View details for PubMedID 30878498

  • Evolution of resilience in protein interactomes across the tree of life. Proceedings of the National Academy of Sciences of the United States of America Zitnik, M., Sosic, R., Feldman, M. W., Leskovec, J. 2019

    Abstract

    Phenotype robustness to environmental fluctuations is a common biological phenomenon. Although most phenotypes involve multiple proteins that interact with each other, the basic principles of how such interactome networks respond to environmental unpredictability and change during evolution are largely unknown. Here we study interactomes of 1,840 species across the tree of life involving a total of 8,762,166 protein-protein interactions. Our study focuses on the resilience of interactomes to network failures and finds that interactomes become more resilient during evolution, meaning that interactomes become more robust to network failures over time. In bacteria, we find that a more resilient interactome is in turn associated with the greater ability of the organism to survive in a more complex, variable, and competitive environment. We find that at the protein family level proteins exhibit a coordinated rewiring of interactions over time and that a resilient interactome arises through gradual change of the network topology. Our findings have implications for understanding molecular network structure in the context of both evolution and environment.

    View details for PubMedID 30765515

  • Does China's Anti-Poverty Relocation and Settlement Program Benefit Ecosystem Services: Evidence from a Household Perspective SUSTAINABILITY Li, C., Kang, B., Wang, L., Li, S., Feldman, M., Li, J. 2019; 11 (3)

    View details for DOI 10.3390/su11030600

    View details for Web of Science ID 000458929500045

  • Sex: The power of randomization. Theoretical population biology Vasylenko, L., Feldman, M. W., Papadimitriou, C., Livnat, A. 2019

    Abstract

    In evolutionary biology, randomness has been perceived as a force that, in and of itself, is capable of inventing: mutation creates new genetic information at random across the genome which leads to phenotypic change, which is then subject to selection. However, in science in general and in computer science in particular, the widespread use of randomness takes a different form. Here, randomization allows for the breaking of pattern, as seen for example in its removal of biases (patterns) in random sampling or random assignment to conditions. Combined with various forms of evaluation, this breaking of pattern becomes an extraordinarily powerful tool, as also seen in many randomized algorithms in computer science. Here we show that this power of randomness is harnessed in nature by sex and recombination. In a finite population, and under the assumption of interactions between genetic variants, sex and recombination allow selection to test how well an allele will perform in a sample of combinations of interacting genetic partners drawn at random from all possible such combinations; consequently, even a small number of tests of genotypes such as takes place in a finite population favors alleles that will most likely perform well in a vast number of yet unrealized genetic combinations. This power of randomization is not manifest in asexual populations.

    View details for PubMedID 30638926

  • The life history of learning: Demographic structure changes cultural outcomes. PLoS computational biology Fogarty, L. n., Creanza, N. n., Feldman, M. W. 2019; 15 (4): e1006821

    Abstract

    Human populations show rich cultural diversity. Underpinning this diversity of tools, rituals, and cultural norms are complex interactions between cultural evolutionary and demographic processes. Most models of cultural change assume that individuals use the same learning modes and methods throughout their lives. However, empirical data on 'learning life histories'-the balance of dominant modes of learning (for example, learning from parents, peers, or unrelated elders) throughout an individual's lifetime-suggest that age structure may play a crucial role in determining learning modes and cultural evolutionary trajectories. Thus, studied in isolation, demographic and cultural evolutionary models show only part of the picture. This paper describes a mathematical and computational framework that combines demographic and cultural evolutionary methods. Using this general framework, we examine interactions between the ways in which culture is spread throughout an individual's lifetime and cultural change across generations. We show that including demographic structure alongside cultural dynamics can help to explain domain-specific patterns of cultural evolution that are a persistent feature of cultural data, and can shed new light on rare but significant demographic events.

    View details for PubMedID 31039147

  • Information diffusion in signed networks. PloS one He, X., Du, H., Feldman, M. W., Li, G. 2019; 14 (10): e0224177

    Abstract

    Information diffusion has been widely discussed in various disciplines including sociology, economics, physics or computer science. In this paper, we generalize the linear threshold model in signed networks consisting of both positive and negative links. We analyze the dynamics of the spread of information based on balance theory, and find that a signed network can generate path dependence while structural balance can help remove the path dependence when seeded with balanced initialized active nodes. Simulation shows that the diffusion of information based on positive links contradicts that based on negative links. More positive links in signed networks are more likely to activate nodes and remove path dependence, but they can reduce predictability that is based on active states. We also find that a balanced structure can facilitate both the magnitude and speed of information diffusion, remove the path dependence, and cause polarization.

    View details for DOI 10.1371/journal.pone.0224177

    View details for PubMedID 31661504

  • Understanding Niche Construction as an Evolutionary Process EVOLUTIONARY CAUSATION: BIOLOGICAL AND PHILOSOPHICAL REFLECTIONS Laland, K. N., Odling-Smee, J., Feldman, M. W., Uller, T., Laland, K. N. 2019: 127–52
  • Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences EVOLUTION MEDICINE AND PUBLIC HEALTH Rosenberg, N. A., Edge, M. D., Pritchard, J. K., Feldman, M. W. 2019: 26–34
  • Beyond uncertainty: A broader scope for "incentive hope" mechanisms and its implications BEHAVIORAL AND BRAIN SCIENCES Linkovski, O., Weinbach, N., Edelman, S., Feldman, M. W., Lotem, A., Kolodny, O. 2019; 42
  • Beyond uncertainty: A broader scope for "incentive hope" mechanisms and its implications. The Behavioral and brain sciences Linkovski, O., Weinbach, N., Edelman, S., Feldman, M. W., Lotem, A., Kolodny, O. 2019; 42: e44

    Abstract

    We propose that food-related uncertainty is but one of multiple cues that predicts harsh conditions and may activate "incentive hope." An evolutionarily adaptive response to these would have been to shift to a behavioral-metabolic phenotype geared toward facing hardship. In modernity, this phenotype may lead to pathologies such as obesity and hoarding. Our perspective suggests a novel therapeutic approach.

    View details for PubMedID 30940254

  • PERFORMANCE OF POLYGENIC SCORES ACROSS ANCESTRALLY DIVERSE POPULATIONS: SCIENTIFIC AND ETHICAL CONSIDERATIONS Duncan, L., Shen, H., Pritchard, J., Feldman, M., Ressler, K., Harris, K., Domingue, B. ELSEVIER SCIENCE BV. 2019: S833–S834
  • Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evolution, medicine, and public health Rosenberg, N. A., Edge, M. D., Pritchard, J. K., Feldman, M. W. 2019; 2019 (1): 26–34

    Abstract

    Recent analyses of polygenic scores have opened new discussions concerning the genetic basis and evolutionary significance of differences among populations in distributions of phenotypes. Here, we highlight limitations in research on polygenic scores, polygenic adaptation and population differences. We show how genetic contributions to traits, as estimated by polygenic scores, combine with environmental contributions so that differences among populations in trait distributions need not reflect corresponding differences in genetic propensity. Under a null model in which phenotypes are selectively neutral, genetic propensity differences contributing to phenotypic differences among populations are predicted to be small. We illustrate this null hypothesis in relation to health disparities between African Americans and European Americans, discussing alternative hypotheses with selective and environmental effects. Close attention to the limitations of research on polygenic phenomena is important for the interpretation of their relationship to human population differences.

    View details for PubMedID 30838127

  • The decline in China's fertility level: a decomposition analysis. Journal of biosocial science Jiang, Q. n., Yang, S. n., Li, S. n., Feldman, M. W. 2019: 1–14

    Abstract

    Many factors have contributed to the decline in China's fertility level. Using China's population census data from 1990, 2000 and 2010, the present study investigates the factors causing the decline in China's fertility rate by decomposing changes in two fertility indices: the total fertility rate (TFR) and the net reproduction rate (NRR). The change in the TFR is decomposed into the change in the marital fertility rate (MFR) and the change in the proportion of married women (PMW). Four factors contribute to the change in the NRR. The following are the main findings. A drop in the MFR caused a decrease in the TFR and the NRR between 1989 and 2000. However, the change in MFR increased TFR and NRR between 2000 and 2010. Marriage postponement caused a decline in the fertility level between 1989 and 2000 as well as between 2000 and 2010. The effect of the MFR and marriage postponement varied with age and region and also between urban and rural areas.

    View details for DOI 10.1017/S0021932019000038

    View details for PubMedID 31156077

  • Predicting microbial growth in a mixed culture from growth curve data. Proceedings of the National Academy of Sciences of the United States of America Ram, Y. n., Dellus-Gur, E. n., Bibi, M. n., Karkare, K. n., Obolski, U. n., Feldman, M. W., Cooper, T. F., Berman, J. n., Hadany, L. n. 2019

    Abstract

    Determining the fitness of specific microbial genotypes has extensive application in microbial genetics, evolution, and biotechnology. While estimates from growth curves are simple and allow high throughput, they are inaccurate and do not account for interactions between costs and benefits accruing over different parts of a growth cycle. For this reason, pairwise competition experiments are the current "gold standard" for accurate estimation of fitness. However, competition experiments require distinct markers, making them difficult to perform between isolates derived from a common ancestor or between isolates of nonmodel organisms. In addition, competition experiments require that competing strains be grown in the same environment, so they cannot be used to infer the fitness consequence of different environmental perturbations on the same genotype. Finally, competition experiments typically consider only the end-points of a period of competition so that they do not readily provide information on the growth differences that underlie competitive ability. Here, we describe a computational approach for predicting density-dependent microbial growth in a mixed culture utilizing data from monoculture and mixed-culture growth curves. We validate this approach using 2 different experiments with Escherichia coli and demonstrate its application for estimating relative fitness. Our approach provides an effective way to predict growth and infer relative fitness in mixed cultures.

    View details for DOI 10.1073/pnas.1902217116

    View details for PubMedID 31253703

  • Coordinated change at the colony level in fruit bat fur microbiomes through time. Nature ecology & evolution Kolodny, O., Weinberg, M., Reshef, L., Harten, L., Hefetz, A., Gophna, U., Feldman, M. W., Yovel, Y. 2018

    Abstract

    The host-associated microbiome affects individual health and behaviour, and may be influenced by local environmental conditions. However, little is known about microbiomes' temporal dynamics in free-living species compared with their dynamics in humans and model organisms, especially in body sites other than the gut. Here, we investigate longitudinal changes in the fur microbiome of captive and free-living Egyptian fruit bats. We find that, in contrast to patterns described in humans and other mammals, the prominent dynamics is of change over time at the level of the colony as a whole. On average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats' ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats' fur, but differs from the more individualized pattern found in the bats' gut microbiome.

    View details for PubMedID 30532043

  • Cryptic selection forces and dynamic heritability in generalized phenotypic evolution. Theoretical population biology Gilpin, W., Feldman, M. W. 2018

    Abstract

    Individuals with different phenotypes can have widely-varying responses to natural selection, yet many classical approaches to evolutionary dynamics emphasize only how a population's average phenotype increases in fitness over time. However, recent experimental results have produced examples of populations that have multiple fitness peaks, or that experience frequency-dependence that affects the direction and strength of selection on certain individuals. Here, we extend classical fitness gradient formulations of natural selection in order to describe the dynamics of a phenotype distribution in terms of its moments-such as the mean, variance, and skewness. The number of governing equations in our model can be adjusted in order to capture different degrees of detail about the population. We compare our simplified model to direct Wright-Fisher simulations of evolution in several canonical fitness landscapes, and we find that our model provides a low-dimensional description of complex dynamics not typically explained by classical theory, such as cryptic selection forces due to selection on trait ranges, time-variation of the heritability, and nonlinear responses to stabilizing or disruptive selection due to asymmetric trait distributions. In addition to providing a framework for extending general understanding of common qualitative concepts in phenotypic evolution - such as fitness gradients, selection pressures, and heritability - our approach has practical importance for studying evolution in contexts in which genetic analysis is infeasible.

    View details for PubMedID 30528351

  • Vertical and oblique cultural transmission fluctuating in time and in space. Theoretical population biology Ram, Y., Liberman, U., Feldman, M. W. 2018

    View details for PubMedID 30465795

  • Advancing front of old-age human survival. Proceedings of the National Academy of Sciences of the United States of America Zuo, W., Jiang, S., Guo, Z., Feldman, M. W., Tuljapurkar, S. 2018; 115 (44): 11209–14

    Abstract

    Old-age mortality decline has driven recent increases in lifespans, but there is no agreement about trends in the age pattern of old-age deaths. Some argue that old-age deaths should become compressed at advanced ages, others argue that old-age deaths should become more dispersed with age, and yet others argue that old-age deaths are consistent with little change in dispersion. However, direct analysis of old-age deaths presents unusual challenges: Death rates at the oldest ages are always noisy, published life tables must assume an asymptotic age pattern of deaths, and the definition of "old-age" changes as lives lengthen. Here we use robust percentile-based methods to overcome some of these challenges and show, for five decades in 20 developed countries, that old-age survival follows an advancing front, like a traveling wave. The front lies between the 25th and 90th percentiles of old-age deaths, advancing with nearly constant long-term shape but annual fluctuations in speed. The existence of this front leads to several predictions that we verify, e.g., that advances in life expectancy at age 65 y are highly correlated with the advance of the 25th percentile, but not with distances between higher percentiles. Our unexpected result has implications for biological hypotheses about human aging and for future mortality change.

    View details for PubMedID 30327342

  • The evolution of cooperation in signed networks under the impact of structural balance PLOS ONE He, X., Du, H., Cai, M., Feldman, M. W. 2018; 13 (10): e0205084

    Abstract

    Structural balance plays an important role in the dynamics of signed networks. Based on structural balance, we generalize the evolution of cooperation in signed networks. Here we develop a new simulation model to study the impact of structural balance on the evolution of cooperation in signed networks. The simulation shows that cooperation prevails when an individual has a higher probability of adjusting the signs of its relations. We also find that structural balance forces the coexistence of cooperators and defectors, while the initial attributes of networks have little impact on the evolution of cooperation in the presence of structural balance, although they have a strong effect on the evolution of structural balance.

    View details for PubMedID 30296278

  • Modeling the implementation of population-level isoniazid preventive therapy for tuberculosis control in a high HIV-prevalence setting. AIDS (London, England) Rhines, A. S., Feldman, M. W., Bendavid, E. 2018

    Abstract

    BACKGROUND: We model the epidemiological impact of providing isoniazid preventive therapy (IPT) to South African adolescents, among whom HIV prevalence is low, latent TB prevalence is high, and school-based programs may enable population-level coverage.METHODS: We simulate a dynamic compartmental model of age-structured HIV and TB co-epidemics in South Africa. HIV dynamics are modeled by infection status, CD4 count, and antiretroviral therapy; TB dynamics are modeled by disease stage, diagnosis, treatment, and IPT status. We analyze the effects of continuous IPT coverage among adolescents from 5% (baseline) to 90%.RESULTS: Our model is calibrated to WHO and UNAIDS epidemiological estimates. In simulations, increasing IPT coverage to 50% among adolescents reduced active TB incidence by 5% to 34%. Increasing coverage to 90% led to a 9% to 40% reduction in active TB incidence. Expanded IPT access causes TB incidence to decline in the general population of HIV-positive individuals, as well as in adult HIV-positive individuals.CONCLUSIONS: Targeting IPT to a secondary school population with high latent TB prevalence and low HIV prevalence, where risk of false-negative diagnosis of active TB is low and IPT benefits are more established, could have substantial benefits to adolescents and spillover benefits to the adult population.

    View details for PubMedID 30096067

  • Assessing Livelihood Reconstruction in Resettlement Program for Disaster Prevention at Baihe County of China: Extension of the Impoverishment Risks and Reconstruction (IRR) Model SUSTAINABILITY Xiao, Q., Liu, H., Feldman, M. 2018; 10 (8)

    View details for DOI 10.3390/su10082913

    View details for Web of Science ID 000446767700329

  • Reversing structural balance in signed networks PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS Du, H., He, X., Wang, J., Feldman, M. W. 2018; 503: 780–92
  • Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck NATURE COMMUNICATIONS Zeng, T., Aw, A. J., Feldman, M. W. 2018; 9: 2077

    Abstract

    In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000-7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

    View details for PubMedID 29802241

  • Gene-culture coevolution under selection THEORETICAL POPULATION BIOLOGY Behar, H., Feldman, M. W. 2018; 121: 33–44

    Abstract

    The joint evolutionary dynamics of phenotypes and genotypes are usually couched in terms of genetic variance contributions to changes in the phenotypic mean. Here, we study the evolution of a dichotomous phenotype whose transmission is controlled by one multi-allelic locus. The phenotype is under selection, which may be genotype-dependent. We answer classical population genetic questions about the phenogenotypic evolution, including the conditions for phenotypic and genotypic polymorphism, in terms of selection coefficients and rates of phenotypic transmission.

    View details for PubMedID 29641980

  • Integrative studies of cultural evolution: crossing disciplinary boundaries to produce new insights PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Kolodny, O., Feldman, M. W., Creanza, N. 2018; 373 (1743)

    Abstract

    Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-by-minute behaviour to millennia of cultural accumulation that give rise to population-level differences. These dynamics act on a range of entities-including behavioural sequences, ideas and artefacts as well as individuals, populations and whole species-and involve mechanisms at multiple levels, from neurons in brains to inter-population interactions. Studying such complex phenomena requires an integration of perspectives from a diverse array of fields, as well as bridging gaps between traditionally disparate areas of study. In this article, which also serves as an introduction to the current special issue, we highlight some specific respects in which the study of cultural evolution has benefited and should continue to benefit from an integrative approach. We showcase a number of pioneering studies of cultural evolution that bring together numerous disciplines. These studies illustrate the value of perspectives from different fields for understanding cultural evolution, such as cognitive science and neuroanatomy, behavioural ecology, population dynamics, and evolutionary genetics. They also underscore the importance of understanding cultural processes when interpreting research about human genetics, neuroscience, behaviour and evolution.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'.

    View details for PubMedID 29440515

    View details for PubMedCentralID PMC5812962

  • Missing compared to what? Revisiting heritability, genes and culture PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Feldman, M. W., Ramachandran, S. 2018; 373 (1743)

    Abstract

    Standard models for the determination of phenotypes from genes are grounded in simple assumptions that are inherent in the modern evolutionary synthesis (MES), which was developed in the 1930s, 1940s and 1950s. The MES was framed in the context of Mendelian genetic transmission enhanced by the Fisherian view of the way discretely inherited genes determine continuously quantitative phenotypes. The statistical models that are used to estimate and interpret genetic contributions to human phenotypes-including behavioural traits-are constructed within the framework of the MES. Variance analysis constitutes the main tool and is used under this framework to characterize genetic inheritance, and hence determination of phenotypes. In this essay, we show that cultural inheritance, when incorporated into models for the determination of phenotypes, can sharply reduce estimates of the genetic contribution to these phenotypes. Recognition of the importance of non-genetic transmission of many human traits is becoming ever more necessary to prevent regression to the debates of the 1970s and 1980s concerning policies based on genetic determination of complex human phenotypes.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'.

    View details for PubMedID 29440529

    View details for PubMedCentralID PMC5812976

  • Bridging cultural gaps: interdisciplinary studies in human cultural evolution PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Kolodny, O., Feldman, M. W., Creanza, N. 2018; 373 (1743)

    View details for PubMedID 29440530

    View details for PubMedCentralID PMC5812977

  • A comparison of worldwide phonemic and genetic variation in populations in Asia Surowiec, A., Ramachandran, S., Feldman, M. W., Creanza, N. WILEY. 2018: 268
  • The impact on rural livelihoods and ecosystem services of a major relocation and settlement program: A case in Shaanxi, China AMBIO Li, C., Li, S., Feldman, M. W., Li, J., Zheng, H., Daily, G. C. 2018; 47 (2): 245–59

    Abstract

    China's largest-ever resettlement program is underway, aiming to restore ecosystems and lift ecosystem service providers out of the poverty trap and into sustainable livelihoods. We examine the impact of the relocation and settlement program (RSP) to date, reporting on an ecosystem services (ES) assessment and a 1400-household survey. The RSP generally achieves the goals of ES increase and livelihood restore. In biophysical terms, the RSP improves water quality, sediment retention, and carbon sequestration. In social terms, resettled households so far report transformation of livelihoods activities from traditional inefficient agricultural and forest production to non-farm activities. Increased income contributes to decrease the poverty rate and improve resettled households' living condition and standard. Meanwhile, the RSP decreases households' dependence on ES in terms of provisioning services. Difficulty and challenge also showed up subsequently after relocation. A major current challenge is to enable poorer households to move, while providing greater follow-up support to relocated households. While the program is unique to China, it illuminates widespread opportunities for addressing environmental and poverty-related concerns in a rapidly changing world.

    View details for PubMedID 28983793

    View details for PubMedCentralID PMC5794687

  • Adopted daughters and adopted daughters-in-law in Taiwan: a mortality analysis ROYAL SOCIETY OPEN SCIENCE Mattison, S. M., Seabright, E., Reynolds, A. Z., Cao, J., Brown, M. J., Feldman, M. W. 2018; 5 (3): 171745

    Abstract

    Adoption is sometimes considered paradoxical from an evolutionary perspective because the costs spent supporting an adopted child would be better spent on rearing one's own. Kin selection theory is commonly used to solve this paradox, because the adoption of closely related kin contributes to the inclusive fitness of the adoptive parent. In this paper, we perform a novel test of kin selection theory in the context of adoption by asking whether adopted daughters-in-law, who contribute directly (i.e. genealogically) to the perpetuation of their adoptive families' lineages, experience lower mortality than daughters adopted for other purposes in historical Taiwan. We show that both classes of adopted daughter suffer lower mortality than biological daughters, but that the protective effect of adoption is stronger among daughters who were not adopted with the intention of perpetuating the family lineage. We speculate as to the possible benefits of such a pattern and emphasize the need to move beyond typological definitions of adoption to understand the specific costs and benefits involved in different forms of caring for others' children.

    View details for PubMedID 29657778

  • Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium JOURNAL OF THE ROYAL SOCIETY INTERFACE Garcia, V., Glassberg, E. C., Harpak, A., Feldman, M. W. 2018; 15 (140)

    Abstract

    Within-host adaptation of pathogens such as human immunodeficiency virus (HIV) often occurs at more than two loci. Multiple beneficial mutations may arise simultaneously on different genetic backgrounds and interfere, affecting each other's fixation trajectories. Here, we explore how these evolutionary dynamics are mirrored in multilocus linkage disequilibrium (MLD), a measure of multi-way associations between alleles. In the parameter regime corresponding to HIV, we show that deterministic early infection models induce MLD to oscillate over time in a wavelet-like fashion. We find that the frequency of these oscillations is proportional to the rate of adaptation. This signature is robust to drift, but can be eroded by high variation in fitness effects of beneficial mutations. Our findings suggest that MLD oscillations could be used as a signature of interference among multiple equally advantageous mutations and may aid the interpretation of MLD in data.

    View details for PubMedID 29563246

    View details for PubMedCentralID PMC5908532

  • Generation of variation and a modified mean fitness principle: Necessity is the mother of genetic invention. Theoretical population biology Ram, Y., Altenberg, L., Liberman, U., Feldman, M. W. 2018

    Abstract

    Generation of variation may be detrimental in well-adapted populationsevolving under constant selection. In a constant environment, genetic modifiers that reduce the rate at which variation is generated by processes such as mutation and migration, succeed. However, departures from this reduction principle have been demonstrated. Here we analyze a general model of evolution under constant selection where the rate at which variation is generated depends on the individual. We find that if a modifier allele increases the rate at which individuals of below-average fitness generate variation, then it will increase in frequency and increase the population mean fitness. This principle applies to phenomena such as stress-induced mutagenesis and condition-dependent dispersal, and exemplifies "Necessity is the mother of genetic invention."

    View details for PubMedID 29496474

  • Evolution of vertical and oblique transmission under fluctuating selection PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ram, Y., Liberman, U., Feldman, M. W. 2018; 115 (6): E1174–E1183

    Abstract

    The evolution and maintenance of social learning, in competition with individual learning, under fluctuating selection have been well-studied in the theory of cultural evolution. Here, we study competition between vertical and oblique cultural transmission of a dichotomous phenotype under constant, periodically cycling, and randomly fluctuating selection. Conditions are derived for the existence of a stable polymorphism in a periodically cycling selection regime. Under such a selection regime, the fate of a genetic modifier of the rate of vertical transmission depends on the length of the cycle and the strength of selection. In general, the evolutionarily stable rate of vertical transmission differs markedly from the rate that maximizes the geometric mean fitness of the population. The evolution of rules of transmission has dramatically different dynamics from the more frequently studied modifiers of recombination, mutation, or migration.

    View details for PubMedID 29363602

  • Ecocultural range-expansion scenarios for the replacement or assimilation of Neanderthals by modern humans THEORETICAL POPULATION BIOLOGY Wakano, J., Gilpin, W., Kadowaki, S., Feldman, M. W., Aoki, K. 2018; 119: 3–14

    Abstract

    Recent archaeological records no longer support a simple dichotomous characterization of the cultures/behaviors of Neanderthals and modern humans, but indicate much cultural/behavioral variability over time and space. Thus, in modeling the replacement or assimilation of Neanderthals by modern humans, it is of interest to consider cultural dynamics and their relation to demographic change. The ecocultural framework for the competition between hominid species allows their carrying capacities to depend on some measure of the levels of culture they possess. In the present study both population densities and the densities of skilled individuals in Neanderthals and modern humans are spatially distributed and subject to change by spatial diffusion, ecological competition, and cultural transmission within each species. We analyze the resulting range expansions in terms of the demographic, ecological and cultural parameters that determine how the carrying capacities relate to the local densities of skilled individuals in each species. Of special interest is the case of cognitive and intrinsic-demographic equivalence of the two species. The range expansion dynamics may consist of multiple wave fronts of different speeds, each of which originates from a traveling wave solution. Properties of these traveling wave solutions are mathematically derived. Depending on the parameters, these traveling waves can result in replacement of Neanderthals by modern humans, or assimilation of the former by the latter. In both the replacement and assimilation scenarios, the first wave of intrusive modern humans is characterized by a low population density and a low density of skilled individuals, with implications for archaeological visibility. The first invasion is due to weak interspecific competition. A second wave of invasion may be induced by cultural differences between moderns and Neanderthals. Spatially and temporally extended coexistence of the two species, which would have facilitated the transfer of genes from Neanderthal into modern humans and vice versa, is observed in the traveling waves, except when niche overlap between the two species is extremely high. Archaeological findings on the spatial and temporal distributions of the Initial Upper Palaeolithic and the Early Upper Palaeolithic and of the coexistence of Neanderthals and modern humans are discussed.

    View details for PubMedID 29032037

  • Female fertility history and mid-late-life health: Findings from China JOURNAL OF WOMEN & AGING Li, X., Jiang, Q., Li, S., Feldman, M. W. 2018; 30 (1): 62–74
  • A Genetic Simulated Annealing Algorithm to Optimize the Small-World Network Generating Process COMPLEXITY Du, H., Fan, J., He, X., Feldman, M. W. 2018
  • How does trust affect acceptance of a nuclear power plant (NPP): A survey among people living with Qinshan NPP in China PLOS ONE Xiao, Q., Liu, H., Feldman, M. W. 2017; 12 (11)
  • How does trust affect acceptance of a nuclear power plant (NPP): A survey among people living with Qinshan NPP in China. PloS one Xiao, Q., Liu, H., Feldman, M. W. 2017; 12 (11): e0187941

    Abstract

    It is difficult to know whether different dimensions of trust have different effects on local residents' acceptance of nuclear power plants (NPPs). In previous research such trust has been considered as a single dimensional concept. This paper divides trust into goodwill trust and competence trust, and we explore the ways in which trust affects acceptance of NPPs through structural equation modeling. A survey of 491 people was conducted in Haiyan County, China, where the Qinshan nuclear power plant is located. We find that goodwill trust is significantly correlated with competence trust, and each can indirectly promote residents' acceptance of NPPs but by different paths. Goodwill trust improves acceptance of NPPs by decreasing risk perception, while competence trust improves acceptance of NPPs by increasing benefit perception. However, the associations between goodwill trust and benefit perception, competence trust and risk perception, are not significant.

    View details for DOI 10.1371/journal.pone.0187941

    View details for PubMedID 29176852

    View details for PubMedCentralID PMC5703464

  • Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wittmann, M. J., Bergland, A. O., Feldman, M. W., Schmidt, P. S., Petrov, D. A. 2017; 114 (46): E9932–E9941

    Abstract

    Most natural populations are affected by seasonal changes in temperature, rainfall, or resource availability. Seasonally fluctuating selection could potentially make a large contribution to maintaining genetic polymorphism in populations. However, previous theory suggests that the conditions for multilocus polymorphism are restrictive. Here, we explore a more general class of models with multilocus seasonally fluctuating selection in diploids. In these models, the multilocus genotype is mapped to fitness in two steps. The first mapping is additive across loci and accounts for the relative contributions of heterozygous and homozygous loci-that is, dominance. The second step uses a nonlinear fitness function to account for the strength of selection and epistasis. Using mathematical analysis and individual-based simulations, we show that stable polymorphism at many loci is possible if currently favored alleles are sufficiently dominant. This general mechanism, which we call "segregation lift," requires seasonal changes in dominance, a phenomenon that may arise naturally in situations with antagonistic pleiotropy and seasonal changes in the relative importance of traits for fitness. Segregation lift works best under diminishing-returns epistasis, is not affected by problems of genetic load, and is robust to differences in parameters across loci and seasons. Under segregation lift, loci can exhibit conspicuous seasonal allele-frequency fluctuations, but often fluctuations may be small and hard to detect. An important direction for future work is to formally test for segregation lift in empirical data and to quantify its contribution to maintaining genetic variation in natural populations.

    View details for PubMedID 29087300

  • A parsimonious neutral model suggests Neanderthal replacement was determined by migration and random species drift NATURE COMMUNICATIONS Kolodny, O., Feldman, M. W. 2017; 8: 1040

    Abstract

    Most hypotheses in the heated debate about the Neanderthals' replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals' demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals' replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated migration of modern humans from Africa into Eurasia.

    View details for PubMedID 29089499

  • Worldwide patterns of human epigenetic variation NATURE ECOLOGY & EVOLUTION Carja, O., Maclsaac, J. L., Mah, S. M., Henn, B. M., Kobor, M. S., Feldman, M. W., Fraser, H. B. 2017; 1 (10): 1577–83
  • Worldwide patterns of human epigenetic variation. Nature ecology & evolution Carja, O., MacIsaac, J. L., Mah, S. M., Henn, B. M., Kobor, M. S., Feldman, M. W., Fraser, H. B. 2017; 1 (10): 1577-1583

    Abstract

    DNA methylation is an epigenetic modification, influenced by both genetic and environmental variation, that plays a key role in transcriptional regulation and many organismal phenotypes. Although patterns of DNA methylation have been shown to differ between human populations, it remains to be determined how epigenetic diversity relates to the patterns of genetic and gene expression variation at a global scale. Here we measured DNA methylation at 485,000 CpG sites in five diverse human populations, and analysed these data together with genome-wide genotype and gene expression data. We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity, as well as initial estimates of the rate of epigenetic divergence in recent human evolution.

    View details for DOI 10.1038/s41559-017-0299-z

    View details for PubMedID 29185505

  • A reversed gender pattern? A meta-analysis of gender differences in the prevalence of non-suicidal self-injurious behaviour among Chinese adolescents BMC PUBLIC HEALTH Yang, X., Feldman, M. W. 2017; 18: 66

    Abstract

    A reversed gender pattern has been observed in the suicide rate in China compared to elsewhere. Like suicidal behaviour, non-suicidal self-injurious (NSSI) behaviour is a health-risk behaviour. We examined whether a reversed gender pattern existed in the prevalence of NSSI.Online literature databases were searched for English and Chinese articles on NSSI behaviours among the Chinese. A meta-analysis with a random-effects model and a subgroup analysis were used to estimate the odds ratios of gender differences in NSSI prevalence among Chinese adolescents including college students, middle school students, and clinical samples, as well as rural, urban, and Hong Kong middle school students.There was a male bias in NSSI prevalence among college students (OR = 1.56, 95% CI = [1.30, 1.87], p < 0.001), and a female bias among middle school students (OR = 0.83, 95% CI = [0.73, 0.94], p < 0.01), but there was no gender difference among clinical samples (OR = 0.88, 95% CI = [0.41, 1.89], p > 0.1). The NSSI prevalence among middle school students had a female bias in the rural (OR = 0.58, 95% CI = [0.47, 0.72], p < 0.001) and Hong Kong areas (OR = 0.91, 95% CI = [0.86, 0.96], p < 0.001), with the gender difference in NSSI prevalence in the Hong Kong areas being greater than in rural areas. No gender difference in NSSI prevalence was found in urban areas (OR = 1.01, 95% CI = [0.84, 1.22], p > 0.1) among middle school students.Our analysis indicated the existence of specific gender and age patterns in NSSI prevalence among Chinese adolescents. The sample type, age, and the areas that have different gender norms and culture could partly explain this pattern.

    View details for PubMedID 28754108

  • The extension of biology through culture. Proceedings of the National Academy of Sciences of the United States of America Whiten, A., Ayala, F. J., Feldman, M. W., Laland, K. N. 2017

    View details for DOI 10.1073/pnas.1707630114

    View details for PubMedID 28739924

    View details for PubMedCentralID PMC5544333

  • Cultural evolutionary theory: How culture evolves and why it matters. Proceedings of the National Academy of Sciences of the United States of America Creanza, N., Kolodny, O., Feldman, M. W. 2017

    Abstract

    Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.

    View details for DOI 10.1073/pnas.1620732114

    View details for PubMedID 28739941

    View details for PubMedCentralID PMC5544263

  • Maximizing influence in a social network: Improved results using a genetic algorithm PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS Zhang, K., Du, H., Feldman, M. W. 2017; 478: 20-30
  • Why Gupta et al.'s critique of niche construction theory is off target. Journal of genetics Feldman, M. W., Odling-Smee, J., Laland, K. N. 2017; 96 (3): 505-508

    Abstract

    Gupta et al., in their article in this issue ('Niche construction in evolutionary theory: the construction of an academic niche?'. doi:10.1007/s12041-017-0787-6), lament 'serious problems with the way science is being done' and suggest that 'niche construction theory exemplifies this state of affairs.' However, their aggressively confrontational but superficial critique of niche construction theory (NCT) only contributes to these problems by attacking claims that NCT does not make. This is unfortunate, as their poor scholarship has done a disservice to the evolutionary biology community through propagating misinformation.We correct Gupta et al.'s misunderstandings, stressing that NCT does not suggest that the fact that organisms engage in niche construction is neglected, nor does it make strong claims on the basis of its formal theory. Moreover, the treatment of niche construction as an evolutionary process has been highly productive, and is both theoretically and empirically well-validated.We end by reflecting on the potentially deleterious implications of their publication for evolutionary science.

    View details for PubMedID 28761013

  • A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape. PLoS computational biology Gilpin, W., Feldman, M. W. 2017; 13 (7): e1005644

    Abstract

    In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the "edge of chaos" while creating a wide distribution of opportunities for speciation during epochs of disruptive selection-a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies.

    View details for DOI 10.1371/journal.pcbi.1005644

    View details for PubMedID 28678792

    View details for PubMedCentralID PMC5517034

  • Trends in DNA Methylation with Age Replicate Across Diverse Human Populations. Genetics Gopalan, S., Carja, O., Fagny, M., Patin, E., Myrick, J. W., McEwen, L. M., Mah, S. M., Kobor, M. S., Froment, A., Feldman, M. W., Quintana-Murci, L., Henn, B. M. 2017

    Abstract

    Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva- and whole blood-derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rain forest and the ≠Khomani San of the South African Kalahari Desert. We identified hundreds of CpG sites whose methylation levels are significantly associated with age, thousands that are significant in a meta-analysis, and replicate trends previously reported in populations of non-African descent. We confirmed that an age-associated site in the promoter of the gene ELOVL2 shows a remarkably congruent relationship with aging in humans, despite extensive genetic and environmental variation across populations. We also demonstrate that genotype state at methylation quantitative trait loci (meQTLs) can affect methylation trends at some age-associated CpG sites. Our study explores the relationship between CpG methylation and chronological age in populations of African hunter-gatherers, who rely on different diets across diverse ecologies. While many age-related CpG sites replicate across populations, we show that considering common genetic variation at meQTLs further improves our ability to detect previously identified age associations.

    View details for DOI 10.1534/genetics.116.195594

    View details for PubMedID 28533441

  • Greater than the sum of its parts? Modelling population contact and interaction of cultural repertoires. Journal of the Royal Society, Interface Creanza, N., Kolodny, O., Feldman, M. W. 2017; 14 (130)

    Abstract

    Evidence for interactions between populations plays a prominent role in the reconstruction of historical and prehistoric human dynamics; these interactions are usually interpreted to reflect cultural practices or demographic processes. The sharp increase in long-distance transportation of lithic material between the Middle and Upper Palaeolithic, for example, is seen as a manifestation of the cultural revolution that defined the transition between these epochs. Here, we propose that population interaction is not only a reflection of cultural change but also a potential driver of it. We explore the possible effects of inter-population migration on cultural evolution when migrating individuals possess core technological knowledge from their original population. Using a computational framework of cultural evolution that incorporates realistic aspects of human innovation processes, we show that migration can lead to a range of outcomes, including punctuated but transient increases in cultural complexity, an increase of cultural complexity to an elevated steady state and the emergence of a positive feedback loop that drives ongoing acceleration in cultural accumulation. Our findings suggest that population contact may have played a crucial role in the evolution of hominin cultures and propose explanations for observations of Palaeolithic cultural change whose interpretations have been hotly debated.

    View details for DOI 10.1098/rsif.2017.0171

    View details for PubMedID 28468920

  • Within-Epitope Interactions Can Bias CTL Escape Estimation in Early HIV Infection. Frontiers in immunology Garcia, V., Feldman, M. W. 2017; 8: 423

    Abstract

    As human immunodeficiency virus (HIV) begins to replicate within hosts, immune responses are elicited against it. Escape mutations in viral epitopes-immunogenic peptide parts presented on the surface of infected cells-allow HIV to partially evade these responses, and thus rapidly go to fixation. The faster they go to fixation, i.e., the higher their escape rate, the larger the selective pressure exerted by the immune system is assumed to be. This relation underpins the rationale for using escapes to assess the strength of immune responses. However, escape rate estimates are often obtained by employing an aggregation procedure, where several mutations that affect the same epitope are aggregated into a single, composite epitope mutation. The aggregation procedure thus rests upon the assumption that all within-epitope mutations have indistinguishable effects on immune recognition. In this study, we investigate how violation of this assumption affects escape rate estimates. To this end, we extend a previously developed simulation model of HIV that accounts for mutation, selection, and recombination to include different distributions of fitness effects (DFEs) and inter-mutational genomic distances. We use this discrete time Wright-Fisher based model to simulate early within-host evolution of HIV for DFEs and apply standard estimation methods to infer the escape rates. We then compare true with estimated escape rate values. We also compare escape rate values obtained by applying the aggregation procedure with values estimated without use of that procedure. We find that across the DFEs analyzed, the aggregation procedure alters the detectability of escape mutations: large-effect mutations are overrepresented while small-effect mutations are concealed. The effect of the aggregation procedure is similar to extracting the largest-effect mutation appearing within an epitope. Furthermore, the more pronounced the over-exponential decay of the DFEs, the more severely true escape rates are underestimated. We conclude that the aggregation procedure has two main consequences. On the one hand, it leads to a misrepresentation of the DFE of fixed mutations. On the other hand, it conceals within-epitope interactions that may generate irregularities in mutation frequency trajectories that are thus left unexplained.

    View details for DOI 10.3389/fimmu.2017.00423

    View details for PubMedID 28507544

    View details for PubMedCentralID PMC5410659

  • A Complex, Polygenic Architecture for Lightened Skin Pigmentation in the Southern African KhoeSan Martin, A. R., Gignoux, C. R., Lin, M., Granka, J. M., Adams, A., Liu, X., Atkinson, E. G., Guenther, C. A., Beleza, S., Werely, C. J., Myrick, J., Moller, M., Kingsley, D. M., Daly, M. J., Feldman, M. W., Hoal, E. G., Bustamante, C. D., Henn, B. M. WILEY. 2017: 277
  • High Heritability and Ancestry Dominance are behind the Genetics of Short Stature in South African KhoeSan Populations Lin, M., Granka, J. M., Martin, A. R., Myrick, J., Atkinson, E. G., Werely, C. J., Gurdasani, D., Pomilla, C., Carstensen, T., Scelza, B., Moller, M., Sandhu, M., Bustamante, C. D., Hoal, E. G., Feldman, M. W., Gignoux, C. R., Henn, B. M. WILEY. 2017: 263–64
  • Unified reduction principle for the evolution of mutation, migration, and recombination. Proceedings of the National Academy of Sciences of the United States of America Altenberg, L., Liberman, U., Feldman, M. W. 2017

    Abstract

    Modifier-gene models for the evolution of genetic information transmission between generations of organisms exhibit the reduction principle: Selection favors reduction in the rate of variation production in populations near equilibrium under a balance of constant viability selection and variation production. Whereas this outcome has been proven for a variety of genetic models, it has not been proven in general for multiallelic genetic models of mutation, migration, and recombination modification with arbitrary linkage between the modifier and major genes under viability selection. We show that the reduction principle holds for all of these cases by developing a unifying mathematical framework that characterizes all of these evolutionary models.

    View details for DOI 10.1073/pnas.1619655114

    View details for PubMedID 28265103

    View details for PubMedCentralID PMC5373362

  • The Driving Forces of Cultural Complexity : Neanderthals, Modern Humans, and the Question of Population Size. Human nature (Hawthorne, N.Y.) Fogarty, L., Wakano, J. Y., Feldman, M. W., Aoki, K. 2017; 28 (1): 39-52

    Abstract

    The forces driving cultural accumulation in human populations, both modern and ancient, are hotly debated. Did genetic, demographic, or cognitive features of behaviorally modern humans (as opposed to, say, early modern humans or Neanderthals) allow culture to accumulate to its current, unprecedented levels of complexity? Theoretical explanations for patterns of accumulation often invoke demographic factors such as population size or density, whereas statistical analyses of variation in cultural complexity often point to the importance of environmental factors such as food stability, in determining cultural complexity. Here we use both an analytical model and an agent-based simulation model to show that a full understanding of the emergence of behavioral modernity, and the cultural evolution that has followed, depends on understanding and untangling the complex relationships among culture, genetically determined cognitive ability, and demographic history. For example, we show that a small but growing population could have a different number of cultural traits from a shrinking population with the same absolute number of individuals in some circumstances.

    View details for DOI 10.1007/s12110-016-9275-6

    View details for PubMedID 27783325

  • Female fertility history and mid-late-life health: Findings from China. Journal of women & aging Li, X., Jiang, Q., Li, S., Feldman, M. W. 2017; 30 (1): 62-74

    Abstract

    China's middle-aged and older women suffer from poorer health than men. Using national baseline data from the China Health and Retirement Longitudinal Study (CHARLS), a survey conducted from 2011 to 2012, this article applies logistic models to investigate the association between female fertility history (parity, early childbearing, late childbearing) and middle-aged and late-life health. We find that parity is related to the mid-late-life health of women. Women with four children or more are more likely to suffer from activities of daily living (ADL) impairment and poorer self-rated health than those with one to three children. Early childbearing is associated with ADL impairment; however, the correlation is mediated by socioeconomic status. Early childbearing is related to self-rated health in later life by an indirect-only mediation effect via educational attainment and personal income.

    View details for DOI 10.1080/08952841.2016.1259445

    View details for PubMedID 28151095

    View details for PubMedCentralID PMC5540811

  • Optimization of the Critical Diameter and Average Path Length of Social Networks COMPLEXITY Du, H., He, X., Du, W., Feldman, M. W. 2017
  • Optimizing transformations of structural balance in signed networks with potential relationships PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS Du, H., He, X., Wang, S., Gong, M., Feldman, M. W. 2017; 465: 414-424
  • An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell Martin, A. R., Lin, M. n., Granka, J. M., Myrick, J. W., Liu, X. n., Sockell, A. n., Atkinson, E. G., Werely, C. J., Möller, M. n., Sandhu, M. S., Kingsley, D. M., Hoal, E. G., Liu, X. n., Daly, M. J., Feldman, M. W., Gignoux, C. R., Bustamante, C. D., Henn, B. M. 2017; 171 (6): 1340–53.e14

    Abstract

    Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

    View details for PubMedID 29195075

  • On the Relationship Between the Marriage Squeeze and the Quality of Life of Rural Men in China. American journal of men's health Yang, X., Li, S., Attané, I., Feldman, M. W. 2016

    Abstract

    China is facing a male marriage squeeze, as there are more men in the marriage market than potential female partners. As a consequence, some men may fail to ever marry. However, while some studies have suggested that most unmarried men affected by the marriage squeeze in rural China feel a sense of failure, the quality of life of the men who remain unmarried against their will remains largely unexplored. Using data collected in rural Hanbin district of Ankang City (Shaanxi, China), this study analyzes the relationship between the marriage squeeze and the quality of life among rural men. Descriptive analyses indicate that the quality of life of unmarried men aged 28 years and older tends to be worse than for both younger unmarried men and married men. Also, the quality of life of men who perceive the marriage squeeze appears to be worse than that of those who do not. Regression analyses reveal that the perceived marriage squeeze and age independently have a significant negative relationship with the quality of life of rural men.

    View details for PubMedID 27923964

  • Evolution of reduced mutation under frequency-dependent selection THEORETICAL POPULATION BIOLOGY Liberman, U., Behar, H., Feldman, M. W. 2016; 112: 52-59

    Abstract

    Most models for the evolution of mutation under frequency-dependent selection involve some form of host-parasite interaction. These generally involve cyclic dynamics under which mutation may increase. Here we show that the reduction principle for the evolution of mutation, which is generally true for frequency-independent selection, also holds under frequency-dependent selection on haploids and diploids that does not involve cyclic dynamics.

    View details for DOI 10.1016/j.tpb.2016.07.004

    View details for Web of Science ID 000389173400006

    View details for PubMedID 27568577

  • A Bibliometric History of the Journal GENETICS GENETICS Telis, N., Lehmann, B. V., Feldman, M. W., Pritchard, J. K. 2016; 204 (4): 1337-1342

    View details for DOI 10.1534/genetics.116.196964

    View details for Web of Science ID 000390765500004

    View details for PubMedID 27927899

    View details for PubMedCentralID PMC5161266

  • Game-Changing Innovations: How Culture Can Change the Parameters of Its Own Evolution and Induce Abrupt Cultural Shifts PLOS COMPUTATIONAL BIOLOGY Kolodny, O., Creanza, N., Feldman, M. W. 2016; 12 (12)

    Abstract

    One of the most puzzling features of the prehistoric record of hominid stone tools is its apparent punctuation: it consists of abrupt bursts of dramatic change that separate long periods of largely unchanging technology. Within each such period, small punctuated cultural modifications take place. Punctuation on multiple timescales and magnitudes is also found in cultural trajectories from historical times. To explain these sharp cultural bursts, researchers invoke such external factors as sudden environmental change, rapid cognitive or morphological change in the hominids that created the tools, or replacement of one species or population by another. Here we propose a dynamic model of cultural evolution that accommodates empirical observations: without invoking external factors, it gives rise to a pattern of rare, dramatic cultural bursts, interspersed by more frequent, smaller, punctuated cultural modifications. Our model includes interdependent innovation processes that occur at different rates. It also incorporates a realistic aspect of cultural evolution: cultural innovations, such as those that increase food availability or that affect cultural transmission, can change the parameters that affect cultural evolution, thereby altering the population's cultural dynamics and steady state. This steady state can be regarded as a cultural carrying capacity. These parameter-changing cultural innovations occur very rarely, but whenever one occurs, it triggers a dramatic shift towards a new cultural steady state. The smaller and more frequent punctuated cultural changes, on the other hand, are brought about by innovations that spur the invention of further, related, technology, and which occur regardless of whether the population is near its cultural steady state. Our model suggests that common interpretations of cultural shifts as evidence of biological change, for example the appearance of behaviorally modern humans, may be unwarranted.

    View details for DOI 10.1371/journal.pcbi.1005302

    View details for Web of Science ID 000392126000057

    View details for PubMedID 28036346

    View details for PubMedCentralID PMC5241012

  • Worldwide genetic and cultural change in human evolution CURRENT OPINION IN GENETICS & DEVELOPMENT Creanza, N., Feldman, M. W. 2016; 41: 85-92

    Abstract

    Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food. Human culture interacts with genes and the environment in complex ways, and studying genes and culture together can deepen our understanding of human evolution.

    View details for DOI 10.1016/j.gde.2016.08.006

    View details for Web of Science ID 000389915800012

    View details for PubMedID 27644074

  • Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models. The Lancet. Global health Houben, R. M., Menzies, N. A., Sumner, T., Huynh, G. H., Arinaminpathy, N., Goldhaber-Fiebert, J. D., Lin, H., Wu, C., Mandal, S., Pandey, S., Suen, S., Bendavid, E., Azman, A. S., Dowdy, D. W., Bacaër, N., Rhines, A. S., Feldman, M. W., Handel, A., Whalen, C. C., Chang, S. T., Wagner, B. G., Eckhoff, P. A., Trauer, J. M., Denholm, J. T., McBryde, E. S., Cohen, T., Salomon, J. A., Pretorius, C., Lalli, M., Eaton, J. W., Boccia, D., Hosseini, M., Gomez, G. B., Sahu, S., Daniels, C., Ditiu, L., Chin, D. P., Wang, L., Chadha, V. K., Rade, K., Dewan, P., Hippner, P., Charalambous, S., Grant, A. D., Churchyard, G., Pillay, Y., Mametja, L. D., Kimerling, M. E., Vassall, A., White, R. G. 2016; 4 (11): e806-e815

    Abstract

    The post-2015 End TB Strategy proposes targets of 50% reduction in tuberculosis incidence and 75% reduction in mortality from tuberculosis by 2025. We aimed to assess whether these targets are feasible in three high-burden countries with contrasting epidemiology and previous programmatic achievements.11 independently developed mathematical models of tuberculosis transmission projected the epidemiological impact of currently available tuberculosis interventions for prevention, diagnosis, and treatment in China, India, and South Africa. Models were calibrated with data on tuberculosis incidence and mortality in 2012. Representatives from national tuberculosis programmes and the advocacy community provided distinct country-specific intervention scenarios, which included screening for symptoms, active case finding, and preventive therapy.Aggressive scale-up of any single intervention scenario could not achieve the post-2015 End TB Strategy targets in any country. However, the models projected that, in the South Africa national tuberculosis programme scenario, a combination of continuous isoniazid preventive therapy for individuals on antiretroviral therapy, expanded facility-based screening for symptoms of tuberculosis at health centres, and improved tuberculosis care could achieve a 55% reduction in incidence (range 31-62%) and a 72% reduction in mortality (range 64-82%) compared with 2015 levels. For India, and particularly for China, full scale-up of all interventions in tuberculosis-programme performance fell short of the 2025 targets, despite preventing a cumulative 3·4 million cases. The advocacy scenarios illustrated the high impact of detecting and treating latent tuberculosis.Major reductions in tuberculosis burden seem possible with current interventions. However, additional interventions, adapted to country-specific tuberculosis epidemiology and health systems, are needed to reach the post-2015 End TB Strategy targets at country level.Bill and Melinda Gates Foundation.

    View details for DOI 10.1016/S2214-109X(16)30199-1

    View details for PubMedID 27720688

  • Structural Balance in Fully Signed Networks COMPLEXITY Du, H., He, X., Feldman, M. W. 2016; 21 (S1): 497-511

    View details for DOI 10.1002/cplx.21764

    View details for Web of Science ID 000388332600040

  • Reply to Yang et al.: GCTA produces unreliable heritability estimates. Proceedings of the National Academy of Sciences of the United States of America Krishna Kumar, S., Feldman, M. W., Rehkopf, D. H., Tuljapurkar, S. 2016; 113 (32): E4581-?

    View details for DOI 10.1073/pnas.1608425113

    View details for PubMedID 27457962

    View details for PubMedCentralID PMC4987787

  • The Italian genome reflects the history of Europe and the Mediterranean basin EUROPEAN JOURNAL OF HUMAN GENETICS Fiorito, G., Di Gaetano, C., Guarrera, S., Rosa, F., Feldman, M. W., Piazza, A., Matullo, G. 2016; 24 (7): 1056-1062

    Abstract

    Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population's ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., 'barbarian invasion' of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.

    View details for DOI 10.1038/ejhg.2015.233

    View details for Web of Science ID 000378098000018

    View details for PubMedID 26554880

  • China's Marriage Squeeze: A Decomposition into Age and Sex Structure SOCIAL INDICATORS RESEARCH Jiang, Q., Li, X., Li, S., Feldman, M. W. 2016; 127 (2): 793-807
  • China's marriage squeeze: A decomposition into age and sex structure. Social indicators research Jiang, Q., Li, X., Li, S., Feldman, M. W. 2016; 127 (2): 793-807

    Abstract

    Most recent studies of marriage patterns in China have emphasized the male-biased sex ratio but have largely neglected age structure as a factor in China's male marriage squeeze. In this paper we develop an index we call "spousal sex ratio" (SSR) to measure the marriage squeeze, and a method of decomposing the proportion of male surplus into age and sex structure effects within a small spousal age difference interval. We project that China's marriage market will be confronted with a relatively severe male squeeze. For the decomposition of the cohort aged 30, from 2010 to 2020 age structure will be dominant, while from 2020 through 2034 the contribution of age structure will gradually decrease and that of sex structure will increase. From then on, sex structure will be dominant. The index and decomposition, concentrated on a specific female birth cohort, can distinguish spousal competition for single cohorts which may be covered by a summary index for the whole marriage market; these can also be used for consecutive cohorts to reflect the situation of the whole marriage market.

    View details for DOI 10.1007/s11205-015-0981-y

    View details for PubMedID 27242390

    View details for PubMedCentralID PMC4883114

  • The Climate Change Challenge and Barriers to the Exercise of Foresight Intelligence BIOSCIENCE Ross, L., Arrow, K., Cialdini, R., Diamond-Smith, N., Diamond, J., Dunne, J., Feldman, M., Horn, R., Kennedy, D., Murphy, C., Pirages, D., Smith, K., York, R., Ehrlich, P. 2016; 66 (5): 363-370
  • Cultural niche construction of repertoire size and learning strategies in songbirds EVOLUTIONARY ECOLOGY Creanza, N., Fogarty, L., Feldman, M. W. 2016; 30 (2): 285-305
  • An introduction to niche construction theory EVOLUTIONARY ECOLOGY Laland, K., Matthews, B., Feldman, M. W. 2016; 30 (2): 191-202
  • An ecocultural model predicts Neanderthal extinction through competition with modern humans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Gilpin, W., Feldman, M. W., Aoki, K. 2016; 113 (8): 2134-2139

    Abstract

    Archaeologists argue that the replacement of Neanderthals by modern humans was driven by interspecific competition due to a difference in culture level. To assess the cogency of this argument, we construct and analyze an interspecific cultural competition model based on the Lotka-Volterra model, which is widely used in ecology, but which incorporates the culture level of a species as a variable interacting with population size. We investigate the conditions under which a difference in culture level between cognitively equivalent species, or alternatively a difference in underlying learning ability, may produce competitive exclusion of a comparatively (although not absolutely) large local Neanderthal population by an initially smaller modern human population. We find, in particular, that this competitive exclusion is more likely to occur when population growth occurs on a shorter timescale than cultural change, or when the competition coefficients of the Lotka-Volterra model depend on the difference in the culture levels of the interacting species.

    View details for DOI 10.1073/pnas.1524861113

    View details for Web of Science ID 000370620300058

    View details for PubMedID 26831111

    View details for PubMedCentralID PMC4776499

  • An introduction to niche construction theory. Evolutionary ecology Laland, K., Matthews, B., Feldman, M. W. 2016; 30: 191-202

    Abstract

    Niche construction refers to the modification of selective environments by organisms. Theoretical and empirical studies of niche construction are increasing in importance as foci in evolutionary ecology. This special edition presents theoretical and empirical research that illustrates the significance of niche construction to the field. Here we set the scene for the following papers by (1) discussing the history of niche construction research, (2) providing clear definitions that distinguish niche construction from related concepts such as ecosystem engineering and the extended phenotype, (3) providing a brief summary of the findings of niche construction research, (4) discussing the contribution of niche construction and ecological inheritance to (a) expanded notions of inheritance, and (b) the extended evolutionary synthesis, and (5) briefly touching on some of the issues that underlie the controversies over niche construction.

    View details for DOI 10.1007/s10682-016-9821-z

    View details for PubMedID 27429507

    View details for PubMedCentralID PMC4922671

  • Investigating the Consequences of Interference between Multiple CD8(+) T Cell Escape Mutations in Early HIV Infection PLOS COMPUTATIONAL BIOLOGY Garcia, V., Feldman, M. W., Regoes, R. R. 2016; 12 (2)

    Abstract

    During early human immunodeficiency virus (HIV) infection multiple CD8+ T cell responses are elicited almost simultaneously. These responses exert strong selective pressures on different parts of HIV's genome, and select for mutations that escape recognition and are thus beneficial to the virus. Some studies reveal that the later these escape mutations emerge, the more slowly they go to fixation. This pattern of escape rate decrease(ERD) can arise by distinct mechanisms. In particular, in large populations with high beneficial mutation rates interference among different escape strains--an effect that can emerge in evolution with asexual reproduction and results in delayed fixation times of beneficial mutations compared to sexual reproduction--could significantly impact the escape rates of mutations. In this paper, we investigated how interference between these concurrent escape mutations affects their escape rates in systems with multiple epitopes, and whether it could be a source of the ERD pattern. To address these issues, we developed a multilocus Wright-Fisher model of HIV dynamics with selection, mutation and recombination, serving as a null-model for interference. We also derived an interference-free null model assuming initial neutral evolution before immune response elicitation. We found that interference between several equally selectively advantageous mutations can generate the observed ERD pattern. We also found that the number of loci, as well as recombination rates substantially affect ERD. These effects can be explained by the underexponential decline of escape rates over time. Lastly, we found that the observed ERD pattern in HIV infected individuals is consistent with both independent, interference-free mutations as well as interference effects. Our results confirm that interference effects should be considered when analyzing HIV escape mutations. The challenge in estimating escape rates and mutation-associated selective coefficients posed by interference effects cannot simply be overcome by improved sampling frequencies or sizes. This problem is a consequence of the fundamental shortcomings of current estimation techniques under interference regimes. Hence, accounting for the stochastic nature of competition between mutations demands novel estimation methodologies based on the analysis of HIV strains, rather than mutation frequencies.

    View details for DOI 10.1371/journal.pcbi.1004721

    View details for Web of Science ID 000376582900002

    View details for PubMedID 26829720

    View details for PubMedCentralID PMC4735108

  • Limitations of GCTA as a solution to the missing heritability problem PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kumar, S. K., Feldman, M. W., Rehkopf, D. H., Tuljapurkar, S. 2016; 113 (1): E61-E70

    Abstract

    Genome-wide association studies (GWASs) seek to understand the relationship between complex phenotype(s) (e.g., height) and up to millions of single-nucleotide polymorphisms (SNPs). Early analyses of GWASs are commonly believed to have "missed" much of the additive genetic variance estimated from correlations between relatives. A more recent method, genome-wide complex trait analysis (GCTA), obtains much higher estimates of heritability using a model of random SNP effects correlated between genotypically similar individuals. GCTA has now been applied to many phenotypes from schizophrenia to scholastic achievement. However, recent studies question GCTA's estimates of heritability. Here, we show that GCTA applied to current SNP data cannot produce reliable or stable estimates of heritability. We show first that GCTA depends sensitively on all singular values of a high-dimensional genetic relatedness matrix (GRM). When the assumptions in GCTA are satisfied exactly, we show that the heritability estimates produced by GCTA will be biased and the standard errors will likely be inaccurate. When the population is stratified, we find that GRMs typically have highly skewed singular values, and we prove that the many small singular values cannot be estimated reliably. Hence, GWAS data are necessarily overfit by GCTA which, as a result, produces high estimates of heritability. We also show that GCTA's heritability estimates are sensitive to the chosen sample and to measurement errors in the phenotype. We illustrate our results using the Framingham dataset. Our analysis suggests that results obtained using GCTA, and the results' qualitative interpretations, should be interpreted with great caution.

    View details for DOI 10.1073/pnas.1520109113

    View details for Web of Science ID 000367520400011

    View details for PubMedCentralID PMC4711841

  • Limitations of GCTA as a solution to the missing heritability problem. Proceedings of the National Academy of Sciences of the United States of America Krishna Kumar, S., Feldman, M. W., Rehkopf, D. H., Tuljapurkar, S. 2016; 113 (1): E61-70

    Abstract

    Genome-wide association studies (GWASs) seek to understand the relationship between complex phenotype(s) (e.g., height) and up to millions of single-nucleotide polymorphisms (SNPs). Early analyses of GWASs are commonly believed to have "missed" much of the additive genetic variance estimated from correlations between relatives. A more recent method, genome-wide complex trait analysis (GCTA), obtains much higher estimates of heritability using a model of random SNP effects correlated between genotypically similar individuals. GCTA has now been applied to many phenotypes from schizophrenia to scholastic achievement. However, recent studies question GCTA's estimates of heritability. Here, we show that GCTA applied to current SNP data cannot produce reliable or stable estimates of heritability. We show first that GCTA depends sensitively on all singular values of a high-dimensional genetic relatedness matrix (GRM). When the assumptions in GCTA are satisfied exactly, we show that the heritability estimates produced by GCTA will be biased and the standard errors will likely be inaccurate. When the population is stratified, we find that GRMs typically have highly skewed singular values, and we prove that the many small singular values cannot be estimated reliably. Hence, GWAS data are necessarily overfit by GCTA which, as a result, produces high estimates of heritability. We also show that GCTA's heritability estimates are sensitive to the chosen sample and to measurement errors in the phenotype. We illustrate our results using the Framingham dataset. Our analysis suggests that results obtained using GCTA, and the results' qualitative interpretations, should be interpreted with great caution.

    View details for DOI 10.1073/pnas.1520109113

    View details for PubMedID 26699465

    View details for PubMedCentralID PMC4711841

  • Evolution of reduced mutation under frequency-dependent selection Theoretical Population Biology Liberman, U., Behar, H., Feldman, M. 2016; 112: 9
  • Evolution in leaps: The punctuated accumulation and loss of cultural innovations PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kolodny, O., Creanza, N., Feldman, M. W. 2015; 112 (49): E6762-E6769

    View details for DOI 10.1073/pnas.1520492112

    View details for PubMedID 26598675

  • Cultural Evolutionary Perspectives on Creativity and Human Innovation TRENDS IN ECOLOGY & EVOLUTION Fogarty, L., Creanza, N., Feldman, M. W. 2015; 30 (12): 736-754

    View details for DOI 10.1016/j.tree.2015.10.004

    View details for PubMedID 26598058

  • The extended evolutionary synthesis: its structure, assumptions and predictions. Proceedings. Biological sciences Laland, K. N., Uller, T., Feldman, M. W., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J. 2015; 282 (1813): 20151019

    Abstract

    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.

    View details for DOI 10.1098/rspb.2015.1019

    View details for PubMedID 26246559

    View details for PubMedCentralID PMC4632619

  • Impacts of conservation and human development policy across stakeholders and scales PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Li, C., Zheng, H., Li, S., Chen, X., Li, J., Zeng, W., Liang, Y., Polasky, S., Feldman, M. W., Ruckelshaus, M., Ouyang, Z., Daily, G. C. 2015; 112 (24): 7396-7401

    Abstract

    Ideally, both ecosystem service and human development policies should improve human well-being through the conservation of ecosystems that provide valuable services. However, program costs and benefits to multiple stakeholders, and how they change through time, are rarely carefully analyzed. We examine one of China's new ecosystem service protection and human development policies: the Relocation and Settlement Program of Southern Shaanxi Province (RSP), which pays households who opt voluntarily to resettle from mountainous areas. The RSP aims to reduce disaster risk, restore important ecosystem services, and improve human well-being. We use household surveys and biophysical data in an integrated economic cost-benefit analysis for multiple stakeholders. We project that the RSP will result in positive net benefits to the municipal government, and to cross-region and global beneficiaries over the long run along with environment improvement, including improved water quality, soil erosion control, and carbon sequestration. However, there are significant short-run relocation costs for local residents so that poor households may have difficulty participating because they lack the resources to pay the initial costs of relocation. Greater subsidies and subsequent supports after relocation are necessary to reduce the payback period of resettled households in the long run. Compensation from downstream beneficiaries for improved water and from carbon trades could be channeled into reducing relocation costs for the poor and sharing the burden of RSP implementation. The effectiveness of the RSP could also be greatly strengthened by early investment in developing human capital and environment-friendly jobs and establishing long-term mechanisms for securing program goals. These challenges and potential solutions pervade ecosystem service efforts globally.

    View details for DOI 10.1073/pnas.1406486112

    View details for Web of Science ID 000356251800034

    View details for PubMedID 26082546

    View details for PubMedCentralID PMC4475968

  • Natural capital and ecosystem services informing decisions: From promise to practice PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Guerry, A. D., Polasky, S., Lubchenco, J., Chaplin-Kramer, R., Daily, G. C., Griffin, R., Ruckelshaus, M., Bateman, I. J., Duraiappah, A., Elmqvist, T., Feldman, M. W., Folke, C., Hoekstra, J., Kareiva, P. M., Keeler, B. L., Li, S., Mckenzie, E., Ouyang, Z., Reyers, B., Ricketts, T. H., Rockstrom, J., Tallis, H., Vira, B. 2015; 112 (24): 7348-7355

    Abstract

    The central challenge of the 21st century is to develop economic, social, and governance systems capable of ending poverty and achieving sustainable levels of population and consumption while securing the life-support systems underpinning current and future human well-being. Essential to meeting this challenge is the incorporation of natural capital and the ecosystem services it provides into decision-making. We explore progress and crucial gaps at this frontier, reflecting upon the 10 y since the Millennium Ecosystem Assessment. We focus on three key dimensions of progress and ongoing challenges: raising awareness of the interdependence of ecosystems and human well-being, advancing the fundamental interdisciplinary science of ecosystem services, and implementing this science in decisions to restore natural capital and use it sustainably. Awareness of human dependence on nature is at an all-time high, the science of ecosystem services is rapidly advancing, and talk of natural capital is now common from governments to corporate boardrooms. However, successful implementation is still in early stages. We explore why ecosystem service information has yet to fundamentally change decision-making and suggest a path forward that emphasizes: (i) developing solid evidence linking decisions to impacts on natural capital and ecosystem services, and then to human well-being; (ii) working closely with leaders in government, business, and civil society to develop the knowledge, tools, and practices necessary to integrate natural capital and ecosystem services into everyday decision-making; and (iii) reforming institutions to change policy and practices to better align private short-term goals with societal long-term goals.

    View details for DOI 10.1073/pnas.1503751112

    View details for Web of Science ID 000356251800027

    View details for PubMedID 26082539

    View details for PubMedCentralID PMC4475956

  • Commercial sex behaviours among involuntary male bachelors: findings from a survey of migrants in Xi'an, China JOURNAL OF PUBLIC HEALTH Yang, X., Li, S., Attane, I., Feldman, M. W. 2015; 37 (2): 305-312

    Abstract

    The highly male-biased sex ratio at birth has produced a severe male 'marriage squeeze' in China. However, with an imbalanced sex ratio, the marriage-squeezed or involuntary bachelors can meet their sexual needs only through ways other than marriage.To investigate the commercial sex behaviours of involuntary bachelors, we conducted a survey on reproductive health and family living among male migrant bachelors in Xi'an City, the capital of Shaanxi Province, from December 2009 to January 2010.The prevalence of commercial sex use was 37.2% among unmarried men, 30.1% among married but separated men and 17.2% among married and cohabitating men (χ(2) = 31.33; P = 0.000; df = 2). Marital status, knowledge about acquired immunodeficiency syndrome (AIDS), age and income were associated with the prevalence and frequency of commercial sex behaviours. Condom use was less frequent among involuntary bachelors and was significantly associated with knowledge about AIDS and other sexually transmitted diseases, the frequency of commercial sex behaviours, marital status and age.The higher prevalence of commercial sex behaviours and the lower frequency of condom use indicate a higher risk of disease from commercial sex among involuntary bachelors, implicating both individual and public health.

    View details for DOI 10.1093/pubmed/fdu047

    View details for Web of Science ID 000356184200019

    View details for PubMedID 25104838

  • Bequest Motives of older people in Rural China: From the Perspective of Intergenerational Support. European journal of ageing Jiang, Q., Li, X., Feldman, M. W. 2015; 12 (2): 141-151

    Abstract

    China, a society long characterized by traditional Confucianism and the practice of filial piety, is undergoing dramatic socioeconomic development and erosion of traditions. In this rapidly changing context, the motives behind rural parental bequests have not been well studied. This paper draws on a survey conducted in rural Anhui province of China and uses hierarchical linear models (HLM) to examine whether three kinds of support from children are associated with older parents' bequest motives. We find that while instrumental support accords with an exchange model of motivation, financial transfer is consistent with an altruistic motivation for parental bequest plans. Offspring gender is strongly associated with parental planning of bequests, when only sons are considered; family division is a strong correlate of parents' bequest plan and reflects exchange motivation. These findings have important implications for research on traditional culture and an evolving social security system.

    View details for DOI 10.1007/s10433-014-0330-z

    View details for PubMedID 27242394

    View details for PubMedCentralID PMC4883116

  • Bequest motives of older people in rural China: from the perspective of intergenerational support EUROPEAN JOURNAL OF AGEING Jiang, Q., Li, X., Feldman, M. W. 2015; 12 (2): 141-151
  • Adoption Does Not Increase the Risk of Mortality among Taiwanese Girls in a Longitudinal Analysis PLOS ONE Mattison, S. M., Brown, M. J., Floyd, B., Feldman, M. W. 2015; 10 (4)

    Abstract

    Adopted children often experience health and well-being disadvantages compared to biological children remaining in their natal households. The degree of genetic relatedness is thought to mediate the level of parental investment in children, leading to poorer outcomes of biologically unrelated children. We explore whether mortality is related to adoption in a historical Taiwanese population where adoption rarely occurred among kin. Using Cox proportional hazards models in which adoption is included as a time-dependent covariate, we show that adoption of girls does not increase the risk of mortality, as previously suggested; in fact, it is either protective or neutral with respect to mortality. These results suggest that socio-structural variables may produce positive outcomes for adopted children, even compared to biological children who remain in the care of their parents.

    View details for DOI 10.1371/journal.pone.0122867

    View details for Web of Science ID 000353711600023

    View details for PubMedID 25923106

    View details for PubMedCentralID PMC4414473

  • Phenotype Accessibility and Noise in Random Threshold Gene Regulatory Networks PLOS ONE Pinho, R., Garcia, V., Feldman, M. W. 2015; 10 (4)
  • Family Structure and Quality of Life of Elders in Rural China: The Role of the New Rural Social Pension JOURNAL OF AGING & SOCIAL POLICY Liu, H., Han, X., Xiao, Q., Li, S., Feldman, M. W. 2015; 27 (2): 123-138

    View details for DOI 10.1080/08959420.2014.977662

    View details for Web of Science ID 000354628000002

    View details for PubMedID 25356822

  • A comparison of worldwide phonemic and genetic variation in human populations. Proceedings of the National Academy of Sciences of the United States of America Creanza, N., Ruhlen, M., Pemberton, T. J., Rosenberg, N. A., Feldman, M. W., Ramachandran, S. 2015; 112 (5): 1265-1272

    Abstract

    Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes-sound units that distinguish meaning between words in languages-to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution.

    View details for DOI 10.1073/pnas.1424033112

    View details for PubMedID 25605893

  • The role of climate and out-of-Africa migration in the frequencies of risk alleles for 21 human diseases. BMC genetics Blair, L. M., Feldman, M. W. 2015; 16 (1): 81-?

    Abstract

    Demography and environmental adaptation can affect the global distribution of genetic variants and possibly the distribution of disease. Population heterozygosity of single nucleotide polymorphisms has been shown to decrease strongly with distance from Africa and this has been attributed to the effect of serial founding events during the migration of humans out of Africa. Additionally, population allele frequencies have been shown to change due to environmental adaptation. Here, we investigate the relationship of Out-of-Africa migration and climatic variables to the distribution of risk alleles for 21 diseases.For each disease, we computed the regression of average heterozygosity and average allele frequency of the risk alleles with distance from Africa and 9 environmental variables. We compared these regressions to a null distribution created by regressing statistics for SNPs not associated with disease on distance from Africa and these environmental variables. Additionally, we used Bayenv 2.0 to assess the signal of environmental adaptation associated with individual risk SNPs. For those SNPs in HGDP and HapMap that are risk alleles for type 2 diabetes, we cannot reject that their distribution is as expected from Out-of-Africa migration. However, the allelic statistics for many other diseases correlate more closely with environmental variables than would be expected from the serial founder effect and show signals of environmental adaptation. We report strong environmental interactions with several autoimmune diseases, and note a particularly strong interaction between asthma and summer humidity. Additionally, we identified several risk genes with strong environmental associations.For most diseases, migration does not explain the distribution of risk alleles and the worldwide pattern of allele frequencies for some diseases may be better explained by environmental associations, which suggests that some selection has acted on these diseases.

    View details for DOI 10.1186/s12863-015-0239-3

    View details for PubMedID 26170196

    View details for PubMedCentralID PMC4501093

  • Marriage Squeeze and Intergenerational Support in Contemporary Rural China: Evidence from X County of Anhui Province INTERNATIONAL JOURNAL OF AGING & HUMAN DEVELOPMENT Jin, X., Guo, Q., Feldman, M. W. 2015; 80 (2): 115-139

    View details for DOI 10.1177/0091415015590304

    View details for PubMedID 26243325

  • Evolution in changing environments: Modifiers of mutation, recombination, and migration PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Carja, O., Liberman, U., Feldman, M. W. 2014; 111 (50): 17935-17940

    Abstract

    The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental changes in the patterns of this variation have been important areas of focus in population genetics. On one hand, periods of constant selection pull the genetic makeup of populations toward local fitness optima. On the other, to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced--such as the rates of recombination, mutation, or migration--populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation, and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that the shape, size, variance, and asymmetry of environmental fluctuation have different but predictable effects on evolutionary dynamics.

    View details for DOI 10.1073/pnas.1417664111

    View details for Web of Science ID 000346366500070

    View details for PubMedID 25427794

    View details for PubMedCentralID PMC4273399

  • Echoes of the Past: Hereditarianism and A Troublesome Inheritance PLOS GENETICS Feldman, M. 2014; 10 (12)

    View details for DOI 10.1371/journal.pgen.1004817

    View details for Web of Science ID 000346649900022

    View details for PubMedID 25502763

    View details for PubMedCentralID PMC4263368

  • The role of migration in the evolution of phenotypic switching PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Carja, O., Furrow, R. E., Feldman, M. W. 2014; 281 (1794)
  • The role of migration in the evolution of phenotypic switching. Proceedings. Biological sciences / The Royal Society Carja, O., Furrow, R. E., Feldman, M. W. 2014; 281 (1794)

    Abstract

    Stochastic switching is an example of phenotypic bet hedging, where an individual can switch between different phenotypic states in a fluctuating environment. Although the evolution of stochastic switching has been studied when the environment varies temporally, there has been little theoretical work on the evolution of phenotypic switching under both spatially and temporally fluctuating selection pressures. Here, we explore the interaction of temporal and spatial change in determining the evolutionary dynamics of phenotypic switching. We find that spatial variation in selection is important; when selection pressures are similar across space, migration can decrease the rate of switching, but when selection pressures differ spatially, increasing migration between demes can facilitate the evolution of higher rates of switching. These results may help explain the diverse array of non-genetic contributions to phenotypic variability and phenotypic inheritance observed in both wild and experimental populations.

    View details for DOI 10.1098/rspb.2014.1677

    View details for PubMedID 25232136

  • Stability depends on positive autoregulation in Boolean gene regulatory networks. PLoS computational biology Pinho, R., Garcia, V., Irimia, M., Feldman, M. W. 2014; 10 (11)

    Abstract

    Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific autoregulatory motifs are selected during evolution and how this relates to robustness is largely unknown. Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. We ran evolutionary simulation experiments for different models of selection, including mutation and recombination. Each generation simulated the development of a population of organisms modeled by GRNs. We found that stability and robustness positively correlate with autoregulation; in all investigated scenarios, stable networks had mostly positive autoregulation. Assuming biological networks correspond to stable networks, these results suggest that biological networks should often be dominated by positive autoregulatory loops. This seems to be the case for most studied eukaryotic transcription factor networks, including those in yeast, flies and mammals.

    View details for DOI 10.1371/journal.pcbi.1003916

    View details for PubMedID 25375153

    View details for PubMedCentralID PMC4222607

  • Social Support and Psychological Well-Being Under Social Change in Urban and Rural China SOCIAL INDICATORS RESEARCH Liu, H., Li, S., Xiao, Q., Feldman, M. W. 2014; 119 (2): 979-996
  • Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks PLOS COMPUTATIONAL BIOLOGY Pinho, R., Garcia, V., Irimia, M., Feldman, M. W. 2014; 10 (11)

    View details for DOI 10.1371/journal.pcbi.1003916

    View details for Web of Science ID 000345454400013

    View details for PubMedID 25375153

  • Complexity in models of cultural niche construction with selection and homophily. Proceedings of the National Academy of Sciences of the United States of America Creanza, N., Feldman, M. W. 2014; 111: 10830-10837

    Abstract

    Niche construction is the process by which organisms can alter the ecological environment for themselves, their descendants, and other species. As a result of niche construction, differences in selection pressures may be inherited across generations. Homophily, the tendency of like phenotypes to mate or preferentially associate, influences the evolutionary dynamics of these systems. Here we develop a model that includes selection and homophily as independent culturally transmitted traits that influence the fitness and mate choice determined by another focal cultural trait. We study the joint dynamics of a focal set of beliefs, a behavior that can differentially influence the fitness of those with certain beliefs, and a preference for partnering based on similar beliefs. Cultural transmission, selection, and homophily interact to produce complex evolutionary dynamics, including oscillations, stable polymorphisms of all cultural phenotypes, and simultaneous stability of oscillation and fixation, which have not previously been observed in models of cultural evolution or gene-culture interactions. We discuss applications of this model to the interaction of beliefs and behaviors regarding education, contraception, and animal domestication.

    View details for DOI 10.1073/pnas.1400824111

    View details for PubMedID 25024189

    View details for PubMedCentralID PMC4113930

  • Back to Little Havana: Controlling Gentrification in the Heart of Cuban Miami INTERNATIONAL JOURNAL OF URBAN AND REGIONAL RESEARCH Feldman, M., Jolivet, V. 2014; 38 (4): 1266-1285
  • ASSORTATIVE SOCIAL LEARNING AND ITS IMPLICATIONS FOR HUMAN (AND ANIMAL?) SOCIETIES EVOLUTION Katsnelson, E., Lotem, A., Feldman, M. W. 2014; 68 (7): 1894-1906

    Abstract

    Choosing from whom to learn is an important element of social learning. It affects learner success and the profile of behaviors in the population. Because individuals often differ in their traits and capabilities, their benefits from different behaviors may also vary. Homophily, or assortment, the tendency of individuals to interact with other individuals with similar traits, is known to affect the spread of behaviors in humans. We introduce models to study the evolution of assortative social learning (ASL), where assorting on a trait acts as an individual-specific mechanism for filtering relevant models from which to learn when that trait varies. We show that when the trait is polymorphic, ASL may maintain a stable behavioral polymorphism within a population (independently of coexistence with individual learning in a population). We explore the evolution of ASL when assortment is based on a nonheritable or partially heritable trait, and when ASL competes with different non-ASL strategies: oblique (learning from the parental generation) and vertical (learning from the parent). We suggest that the tendency to assort may be advantageous in the context of social learning, and that ASL might be an important concept for the evolutionary theory of social learning.

    View details for DOI 10.1111/evo.12403

    View details for Web of Science ID 000339052000005

    View details for PubMedID 24628026

  • Evolution of division of labor: Emergence of different activities among group members JOURNAL OF THEORETICAL BIOLOGY Nakahashi, W., Feldman, M. W. 2014; 348: 65-79

    Abstract

    The division of labor is an important component of the organization of human society. However, why this division evolved in hominids requires further investigation. Archeological evidence suggests that it appeared after the emergence of Homo sapiens and contributed to the great success of our species. We develop a mathematical model to investigate under what conditions division of labor should evolve. We assume two types of resources the acquisition of which demands different skills, and study the evolution of the strategy that an individual should use to divide its lifetime into learning and using each skill. We show that division of labor likely evolves when group size is large, skill learning is important for acquiring resources, and there is food sharing within a group. We also investigate division of labor by gender under the assumption that the genders have different efficiencies in acquiring each resource. We show that division of labor by gender likely evolves when skill learning is important and the difference in efficiencies between genders in acquiring resources is large. We discuss how the results of our analysis might apply to the evolution of division of labor in hominids.

    View details for DOI 10.1016/j.jtbi.2014.01.027

    View details for Web of Science ID 000334324600007

    View details for PubMedID 24486228

  • An arms race between producers and scroungers can drive the evolution of social cognition BEHAVIORAL ECOLOGY Arbilly, M., Weissman, D. B., Feldman, M. W., Grodzinski, U. 2014; 25 (3): 487-495
  • An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral ecology : official journal of the International Society for Behavioral Ecology Arbilly, M., Weissman, D. B., Feldman, M. W., Grodzinski, U. 2014; 25 (3): 487-495

    Abstract

    The "social intelligence hypothesis" states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.

    View details for DOI 10.1093/beheco/aru002

    View details for PubMedID 24822021

    View details for PubMedCentralID PMC4014306

  • Marriage Squeeze, Never-Married Proportion, and Mean Age at First Marriage in China. Population research and policy review Jiang, Q., Feldman, M. W., Li, S. 2014; 33: 189-204

    Abstract

    China's sex ratio imbalance and the surplus of males have received a great deal of attention, but measures of the extent of the marriage squeeze do not take into account the marital status of population. In this paper, we devise an index of the marriage squeeze for the never-married population and use it to project the male marriage squeeze from 2000 to 2060. From the predicted population and nuptiality tables, we estimate trends in the proportion of men that never marry by age 50 and the mean age at first marriage. We find that the marriage squeeze is much more intense if only the never-married population is considered, rather than including all people without distinguishing their marital status. As the lifelong never-married proportion increases, mean age at first marriage rises first and then declines.

    View details for DOI 10.1007/s11113-013-9283-8

    View details for PubMedID 24634556

    View details for PubMedCentralID PMC3948615

  • Marriage Squeeze, Never-Married Proportion, and Mean Age at First Marriage in China POPULATION RESEARCH AND POLICY REVIEW Jiang, Q., Feldman, M. W., Li, S. 2014; 33 (2): 189-204
  • The evolution of phenotypic switching in subdivided populations. Genetics Carja, O., Liberman, U., Feldman, M. W. 2014; 196 (4): 1185-1197

    Abstract

    Stochastic switching is an example of phenotypic bet hedging, where offspring can express a phenotype different from that of their parents. Phenotypic switching is well documented in viruses, yeast, and bacteria and has been extensively studied when the selection pressures vary through time. However, there has been little work on the evolution of phenotypic switching under both spatially and temporally fluctuating selection pressures. Here we use a population genetic model to explore the interaction of temporal and spatial variation in determining the evolutionary dynamics of phenotypic switching. We find that the stable switching rate is mainly determined by the rate of environmental change and the migration rate. This stable rate is also a decreasing function of the recombination rate, although this is a weaker effect than those of either the period of environmental change or the migration rate. This study highlights the interplay of spatial and temporal environmental variability, offering new insights into how migration can influence the evolution of phenotypic switching rates, mutation rates, or other sources of phenotypic variation.

    View details for DOI 10.1534/genetics.114.161364

    View details for PubMedID 24496012

  • Male Marriage Squeeze and Inter-provincial Marriage in Central China: evidence from Anhui JOURNAL OF CONTEMPORARY CHINA Liu, L., Jin, X., Brown, M. J., Feldman, M. W. 2014; 23 (86): 351-371

    Abstract

    Since the 1990s, inter-provincial female migration for marriage has become important in central and eastern rural China. Using survey data from X County in rural Anhui Province, we explore the arrangement of inter-provincial marriages, as well as the characteristics of husbands and wives, marital satisfaction, and marital stability for these marriages. We find that inter-provincial marriage is an important option for local men to respond to the marriage squeeze and the increasing expense of marriage. It helps to relieve the shortage of marriageable women in the local marriage market. Because this kind of marriage is based on economic exchange, but not affection, it is often subject to a higher risk of marriage instability, and can lead to such illegal behaviors as marriage fraud and mercenary marriage.

    View details for DOI 10.1080/10670564.2013.832541

    View details for Web of Science ID 000331361200009

    View details for PubMedID 26594102

    View details for PubMedCentralID PMC4650892

  • Genetic variation and the evolution of epigenetic regulation. Evolution; international journal of organic evolution Furrow, R. E., Feldman, M. W. 2014; 68 (3): 673-683

    Abstract

    Epigenetic variation has been observed in a range of organisms, leading to questions of the adaptive significance of this variation. In this study, we present a model to explore the ecological and genetic conditions that select for epigenetic regulation. We find that the rate of temporal environmental change is a key factor controlling the features of this evolution. When the environment fluctuates rapidly between states with different phenotypic optima, epigenetic regulation may evolve but we expect to observe low transgenerational inheritance of epigenetic states, whereas when this fluctuation occurs over longer time scales, regulation may evolve to generate epigenetic states that are inherited faithfully for many generations. In all cases, the underlying genetic variation at the epigenetically regulated locus is a crucial factor determining the range of conditions that allow for evolution of epigenetic mechanisms.

    View details for DOI 10.1111/evo.12225

    View details for PubMedID 24588347

  • A new network structure entropy based on maximum flow ACTA PHYSICA SINICA Cai Meng, M., Du Hai-Feng, H. F., Feldman, M. W. 2014; 63 (6)
  • Adaptive foraging behaviour of individual pollinators and the coexistence of co-flowering plants PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Song, Z., Feldman, M. W. 2014; 281 (1776)

    Abstract

    Although pollinators can play a central role in determining the structure and stability of plant communities, little is known about how their adaptive foraging behaviours at the individual level, e.g. flower constancy, structure these interactions. Here, we construct a mathematical model that integrates individual adaptive foraging behaviour and population dynamics of a community consisting of two plant species and a pollinator species. We find that adaptive foraging at the individual level, as a complementary mechanism to adaptive foraging at the species level, can further enhance the coexistence of plant species through niche partitioning between conspecific pollinators. The stabilizing effect is stronger than that of unbiased generalists when there is also strong competition between plant species over other resources, but less so than that of multiple specialist species. This suggests that adaptive foraging in mutualistic interactions can have a very different impact on the plant community structure from that in predator-prey interactions. In addition, the adaptive behaviour of individual pollinators may cause a sharp regime shift for invading plant species. These results indicate the importance of integrating individual adaptive behaviour and population dynamics for the conservation of native plant communities.

    View details for DOI 10.1098/rspb.2013.2437

    View details for Web of Science ID 000332381500009

    View details for PubMedID 24352943

    View details for PubMedCentralID PMC3871311

  • Evolution of learning strategies in temporally and spatially variable environments: A review of theory THEORETICAL POPULATION BIOLOGY Aoki, K., Feldman, M. W. 2014; 91: 3-19

    Abstract

    The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change--coevolutionary, two-timescale, and information decay--are compared and shown to sometimes yield contradictory results. The so-called Rogers' paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers' paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent.

    View details for DOI 10.1016/j.tpb.2013.10.004

    View details for Web of Science ID 000329887200002

    View details for PubMedID 24211681

    View details for PubMedCentralID PMC4412376

  • Preface to the Theoretical Population Biology special issue on learning. Theoretical population biology Feldman, M. W., Aoki, K. 2014; 91: 1-2

    View details for DOI 10.1016/j.tpb.2013.09.001

    View details for PubMedID 24055618

  • Phylogenetic resolution power of microsatellites and various single-nucleotide polymorphism types assessed in 10 divergent chicken populations ANIMAL GENETICS Granevitze, Z., David, L., Twito, T., Weigend, S., Feldman, M., Hillel, J. 2014; 45 (1): 87-95

    Abstract

    There has been some debate over the question of which types of DNA variation are most appropriate to accurately reconstruct evolutionary events. We compared the capacity of microsatellites (STRs) and various types of single-nucleotide polymorphism (SNP) loci in the chicken genome. The SNP types differ in their location: in exons, introns and promoters. Genetic distances between all possible pairs of 10 populations were calculated for each marker type. STR loci, which are much more polymorphic than are SNPs, are considered to have occurred at recent time compared with old evolutionary events of SNPs. Using structure software, STR loci assigned individuals to their population much more correctly than did any other marker types, whereas SNPs at promoter regions gave the poorest ascription. Furthermore, 29 STR markers were even better than all 152 SNPs together. Ancient evolutionary events that produced genetic differences between the most distant populations such as Red Jungle Fowl and domestic chicken were detected better by exons and introns than by STR loci and promoters. The significant interactions found between marker types and populations suggest that marker types had different phylogenetic histories, possibly related to a different timescale.

    View details for DOI 10.1111/age.12088

    View details for Web of Science ID 000329456900010

    View details for PubMedID 24028291

  • Exome capture from saliva produces high quality genomic and metagenomic data. BMC genomics Kidd, J. M., Sharpton, T. J., Bobo, D., Norman, P. J., Martin, A. R., Carpenter, M. L., Sikora, M., Gignoux, C. R., Nemat-Gorgani, N., Adams, A., Guadalupe, M., Guo, X., Feng, Q., Li, Y., Liu, X., Parham, P., Hoal, E. G., Feldman, M. W., Pollard, K. S., Wall, J. D., Bustamante, C. D., Henn, B. M. 2014; 15 (1): 262-?

    Abstract

    Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research.We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data.DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.

    View details for DOI 10.1186/1471-2164-15-262

    View details for PubMedID 24708091

    View details for PubMedCentralID PMC4051168

  • Exome capture from saliva produces high quality genomic and metagenomic data. BMC genomics Kidd, J. M., Sharpton, T. J., Bobo, D., Norman, P. J., Martin, A. R., Carpenter, M. L., Sikora, M., Gignoux, C. R., Nemat-Gorgani, N., Adams, A., Guadalupe, M., Guo, X., Feng, Q., Li, Y., Liu, X., Parham, P., Hoal, E. G., Feldman, M. W., Pollard, K. S., Wall, J. D., Bustamante, C. D., Henn, B. M. 2014; 15: 262-?

    Abstract

    Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research.We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data.DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.

    View details for DOI 10.1186/1471-2164-15-262

    View details for PubMedID 24708091

  • Phenotype accessibility and noise in random threshold gene regulatory networks. PloS one Pinho, R., Garcia, V., Feldman, M. W. 2014; 10 (4)

    Abstract

    Evolution requires phenotypic variation in a population of organisms for selection to function. Gene regulatory processes involved in organismal development affect the phenotypic diversity of organisms. Since only a fraction of all possible phenotypes are predicted to be accessed by the end of development, organisms may evolve strategies to use environmental cues and noise-like fluctuations to produce additional phenotypic diversity, and hence to enhance the speed of adaptation. We used a generic model of organismal development --gene regulatory networks-- to investigate how different levels of noise on gene expression states (i.e. phenotypes) may affect access to new, unique phenotypes, thereby affecting phenotypic diversity. We studied additional strategies that organisms might adopt to attain larger phenotypic diversity: either by augmenting their genome or the number of gene expression states. This was done for different types of gene regulatory networks that allow for distinct levels of regulatory influence on gene expression or are more likely to give rise to stable phenotypes. We found that if gene expression is binary, increasing noise levels generally decreases phenotype accessibility for all network types studied. If more gene expression states are considered, noise can moderately enhance the speed of discovery if three or four gene expression states are allowed, and if there are enough distinct regulatory networks in the population. These results were independent of the network types analyzed, and were robust to different implementations of noise. Hence, for noise to increase the number of accessible phenotypes in gene regulatory networks, very specific conditions need to be satisfied. If the number of distinct regulatory networks involved in organismal development is large enough, and the acquisition of more genes or fine tuning of their expression states proves costly to the organism, noise can be useful in allowing access to more unique phenotypes.

    View details for DOI 10.1371/journal.pone.0119972

    View details for PubMedID 25919290

    View details for PubMedCentralID PMC4412837

  • INVOLUNTARY BACHELORHOOD IN RURAL CHINA: A SOCIAL NETWORK PERSPECTIVE POPULATION Liu, L., Jin, X., Brown, M. J., Feldman, M. W. 2014; 69 (1): 109-133
  • On the stability of the Bayenv method in assessing human SNP-environment associations. Human genomics Blair, L. M., Granka, J. M., Feldman, M. W. 2014; 8 (1): 1-?

    Abstract

    Phenotypic variation along environmental gradients has been documented among and within many species, and in some cases, genetic variation has been shown to be associated with these gradients. Bayenv is a relatively new method developed to detect patterns of polymorphisms associated with environmental gradients. Using a Bayesian Markov Chain Monte Carlo (MCMC) approach, Bayenv evaluates whether a linear model relating population allele frequencies to environmental variables is more probable than a null model based on observed frequencies of neutral markers. Although this method has been used to detect environmental adaptation in a number of species, including humans, plants, fish, and mosquitoes, stability between independent runs of this MCMC algorithm has not been characterized. In this paper, we explore the variability of results between runs and the factors contributing to it.Independent runs of the Bayenv program were carried out using genome-wide single-nucleotide polymorphism (SNP) data from samples from 60 worldwide human populations following previous applications of the Bayenv method. To assess factors contributing to the method's stability, we used varying numbers of MCMC iterations and also analyzed a second modified data set that excluded two Siberian populations with extreme climate variables. Between any two runs, correlations between Bayes factors and the overlap of SNPs in the empirical p value tails were surprisingly low. Enrichments of genic versus non-genic SNPs in the empirical tails were more robust than the empirical p values; however, the significance of the enrichments for some environmental variables still varied among runs, contradicting previously published conclusions. Runs with a greater number of MCMC iterations slightly reduced run-to-run variability, and excluding the Siberian populations did not have a large effect on the stability of the runs.Because of high run-to-run variability, we advise against making conclusions about genome-wide patterns of adaptation based on only one run of the Bayenv algorithm and recommend caution in interpreting previous studies that have used only one run. Moving forward, we suggest carrying out multiple independent runs of Bayenv and averaging Bayes factors between runs to produce more stable and reliable results. With these modifications, future discoveries of environmental adaptation within species using the Bayenv method will be more accurate, interpretable, and easily compared between studies.

    View details for DOI 10.1186/1479-7364-8-1

    View details for PubMedID 24405978

    View details for PubMedCentralID PMC3896655

  • Genetics and the History of the Samaritans: Y-Chromosomal Microsatellites and Genetic Affinity between Samaritans and Cohanim HUMAN BIOLOGY Oefner, P. J., Hoelzl, G., Shen, P., Shpirer, I., Gefel, D., Lavi, T., Woolf, E., Cohen, J., Cinnioglu, C., Underhill, P. A., Rosenberg, N. A., Hochrein, J., Granka, J. M., Hillel, J., Feldman, M. W. 2013; 85 (6): 825-857
  • Genetics and the History of the Samaritans: Y-Chromosomal Microsatellites and Genetic Affinity between Samaritans and Cohanim. Human biology Oefner, P. J., Hölzi, G., Shen, P., Shpirer, I., Gefel, D., Lavi, T., Woolf, E., Cohen, J., Cinnioglu, C., Underhill, P. A., Rosenberg, N. A., Hochrein, J., Granka, J. M., Hillel, J., Feldman, M. W. 2013; 85 (6): 825-858

    Abstract

    The Samaritans are a group of some 750 indigenous Middle Eastern people, about half of whom live in Holon, a suburb of Tel Aviv, and the other half near Nablus. The Samaritan population is believed to have numbered more than a million in late Roman times but less than 150 in 1917. The ancestry of the Samaritans has been subject to controversy from late Biblical times to the present. In this study, liquid chromatography/electrospray ionization/quadrupole ion trap mass spectrometry was used to allelotype 13 Y-chromosomal and 15 autosomal microsatellites in a sample of 12 Samaritans chosen to have as low a level of relationship as possible, and 461 Jews and non-Jews. Estimation of genetic distances between the Samaritans and seven Jewish and three non-Jewish populations from Israel, as well as populations from Africa, Pakistan, Turkey, and Europe, revealed that the Samaritans were closely related to Cohanim. This result supports the position of the Samaritans that they are descendants from the tribes of Israel dating to before the Assyrian exile in 722-720 BCE. In concordance with previously published single-nucleotide polymorphism haplotypes, each Samaritan family, with the exception of the Samaritan Cohen lineage, was observed to carry a distinctive Y-chromosome short tandem repeat haplotype that was not more than one mutation removed from the six-marker Cohen modal haplotype.

    View details for PubMedID 25079122

  • Gender in Marriage and Life Satisfaction Under Gender Imbalance in China: The Role of Intergenerational Support and SES SOCIAL INDICATORS RESEARCH Liu, H., Li, S., Feldman, M. W. 2013; 114 (3): 915-933
  • The role of beginner's luck in learning to prefer risky patches by socially foraging house sparrows BEHAVIORAL ECOLOGY Ilan, T., Katsnelson, E., Motro, U., Feldman, M. W., Lotem, A. 2013; 24 (6): 1398-1406
  • "Bare Branches" and the Marriage Market in Rural China Preliminary Evidence from a Village-Level Survey CHINESE SOCIOLOGICAL REVIEW Jin, X., Liu, L., Li, Y., Feldman, M. W., Li, S. 2013; 46 (1): 83-104
  • The role of cultural transmission in human demographic change: An age-structured model. Theoretical population biology Fogarty, L., Creanza, N., Feldman, M. W. 2013; 88: 68-77

    Abstract

    Human populations vary demographically with population sizes ranging from small groups of hunter-gatherers with less than fifty individuals to vast cities containing many millions. Here we investigate how the cultural transmission of traits affecting survival, fertility, or both can influence the birth rate, age structure, and asymptotic growth rate of a population. We show that the strong spread of such a trait can lead to a demographic transition, similar to that experienced in Europe in the late 19th and early 20th centuries, without using ecological or economic optimizing models. We also show that the spread of a cultural trait that increases fertility, but not survival, can cause demographic change similar to the 'Neolithic demographic transition': a period of increased population growth that is thought to have accompanied the transition from hunter-gatherer to agricultural lifestyles. We investigate the roles of vertical, oblique, and horizontal learning of such a trait in this transition and find that compared to vertical learning alone, horizontal and oblique learning can accelerate the trait's spread, lead to faster population growth, and increase its equilibrium frequency.

    View details for DOI 10.1016/j.tpb.2013.06.006

    View details for PubMedID 23867394

  • Plant-animal mutualism in biological markets: Evolutionary and ecological dynamics driven by non-heritable phenotypic variance THEORETICAL POPULATION BIOLOGY Song, Z., Feldman, M. W. 2013; 88: 20-30

    Abstract

    Mutualism between plants and animals, such as in pollination and seed dispersal, is a fundamental mechanism facilitating the productivity and biodiversity of ecosystems, and it is often considered as an analog of a free-market economy. The coevolution of plant reward and animal choosiness, however, involves an apparent paradox due to incomplete information and limited mutation rates: plant rewards evolve only when animals are choosy, but choosy animals purge the heritable variations of plants, which then favors less choosy animals. Here we use a two-species mathematical model to illustrate how non-heritable phenotypic variances of plants may facilitate the coevolution of rewards and choosiness and solve the paradox with low mutation rates. We simultaneously track the ecological and evolutionary dynamics and show that the population ratio links the two processes and tunes the stable eco-evolutionary equilibrium. Numerical simulations confirm the analytic prediction with varying mutation rates (heritable variance). The efficiency of a biological market is generally suboptimal due to the information constraint and individual competition.

    View details for DOI 10.1016/j.tpb.2013.06.002

    View details for Web of Science ID 000324508700003

    View details for PubMedID 23791699

  • Social Management of Gender Imbalance in China: A Holistic Governance Framework. Economic and political weekly Shuzhuo, L., Zijuan, S., Feldman, M. W. 2013; 48 (35): 79-86

    Abstract

    Since the 1980s, the sex ratio at birth (abbreviated as SRB) in China has been rising and has remained extremely high. With rapid social transition, gender imbalance has become one of the most significant issues of China's social management and has raised many problems and challenges. Innovation in the management principles and public policies of social management urgently needs a new perspective of holistic governance framework. Based on the latest trends in gender imbalance, using data from China's 2010 Population Census, this paper firstly reviews China's strategic policy responses and actions concerning the governance of the male-skewed SRB. With holistic governance theory, we focus on China's "Care for Girls" campaign to analyze the current public policy system. This paper then reveals fragmentation in the current management of China's gender imbalance. Finally we propose a social management framework for addressing China's gender imbalance. The public system needs to be strengthened, and the Chinese government should focus more on vulnerable groups such as forced bachelors in rural areas, and try to bring those groups into the policy framework for governance of gender imbalance. The proposed theoretical framework may help Chinese governments at various levels to design and implement improved social management of gender imbalance issues.

    View details for PubMedID 26663948

    View details for PubMedCentralID PMC4673002

  • The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations PLOS PATHOGENS Pepperell, C. S., Casto, A. M., Kitchen, A., Granka, J. M., Cornejo, O. E., Holmes, E. C., Birren, B., Galagan, J., Feldman, M. W. 2013; 9 (8)

    Abstract

    Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new host every second. While analyses of genetic data from natural populations of M.tb have emphasized the role of genetic drift in shaping patterns of diversity, the influence of natural selection on this successful pathogen is less well understood. We investigated the effects of natural selection on patterns of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence of strong purifying selection, with an estimated genome-wide selection coefficient equal to -9.5 × 10(-4) (95% CI -1.1 × 10(-3) to -6.8 × 10(-4)); this is several orders of magnitude higher than recent estimates for eukaryotic and prokaryotic organisms. We also identified different patterns of variation across categories of gene function. Genes involved in transport and metabolism of inorganic ions exhibited very low levels of non-synonymous polymorphism, equivalent to categories under strong purifying selection (essential and translation-associated genes). The highest levels of non-synonymous variation were seen in a group of transporter genes, likely due to either diversifying selection or local selective sweeps. In addition to selection, we identified other important influences on M.tb genetic diversity, such as a 25-fold expansion of global M.tb populations coincident with explosive growth in human populations (estimated timing 1684 C.E., 95% CI 1620-1713 C.E.). These results emphasize the parallel demographic histories of this obligate pathogen and its human host, and suggest that the dominant effect of selection on M.tb is removal of novel variants, with exceptions in an interesting group of genes involved in transportation and defense. We speculate that the hostile environment within a host imposes strict demands on M.tb physiology, and thus a substantial fitness cost for most new mutations. In this respect, obligate bacterial pathogens may differ from other host-associated microbes such as symbionts.

    View details for DOI 10.1371/journal.ppat.1003543

    View details for Web of Science ID 000323888200037

    View details for PubMedID 23966858

  • The Role of Social Networks in the Integration of Chinese Rural-Urban Migrants: A Migrant-Resident Tie Perspective URBAN STUDIES Yue, Z., Li, S., Jin, X., Feldman, M. W. 2013; 50 (9): 1704-1723
  • Evolution with stochastic fitnesses: A role for recombination. Theoretical population biology Carja, O., Liberman, U., Feldman, M. W. 2013; 86: 29-42

    Abstract

    Phenotypic adaptation to fluctuating environments has been an important focus in the population genetic literature. Previous studies have shown that evolution under temporal variation is determined not only by expected fitness in a given generation, but also by the degree of variation in fitness over generations; in an uncertain environment, alleles that increase the geometric mean fitness can invade a randomly mating population at equilibrium. This geometric mean principle governs the evolutionary interplay of genes controlling mean phenotype and genes controlling phenotypic variation, such as genetic regulators of the epigenetic machinery. Thus, it establishes an important role for stochastic epigenetic variation in adaptation to fluctuating environments: by modifying the geometric mean fitness, variance-modifying genes can change the course of evolution and determine the long-term trajectory of the evolving system. The role of phenotypic variance has previously been studied in systems in which the only driving force is natural selection, and there is no recombination between mean- and variance-modifying genes. Here, we develop a population genetic model to investigate the effect of recombination between mean- and variance-modifiers of phenotype on the geometric mean principle under different environmental regimes and fitness landscapes. We show that interactions of recombination with stochastic epigenetic variation and environmental fluctuations can give rise to complex evolutionary dynamics that differ from those in systems with no recombination.

    View details for DOI 10.1016/j.tpb.2013.02.005

    View details for PubMedID 23517905

  • Long-term evolution is surprisingly predictable in lattice proteins JOURNAL OF THE ROYAL SOCIETY INTERFACE Palmer, M. E., Moudgil, A., Feldman, M. W. 2013; 10 (82)

    Abstract

    It has long been debated whether natural selection acts primarily upon individual organisms, or whether it also commonly acts upon higher-level entities such as lineages. Two arguments against the effectiveness of long-term selection on lineages have been (i) that long-term evolutionary outcomes will not be sufficiently predictable to support a meaningful long-term fitness and (ii) that short-term selection on organisms will almost always overpower long-term selection. Here, we use a computational model of protein folding and binding called 'lattice proteins'. We quantify the long-term evolutionary success of lineages with two metrics called the k-fitness and k-survivability. We show that long-term outcomes are surprisingly predictable in this model: only a small fraction of the possible outcomes are ever realized in multiple replicates. Furthermore, the long-term fitness of a lineage depends only partly on its short-term fitness; other factors are also important, including the 'evolvability' of a lineage-its capacity to produce adaptive variation. In a system with a distinct short-term and long-term fitness, evolution need not be 'short-sighted': lineages may be selected for their long-term properties, sometimes in opposition to short-term selection. Similar evolutionary basins of attraction have been observed in vivo, suggesting that natural biological lineages will also have a predictive long-term fitness.

    View details for DOI 10.1098/rsif.2013.0026

    View details for Web of Science ID 000316415600015

    View details for PubMedID 23466559

    View details for PubMedCentralID PMC3627087

  • The coevolution of long-term pair bonds and cooperation. Journal of evolutionary biology Song, Z., Feldman, M. W. 2013; 26 (5): 963-970

    Abstract

    The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair-matching distribution of the population, and the latter often emerges as a collective outcome of individual pair-bonding traits, which are also under selection. Here, we develop an analytical model and individual-based simulations to study the coevolution of long-term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long-term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long-term pair bonds lead to assortative interactions through pair-matching dynamics, they may promote the prevalence of cooperation. In addition to the pay-off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair-bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems.

    View details for DOI 10.1111/jeb.12111

    View details for PubMedID 23496797

  • Development and Validation of a Gender Ideology Scale for Family Planning Services in Rural China PLOS ONE Yang, X., Li, S., Feldman, M. W. 2013; 8 (4)

    Abstract

    The objectives of this study are to develop a scale of gender role ideology appropriate for assessing Quality of Care in family planning services for rural China. Literature review, focus-group discussions and in-depth interviews with service providers and clients from two counties in eastern and western China, as well as experts' assessments, were used to develop a scale for family planning services. Psychometric methodologies were applied to samples of 601 service clients and 541 service providers from a survey in a district in central China to validate its internal consistency, reliability, and construct validity with realistic and strategic dimensions. This scale is found to be reliable and valid, and has prospects for application both academically and practically in the field.

    View details for DOI 10.1371/journal.pone.0059919

    View details for Web of Science ID 000316930900035

    View details for PubMedID 23573222

  • NICHE CONSTRUCTION THEORY: A PRACTICAL GUIDE FOR ECOLOGISTS QUARTERLY REVIEW OF BIOLOGY Odling-Smee, J., Erwin, D. H., Palkovacs, E. P., Feldman, M. W., Laland, K. N. 2013; 88 (1): 3-28
  • Niche construction theory: a practical guide for ecologists. Quarterly review of biology Odling-Smee, J., Erwin, D. H., Palkovacs, E. P., Feldman, M. W., Laland, K. N. 2013; 88 (1): 4-28

    Abstract

    Niche construction theory (NCT) explicitly recognizes environmental modication by organisms ("niche construction") and their legacy overtime ("ecological inheritance") to be evolutionary processes in their own right. Here we illustrate how niche construction theory provides usedl conceptual tools and theoretical insights for integrating ecosystem ecology and evolutionary theory. We begin by briefly describing NCT, and illustrating how it deifers from conventional evolutionary approaches. We then distinguish between two aspects ofniche construction--environment alteration and subsequent evolution in response to constructed environments--equating the first of these with "ecosystem engineering." We describe some of the ecological and evolutionary impacts on ecosystems of niche construction, ecosystem engineering and ecological inheritance, and illustrate how these processes trigger ecological and evolutionary feedbacks and leave detectable ecological signatures that are open to investigation. FIinally, we provide a practical guide to how NCT could be deployed by ecologists and evolutionary biologists to aeplore ecoeoolutionay dynamics. We suggest that, by highlighting the ecological and evolutionay ramifications of changes that organisms bring about in ecosystems, NCT helps link ecosystem ecology to evolutionary biology, potentially leading to a deeper understanding of how ecosystems change over time.

    View details for PubMedID 23653966

  • Asset endowments, non-farm participation and local separability in remote rural China CHINA AGRICULTURAL ECONOMIC REVIEW Liang, Y., Feldman, M. W., Li, S., Daily, G. C. 2013; 5 (1): 66-88
  • "Bare Branches" and the Marriage Market in Rural China: Preliminary Evidence from a village-level survey. Chinese sociological review Jin, X., Liu, L., Li, Y., Feldman, M. W., Li, S. 2013; 46 (1): 83-104

    Abstract

    Using data from a village survey in rural China, this study explores the relationships between current prevalence of involuntary bachelorhood and its causes and social consequences at the village level. We find that bachelors, inter-county marriage and marriage fraud exist in all regions, and are expected to become more frequent with the increasing surplus of males born after 1980 entering the marriage market. The marriage squeeze and social problems related to the bachelors are more serious in less-developed western villages, and heterogeneity within central villages is significant. Economic and socio-demographic factors are shown to be the major causes of the prevalence of bachelors at the village level in contemporary rural China. Our findings confirm the negative consequences of the marriage squeeze, and effective policies are urgently needed to respond to and prevent more negative consequences of gender imbalance in the foreseeable future.

    View details for DOI 10.2753/CSA2162-0555460104

    View details for PubMedID 26213641

    View details for PubMedCentralID PMC4512178

  • China's Population Policy at the Crossroads: Social Impacts and Prospects. Asian journal of social science Jiang, Q., Li, S., Feldman, M. W. 2013; 41 (2): 193-218

    Abstract

    China's total fertility rate fell below replacement level in the 1990s. From the 1970s the fertility rate declined dramatically, mainly as a consequence of the national population policy whose aim has been to limit birth numbers, control population growth and boost economic growth. Having achieved such a low fertility rate, how will China's population policy evolve in the future? This paper first reviews the history of China's population policy since 1970 in terms of three stages: 1970-1979; 1980-1999; and after 2000. We explore the impacts of China's population policy, including relief of pressure on China's environment and resources, fertility decline, the unexpectedly high male-biased sex ratio at birth (SRB), the coming shortage of labor force, and the rapid aging of the population. We also investigate ethical issues raised by the implementation of the policy and its results. Finally we introduce the controversy over potential adjustment of the policy, acknowledging the problems faced by western countries with low fertility and countermeasures they have taken. We offer some suggestions that might be appropriate in the Chinese context.

    View details for DOI 10.1163/15685314-12341298

    View details for PubMedID 26612983

    View details for PubMedCentralID PMC4657744

  • The Life Cycle of Bare Branch Families in China: A Simulation Study CANADIAN STUDIES IN POPULATION Jiang, Q., Guo, Z., Li, S., Feldman, M. W. 2013; 40 (3-4): 134-148
  • Gene-culture co-evolution: teaching, learning, and correlations between relatives ISRAEL JOURNAL OF ECOLOGY & EVOLUTION Feldman, M. W., Christiansen, F. B., Otto, S. P. 2013; 59 (2): 72-91
  • China's Population Policy at the Crossroads: Social Impacts and Prospects ASIAN JOURNAL OF SOCIAL SCIENCE Jiang, Q., Li, S., Feldman, M. W. 2013; 41 (2): 193-218
  • A Tale of Two Haplotypes: The EDA2R/AR Intergenic Region Is the Most Divergent Genomic Segment between Africans and East Asians in the Human Genome HUMAN BIOLOGY Casto, A. M., Henn, B. M., Kidd, J. M., Bustamante, C. D., Feldman, M. W. 2012; 84 (6): 641-694

    Abstract

    Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly differentiated SNPs. Using a publicly available data set of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed by use of a subset of individuals sequenced to high coverage. The first of these haplotypes, the α-haplotype is at high frequencies in most of the African populations surveyed and likely arose before the separation of African populations into distinct genetic entities. The second, the β-haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa before the out-of-Africa migration. We also observed a small group or rare haplotypes with no clear relationship to the α- and β-haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, such as the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α- and β-haplotypes. We suggest that the rise of the α- and β-haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α- and β-haplotypes and of purifying the selection against α/β recombinants.

    View details for Web of Science ID 000322906700002

    View details for PubMedID 23959643

  • Estimates of missing women in twentieth-century China CONTINUITY AND CHANGE Jiang, Q., Li, S., Feldman, M. W., Javier Sanchez-Barricarte, J. 2012; 27: 461-479
  • Limited Evidence for Classic Selective Sweeps in African Populations GENETICS Granka, J. M., Henn, B. M., Gignoux, C. R., Kidd, J. M., Bustamante, C. D., Feldman, M. W. 2012; 192 (3): 1049-?

    Abstract

    While hundreds of loci have been identified as reflecting strong-positive selection in human populations, connections between candidate loci and specific selective pressures often remain obscure. This study investigates broader patterns of selection in African populations, which are underrepresented despite their potential to offer key insights into human adaptation. We scan for hard selective sweeps using several haplotype and allele-frequency statistics with a data set of nearly 500,000 genome-wide single-nucleotide polymorphisms in 12 highly diverged African populations that span a range of environments and subsistence strategies. We find that positive selection does not appear to be a strong determinant of allele-frequency differentiation among these African populations. Haplotype statistics do identify putatively selected regions that are shared across African populations. However, as assessed by extensive simulations, patterns of haplotype sharing between African populations follow neutral expectations and suggest that tails of the empirical distributions contain false-positive signals. After highlighting several genomic regions where positive selection can be inferred with higher confidence, we use a novel method to identify biological functions enriched among populations' empirical tail genomic windows, such as immune response in agricultural groups. In general, however, it seems that current methods for selection scans are poorly suited to populations that, like the African populations in this study, are affected by ascertainment bias and have low levels of linkage disequilibrium, possibly old selective sweeps, and potentially reduced phasing accuracy. Additionally, population history can confound the interpretation of selection statistics, suggesting that greater care is needed in attributing broad genetic patterns to human adaptation.

    View details for DOI 10.1534/genetics.112.144071

    View details for Web of Science ID 000310793900019

    View details for PubMedID 22960214

    View details for PubMedCentralID PMC3522151

  • Learning to Choose Among Social Foraging Strategies in Adult House Sparrows (Passer domesticus) ETHOLOGY Belmaker, A., Motro, U., Feldman, M. W., Lotem, A. 2012; 118 (11): 1111-1121

    View details for DOI 10.1111/eth.12013

    View details for Web of Science ID 000309468900010

  • The great human expansion PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Henn, B. M., Cavalli-Sforza, L. L., Feldman, M. W. 2012; 109 (44): 17758-17764

    Abstract

    Genetic and paleoanthropological evidence is in accord that today's human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth's habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the "serial founder effect." In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution.

    View details for DOI 10.1073/pnas.1212380109

    View details for Web of Science ID 000311149900021

    View details for PubMedID 23077256

    View details for PubMedCentralID PMC3497766

  • China's Missing Girls in the Three Decades from 1980 to 2010 ASIAN WOMEN Jiang, Q., Li, S., Feldman, M. W. 2012; 28 (3): 53-73
  • Models of Cultural Niche Construction with Selection and Assortative Mating PLOS ONE Creanza, N., Fogarty, L., Feldman, M. W. 2012; 7 (8)

    Abstract

    Niche construction is a process through which organisms modify their environment and, as a result, alter the selection pressures on themselves and other species. In cultural niche construction, one or more cultural traits can influence the evolution of other cultural or biological traits by affecting the social environment in which the latter traits may evolve. Cultural niche construction may include either gene-culture or culture-culture interactions. Here we develop a model of this process and suggest some applications of this model. We examine the interactions between cultural transmission, selection, and assorting, paying particular attention to the complexities that arise when selection and assorting are both present, in which case stable polymorphisms of all cultural phenotypes are possible. We compare our model to a recent model for the joint evolution of religion and fertility and discuss other potential applications of cultural niche construction theory, including the evolution and maintenance of large-scale human conflict and the relationship between sex ratio bias and marriage customs. The evolutionary framework we introduce begins to address complexities that arise in the quantitative analysis of multiple interacting cultural traits.

    View details for DOI 10.1371/journal.pone.0042744

    View details for Web of Science ID 000307500800020

    View details for PubMedID 22905167

    View details for PubMedCentralID PMC3419226

  • Genomic Patterns of Homozygosity in Worldwide Human Populations AMERICAN JOURNAL OF HUMAN GENETICS Pemberton, T. J., Absher, D., Feldman, M. W., Myers, R. M., Rosenberg, N. A., Li, J. Z. 2012; 91 (2): 275-292

    Abstract

    Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes-short, intermediate, and long-with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.

    View details for DOI 10.1016/j.ajhg.2012.06.014

    View details for Web of Science ID 000307608700006

    View details for PubMedID 22883143

    View details for PubMedCentralID PMC3415543

  • Out-Migration of Young Adults and Gender Division of Intergenerational Support in Rural China RESEARCH ON AGING Song, L., Li, S., Feldman, M. W. 2012; 34 (4): 399-424
  • Out-migration of Young Adults and Gender Division of Intergenerational Support in Rural China. Research on aging Song, L., Li, S., Feldman, M. W. 2012; 34 (4): 399-424

    Abstract

    Using data from the baseline and follow-up surveys of "Well-being of Elderly in Anhui Province, China" conducted in 2001, in 2003 and in 2006, respectively, by the Institute for Population and Development Studies of Xi'an Jiaotong University, this paper employs random effects models to explore the gender division of intergenerational support in the elderly rural families. Analyses by parents' and children's gender suggest that there are gender differences in intergenerational support because of gender roles and division in family. Our analysis shows that older mothers receive more returns, which reciprocates their support, while older fathers benefit more from the out-migration of adult children. While sons take more responsibility for family support, daughters reciprocate support from their elderly parents more. Enhancement of the role and function of daughters in families has accompanied out-migration of young adults and suggests that gender differences in intergenerational supports between sons and daughters have decreased.

    View details for DOI 10.1177/0164027511436321

    View details for PubMedID 29353946

    View details for PubMedCentralID PMC5772779

  • Survivability Is More Fundamental Than Evolvability PLOS ONE Palmer, M. E., Feldman, M. W. 2012; 7 (6)

    Abstract

    For a lineage to survive over long time periods, it must sometimes change. This has given rise to the term evolvability, meaning the tendency to produce adaptive variation. One lineage may be superior to another in terms of its current standing variation, or it may tend to produce more adaptive variation. However, evolutionary outcomes depend on more than standing variation and produced adaptive variation: deleterious variation also matters. Evolvability, as most commonly interpreted, is not predictive of evolutionary outcomes. Here, we define a predictive measure of the evolutionary success of a lineage that we call the k-survivability, defined as the probability that the lineage avoids extinction for k generations. We estimate the k-survivability using multiple experimental replicates. Because we measure evolutionary outcomes, the initial standing variation, the full spectrum of generated variation, and the heritability of that variation are all incorporated. Survivability also accounts for the decreased joint likelihood of extinction of sub-lineages when they 1) disperse in space, or 2) diversify in lifestyle. We illustrate measurement of survivability with in silico models, and suggest that it may also be measured in vivo using multiple longitudinal replicates. The k-survivability is a metric that enables the quantitative study of, for example, the evolution of 1) mutation rates, 2) dispersal mechanisms, 3) the genotype-phenotype map, and 4) sexual reproduction, in temporally and spatially fluctuating environments. Although these disparate phenomena evolve by well-understood microevolutionary rules, they are also subject to the macroevolutionary constraint of long-term survivability.

    View details for DOI 10.1371/journal.pone.0038025

    View details for Web of Science ID 000305583300018

    View details for PubMedID 22723844

    View details for PubMedCentralID PMC3377627

  • Most Networks in Wagner's Model Are Cycling PLOS ONE Pinho, R., Borenstein, E., Feldman, M. W. 2012; 7 (4)

    Abstract

    In this paper we study a model of gene networks introduced by Andreas Wagner in the 1990s that has been used extensively to study the evolution of mutational robustness. We investigate a range of model features and parameters and evaluate the extent to which they influence the probability that a random gene network will produce a fixed point steady state expression pattern. There are many different types of models used in the literature, (discrete/continuous, sparse/dense, small/large network) and we attempt to put some order into this diversity, motivated by the fact that many properties are qualitatively the same in all the models. Our main result is that random networks in all models give rise to cyclic behavior more often than fixed points. And although periodic orbits seem to dominate network dynamics, they are usually considered unstable and not allowed to survive in previous evolutionary studies. Defining stability as the probability of fixed points, we show that the stability distribution of these networks is highly robust to changes in its parameters. We also find sparser networks to be more stable, which may help to explain why they seem to be favored by evolution. We have unified several disconnected previous studies of this class of models under the framework of stability, in a way that had not been systematically explored before.

    View details for DOI 10.1371/journal.pone.0034285

    View details for Web of Science ID 000305338600021

    View details for PubMedID 22511935

    View details for PubMedCentralID PMC3325246

  • An equilibrium for phenotypic variance in fluctuating environments owing to epigenetics JOURNAL OF THE ROYAL SOCIETY INTERFACE Carja, O., Feldman, M. W. 2012; 9 (69): 613-623

    Abstract

    The connection between random environments and genetic and phenotypic variability has been a major focus in the population genetic literature. By providing differential access to the underlying genetic information, epigenetic variation could play an important role in the interaction between environmental and phenotypic variation. Using simulation, we model epigenetic plasticity during development by investigating the dynamics of genetic regulators of the epigenetic machinery that change the variance of the phenotype, while having no effect on the phenotype's mean. Previous studies have found that increased phenotypic variance is selected for if the environment is fluctuating. Here, we find that when a variance-increasing allele achieves a sufficiently high frequency, it can be out-competed by a variance-reducing allele, with the consequence that the population evolves to an equilibrium phenotypic variability. This equilibrium is shown to be robust to different initial conditions, but to depend heavily on parameters of the model, such as the mutation rate, the fitness landscape and the nature of the environmental fluctuation. Indeed, if there is no mutation at the genes controlling the variance of the phenotype, reduction of this variance is favoured.

    View details for DOI 10.1098/rsif.2011.0390

    View details for Web of Science ID 000300726700002

    View details for PubMedID 21849387

    View details for PubMedCentralID PMC3284130

  • Evolution of learned strategy choice in a frequency-dependent game PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Katsnelson, E., Motro, U., Feldman, M. W., Lotem, A. 2012; 279 (1731): 1176-1184

    Abstract

    In frequency-dependent games, strategy choice may be innate or learned. While experimental evidence in the producer-scrounger game suggests that learned strategy choice may be common, a recent theoretical analysis demonstrated that learning by only some individuals prevents learning from evolving in others. Here, however, we model learning explicitly, and demonstrate that learning can easily evolve in the whole population. We used an agent-based evolutionary simulation of the producer-scrounger game to test the success of two general learning rules for strategy choice. We found that learning was eventually acquired by all individuals under a sufficient degree of environmental fluctuation, and when players were phenotypically asymmetric. In the absence of sufficient environmental change or phenotypic asymmetries, the correct target for learning seems to be confounded by game dynamics, and innate strategy choice is likely to be fixed in the population. The results demonstrate that under biologically plausible conditions, learning can easily evolve in the whole population and that phenotypic asymmetry is important for the evolution of learned strategy choice, especially in a stable or mildly changing environment.

    View details for DOI 10.1098/rspb.2011.1734

    View details for Web of Science ID 000300417000018

    View details for PubMedID 21937494

  • Does household composition matter? The impact of the Grain for Green Program on rural livelihoods in China ECOLOGICAL ECONOMICS Liang, Y., Li, S., Feldman, M. W., Daily, G. C. 2012; 75: 152-160
  • Does Out-migration Reshape Rural Households' Livelihood Capitals in the Source Communities? Recent Evidence from Western China ASIAN AND PACIFIC MIGRATION JOURNAL Li, C., Li, S., Feldman, M. W., Daily, G. C., Li, J. 2012; 21 (1): 1-30
  • Forced bachelors, migration and HIV transmission risk in the context of China's gender imbalance: A meta-analysis AIDS CARE-PSYCHOLOGICAL AND SOCIO-MEDICAL ASPECTS OF AIDS/HIV Liu, H., Li, S., Feldman, M. W. 2012; 24 (12): 1487-1495

    Abstract

    China has experienced continual increase in the sex ratio at birth (SRB) since the 1980s, which has led to a serious gender imbalance. To identify whether the future forced bachelors, especially those who migrate to cities, will increase the risk of HIV spread, a systematic review was carried out of studies published since 2000 that include the sexual risks of male migrants of China. Five studies comparing risk differences between migrants and non-migrants showed male migrants had greater risk of having multiple sexual partners and engaging in commercial sex. Ten studies concerning the relationship between sexual risks and socio-demographic characteristics showed that unmarried male migrants were more likely to engage in commercial sex and be infected with STDs than married migrants, while male migrants with higher income were more likely to have multiple sexual partners and be infected with STDs. In an analysis stratified by sample characteristics, the association between marriage and sexual risk was greater among samples with lower mean age, higher average income and education. In addition, the risk selection on education and income disappeared in the samples of migrants of whom more than half were unmarried.

    View details for DOI 10.1080/09540121.2012.663885

    View details for Web of Science ID 000310484200004

    View details for PubMedID 22519697

  • Environment-Sensitive Epigenetics and the Heritability of Complex Diseases GENETICS Furrow, R. E., Christiansen, F. B., Feldman, M. W. 2011; 189 (4): 1377-?

    Abstract

    Genome-wide association studies have thus far failed to explain the observed heritability of complex human diseases. This is referred to as the "missing heritability" problem. However, these analyses have usually neglected to consider a role for epigenetic variation, which has been associated with many human diseases. We extend models of epigenetic inheritance to investigate whether environment-sensitive epigenetic modifications of DNA might explain observed patterns of familial aggregation. We find that variation in epigenetic state and environmental state can result in highly heritable phenotypes through a combination of epigenetic and environmental inheritance. These two inheritance processes together can produce familial covariances significantly higher than those predicted by models of purely epigenetic inheritance and similar to those expected from genetic effects. The results suggest that epigenetic variation, inherited both directly and through shared environmental effects, may make a key contribution to the missing heritability.

    View details for DOI 10.1534/genetics.111.131912

    View details for Web of Science ID 000298412100020

    View details for PubMedID 21968193

    View details for PubMedCentralID PMC3241426

  • Recombination and the evolution of coordinated phenotypic expression in a frequency-dependent game THEORETICAL POPULATION BIOLOGY Arbilly, M., Motro, U., Feldman, M. W., Lotem, A. 2011; 80 (4): 244-255

    Abstract

    A long standing question in evolutionary biology concerns the maintenance of adaptive combinations of traits in the presence of recombination. This problem may be solved if positive epistasis selects for reducing the rate of recombination between such traits, but this requires sufficiently strong epistasis. Here we use a model that we developed previously to analyze a frequency-dependent strategy game in asexual populations, to study how adaptive combinations of traits may be maintained in the presence of recombination when epistasis is too weak to select for genetic linkage. Previously, in the asexual case, our model demonstrated the evolution of adaptive associations between social foraging strategies and learning rules. We verify that these adaptive associations, which are represented by different two-locus haplotypes, can easily be broken by genetic recombination. We also confirm that a modifier allele that reduces the rate of recombination fails to evolve (due to weak epistasis). However, we find that under the same conditions of weak epistasis, there is an alternative mechanism that allows an association between traits to evolve. This is based on a genetic switch that responds to the presence of one social foraging allele by activating one of the two alternative learning alleles that are carried by all individuals. We suggest that such coordinated phenotypic expression by genetic switches offers a general and robust mechanism for the evolution of adaptive combinations of traits in the presence of recombination.

    View details for DOI 10.1016/j.tpb.2011.09.001

    View details for Web of Science ID 000297538500002

    View details for PubMedID 21945887

  • Evolution of social learning when high expected payoffs are associated with high risk of failure JOURNAL OF THE ROYAL SOCIETY INTERFACE Arbilly, M., Motro, U., Feldman, M. W., Lotem, A. 2011; 8 (64): 1604-1615

    Abstract

    In an environment where the availability of resources sought by a forager varies greatly, individual foraging is likely to be associated with a high risk of failure. Foragers that learn where the best sources of food are located are likely to develop risk aversion, causing them to avoid the patches that are in fact the best; the result is sub-optimal behaviour. Yet, foragers living in a group may not only learn by themselves, but also by observing others. Using evolutionary agent-based computer simulations of a social foraging game, we show that in an environment where the most productive resources occur with the lowest probability, socially acquired information is strongly favoured over individual experience. While social learning is usually regarded as beneficial because it filters out maladaptive behaviours, the advantage of social learning in a risky environment stems from the fact that it allows risk aversion to be circumvented and the best food source to be revisited despite repeated failures. Our results demonstrate that the consequences of individual risk aversion may be better understood within a social context and suggest one possible explanation for the strong preference for social information over individual experience often observed in both humans and animals.

    View details for DOI 10.1098/rsif.2011.0138

    View details for Web of Science ID 000295211200007

    View details for PubMedID 21508013

  • A new network structure entropy based node difference and edge difference ACTA PHYSICA SINICA Cai Meng, M., Du Hai-Feng, H. F., Ren Yi-Ke, Y. K., Feldman, M. W. 2011; 60 (11)
  • The Spread of Inequality PLOS ONE Rogers, D. S., Deshpande, O., Feldman, M. W. 2011; 6 (9)

    Abstract

    The causes of socioeconomic inequality have been debated since the time of Plato. Many reasons for the development of stratification have been proposed, from the need for hierarchical control over large-scale irrigation systems to the accumulation of small differences in wealth over time via inheritance processes. However, none of these explains how unequal societies came to completely displace egalitarian cultural norms over time. Our study models demographic consequences associated with the unequal distribution of resources in stratified societies. Agent-based simulation results show that in constant environments, unequal access to resources can be demographically destabilizing, resulting in the outward migration and spread of such societies even when population size is relatively small. In variable environments, stratified societies spread more and are also better able to survive resource shortages by sequestering mortality in the lower classes. The predictions of our simulation are provided modest support by a range of existing empirical studies. In short, the fact that stratified societies today vastly outnumber egalitarian societies may not be due to the transformation of egalitarian norms and structures, but may instead reflect the more rapid migration of stratified societies and consequent conquest or displacement of egalitarian societies over time.

    View details for DOI 10.1371/journal.pone.0024683

    View details for Web of Science ID 000295262100016

    View details for PubMedID 21957457

    View details for PubMedCentralID PMC3177824

  • SPATIAL ENVIRONMENTAL VARIATION CAN SELECT FOR EVOLVABILITY EVOLUTION Palmer, M. E., Feldman, M. W. 2011; 65 (8): 2345-2356

    Abstract

    Previous studies have shown that temporally fluctuating environments can create indirect selection for modifiers of evolvability. Here, we use a simple computational model to investigate whether spatially varying environments (multiple demes with limited migration among them, and a different, static selective optimum in each) can also create indirect selection for increased evolvability. The answer is surprisingly complicated. Spatial variation in the environment can sharply reduce the survival rate of migrants, because migrants may be maladapted to their new deme, relative to incumbents. The incumbent advantage can be removed by occasional extinctions in single demes. After all incumbents in a particular deme die, incoming migrants from other demes will, on average, be similarly maladapted to the new environment. This sets off a race to adapt rapidly. Over many extinction events, and the subsequent invasions by maladapted immigrants into a new environment, indirect selection for the ability to adapt rapidly, also known as high evolvability, may result.

    View details for DOI 10.1111/j.1558-5646.2011.01283.x

    View details for Web of Science ID 000293182700017

    View details for PubMedID 21790580

  • Demographic Consequences of Gender Discrimination in China: Simulation Analysis of Policy Options POPULATION RESEARCH AND POLICY REVIEW Jiang, Q., Li, S., Feldman, M. W. 2011; 30 (4): 619-638
  • Reply to Hublin and Klein: Locating a geographic point of dispersion in Africa for contemporary humans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Henn, B. M., Bustamante, C. D., Mountain, J. L., Feldman, M. W. 2011; 108 (28): E278-E278
  • Rates of cultural change and patterns of cultural accumulation in stochastic models of social transmission THEORETICAL POPULATION BIOLOGY Aoki, K., Lehmann, L., Feldman, M. W. 2011; 79 (4): 192-202

    Abstract

    Cultural variation in a population is affected by the rate of occurrence of cultural innovations, whether such innovations are preferred or eschewed, how they are transmitted between individuals in the population, and the size of the population. An innovation, such as a modification in an attribute of a handaxe, may be lost or may become a property of all handaxes, which we call "fixation of the innovation." Alternatively, several innovations may attain appreciable frequencies, in which case properties of the frequency distribution-for example, of handaxe measurements-is important. Here we apply the Moran model from the stochastic theory of population genetics to study the evolution of cultural innovations. We obtain the probability that an initially rare innovation becomes fixed, and the expected time this takes. When variation in cultural traits is due to recurrent innovation, copy error, and sampling from generation to generation, we describe properties of this variation, such as the level of heterogeneity expected in the population. For all of these, we determine the effect of the mode of social transmission: conformist, where there is a tendency for each naïve newborn to copy the most popular variant; pro-novelty bias, where the newborn prefers a specific variant if it exists among those it samples; one-to-many transmission, where the variant one individual carries is copied by all newborns while that individual remains alive. We compare our findings with those predicted by prevailing theories for rates of cultural change and the distribution of cultural variation.

    View details for DOI 10.1016/j.tpb.2011.02.001

    View details for Web of Science ID 000290467600007

    View details for PubMedID 21315753

  • Rural household income and inequality under the Sloping Land Conversion Program in western China PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Li, J., Feldman, M. W., Li, S., Daily, G. C. 2011; 108 (19): 7721-7726

    Abstract

    As payment for ecosystem services (PES) programs proliferate globally, assessing their impact upon households' income and livelihood patterns is critical. The Sloping Land Conversion Program (SLCP) is an exceptional PES program, in terms of its ambitious biophysical and socioeconomic objectives, large geographic scale, numbers of people directly affected, and duration of operation. The SLCP has now operated in the poor mountainous areas in China for 10 y and offers a unique opportunity for policy evaluation. Using survey data on rural households' livelihoods in the southern mountain area in Zhouzhi County, Shaanxi Province, we carry out a statistical analysis of the effects of PES and other factors on rural household income. We analyze the extent of income inequality and compare the socio-demographic features and household income of households participating in the SLCP with those that did not. Our statistical analysis shows that participation in SLCP has significant positive impacts upon household income, especially for low- and medium-income households; however, participation also has some negative impacts on the low- and medium-income households. Overall, income inequality is less among households participating in the SLCP than among those that do not after 7 y of the PES program. Different income sources have different effects on Gini statistics; in particular, wage income has opposite effects on income inequality for the participating and nonparticipating households. We find, however, that the SLCP has not increased the transfer of labor toward nonfarming activities in the survey site, as the government expected.

    View details for DOI 10.1073/pnas.1101018108

    View details for Web of Science ID 000290439500022

    View details for PubMedID 21518856

    View details for PubMedCentralID PMC3093530

  • Dispersal of Mycobacterium tuberculosis via the Canadian fur trade PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Pepperell, C. S., Granka, J. M., Alexander, D. C., Behr, M. A., Chui, L., Gordon, J., Guthrie, J. L., Jamieson, F. B., Langlois-Klassen, D., Long, R., Nguyen, D., Wobeser, W., Feldman, M. W. 2011; 108 (16): 6526-6531

    Abstract

    Patterns of gene flow can have marked effects on the evolution of populations. To better understand the migration dynamics of Mycobacterium tuberculosis, we studied genetic data from European M. tuberculosis lineages currently circulating in Aboriginal and French Canadian communities. A single M. tuberculosis lineage, characterized by the DS6(Quebec) genomic deletion, is at highest frequency among Aboriginal populations in Ontario, Saskatchewan, and Alberta; this bacterial lineage is also dominant among tuberculosis (TB) cases in French Canadians resident in Quebec. Substantial contact between these human populations is limited to a specific historical era (1710-1870), during which individuals from these populations met to barter furs. Statistical analyses of extant M. tuberculosis minisatellite data are consistent with Quebec as a source population for M. tuberculosis gene flow into Aboriginal populations during the fur trade era. Historical and genetic analyses suggest that tiny M. tuberculosis populations persisted for ∼100 y among indigenous populations and subsequently expanded in the late 19th century after environmental changes favoring the pathogen. Our study suggests that spread of TB can occur by two asynchronous processes: (i) dispersal of M. tuberculosis by minimal numbers of human migrants, during which small pathogen populations are sustained by ongoing migration and slow disease dynamics, and (ii) expansion of the M. tuberculosis population facilitated by shifts in host ecology. If generalizable, these migration dynamics can help explain the low DNA sequence diversity observed among isolates of M. tuberculosis and the difficulties in global elimination of tuberculosis, as small, widely dispersed pathogen populations are difficult both to detect and to eradicate.

    View details for DOI 10.1073/pnas.1016708108

    View details for Web of Science ID 000289680400042

    View details for PubMedID 21464295

    View details for PubMedCentralID PMC3080970

  • How copying affects the amount, evenness and persistence of cultural knowledge: insights from the social learning strategies tournament PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Rendell, L., Boyd, R., Enquist, M., Feldman, M. W., Fogarty, L., Laland, K. N. 2011; 366 (1567): 1118-1128

    Abstract

    Darwinian processes should favour those individuals that deploy the most effective strategies for acquiring information about their environment. We organized a computer-based tournament to investigate which learning strategies would perform well in a changing environment. The most successful strategies relied almost exclusively on social learning (here, learning a behaviour performed by another individual) rather than asocial learning, even when environments were changing rapidly; moreover, successful strategies focused learning effort on periods of environmental change. Here, we use data from tournament simulations to examine how these strategies might affect cultural evolution, as reflected in the amount of culture (i.e. number of cultural traits) in the population, the distribution of cultural traits across individuals, and their persistence through time. We found that high levels of social learning are associated with a larger amount of more persistent knowledge, but a smaller amount of less persistent expressed behaviour, as well as more uneven distributions of behaviour, as individuals concentrated on exploiting a smaller subset of behaviour patterns. Increased rates of environmental change generated increases in the amount and evenness of behaviour. These observations suggest that copying confers on cultural populations an adaptive plasticity, allowing them to respond to changing environments rapidly by drawing on a wider knowledge base.

    View details for DOI 10.1098/rstb.2010.0376

    View details for Web of Science ID 000287802900020

    View details for PubMedID 21357234

  • Hunter-gatherer genomic diversity suggests a southern African origin for modern humans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Henn, B. M., Gignoux, C. R., Jobin, M., Granka, J. M., Macpherson, J. M., Kidd, J. M., Rodriguez-Botigue, L., Ramachandran, S., Hon, L., Brisbin, A., Lin, A. A., Underhill, P. A., Comas, D., Kidd, K. K., Norman, P. J., Parham, P., Bustamante, C. D., Mountain, J. L., Feldman, M. W. 2011; 108 (13): 5154-5162

    Abstract

    Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

    View details for DOI 10.1073/pnas.1017511108

    View details for Web of Science ID 000288894800009

    View details for PubMedID 21383195

    View details for PubMedCentralID PMC3069156

  • The influence of social niche on cultural niche construction: modelling changes in belief about marriage form in Taiwan PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Lipatov, M., Brown, M. J., Feldman, M. W. 2011; 366 (1566): 901-917

    Abstract

    With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction.

    View details for DOI 10.1098/rstb.2010.0303

    View details for Web of Science ID 000287302400011

    View details for PubMedID 21320903

    View details for PubMedCentralID PMC3048994

  • Measuring school contact networks using wireless sensor technology Jones, J. H., Salathe, M., Feldman, M. W., KAZANDJIEVA, M., Lee, J. W., Levis, P. WILEY-BLACKWELL. 2011: 263–63
  • On the Evolution of Mutation in Changing Environments: Recombination and Phenotypic Switching GENETICS Liberman, U., Van Cleve, J., Feldman, M. W. 2011; 187 (3): 837-851

    Abstract

    Phenotypic switching has been observed in laboratory studies of yeast and bacteria, in which the rate of such switching appears to adjust to match the frequency of environmental changes. Among possible mechanisms of switching are epigenetic influences on gene expression and variation in levels of methylation; thus environmental and/or genetic factors may contribute to the rate of switching. Most previous analyses of the evolution of phenotypic switching have compared exponential growth rates of noninteracting populations, and recombination has been ignored. Our genetic model of the evolution of switching rates is framed in terms of a mutation-modifying gene, environments that cause periodic changes in fitness, and recombination between the mutation modifier and the gene under selection. Exact results are obtained for all recombination rates and symmetric fitnesses that strongly generalize earlier results obtained under complete linkage and strong constraints on the relation between fitness and period of switching. Our analytical and numerical results suggest a general principle that recombination reduces the stable rate of switching in symmetric and asymmetric fitness regimes and when the period of switching is random. As the recombination rate increases, it becomes less likely that there is a stable nonzero rate of switching.

    View details for DOI 10.1534/genetics.110.123620

    View details for Web of Science ID 000288457800017

    View details for PubMedID 21212229

  • Individual-learning ability predicts social-foraging strategy in house sparrows PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Katsnelson, E., Motro, U., Feldman, M. W., Lotem, A. 2011; 278 (1705): 582-589

    Abstract

    Social foragers can use either a 'producer' strategy, which involves searching for food, or a 'scrounger' strategy, which involves joining others' food discoveries. While producers rely on personal information and past experience, we may ask whether the tendency to forage as a producer is related to being a better learner. To answer this question, we hand-raised house sparrow (Passer domesticus) nestlings that upon independence were given an individual-learning task that required them to associate colour signal and food presence. Following the testing phase, all fledglings were released into a shared aviary, and their social-foraging tendencies were measured. We found a significant positive correlation between individual's performance in the individual-learning task and subsequent tendency to use searching (producing) behaviour. Individual-learning score was negatively correlated with initial fear of the test apparatus and with body weight. However, the correlation between individual learning and searching remained significant after controlling for these variables. Since it was measured before the birds entered a social group, individual-learning ability could not be the outcome of being a producer. However, the two traits may be initially associated, or individual learning could facilitate producing behaviour. To our knowledge, this is the first evidence that associates individual-learning abilities with social-foraging strategies in animal groups.

    View details for DOI 10.1098/rspb.2010.1151

    View details for Web of Science ID 000286093900016

    View details for PubMedID 20810440

  • On the number of independent cultural traits carried by individuals and populations PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Lehmann, L., Aoki, K., Feldman, M. W. 2011; 366 (1563): 424-435

    Abstract

    In species subject to individual and social learning, each individual is likely to express a certain number of different cultural traits acquired during its lifetime. If the process of trait innovation and transmission reaches a steady state in the population, the number of different cultural traits carried by an individual converges to some stationary distribution. We call this the trait-number distribution. In this paper, we derive the trait-number distributions for both individuals and populations when cultural traits are independent of each other. Our results suggest that as the number of cultural traits becomes large, the trait-number distributions approach Poisson distributions so that their means characterize cultural diversity in the population. We then analyse how the mean trait number varies at both the individual and population levels as a function of various demographic features, such as population size and subdivision, and social learning rules, such as conformism and anti-conformism. Diversity at the individual and population levels, as well as at the level of cultural homogeneity within groups, depends critically on the details of population demography and the individual and social learning rules.

    View details for DOI 10.1098/rstb.2010.0313

    View details for Web of Science ID 000285793800011

    View details for PubMedID 21199846

  • Genome-Wide Association Study SNPs in the Human Genome Diversity Project Populations: Does Selection Affect Unlinked SNPs with Shared Trait Associations? PLOS GENETICS Casto, A. M., Feldman, M. W. 2011; 7 (1)

    Abstract

    Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human fitness, including many immunological, metabolic, cardiovascular, and behavioral phenotypes. Given the polygenic nature of complex traits, selection may exert its influence on them by altering allele frequencies at many associated loci, a possibility which has yet to be explored empirically. Here we use 38 different measures of allele frequency variation and 8 iHS scores to characterize over 1,300 GWAS SNPs in 53 globally distributed human populations. We apply these same techniques to evaluate SNPs grouped by trait association. We find that groups of SNPs associated with pigmentation, blood pressure, infectious disease, and autoimmune disease traits exhibit unusual allele frequency patterns and elevated iHS scores in certain geographical locations. We also find that GWAS SNPs have generally elevated scores for measures of allele frequency variation and for iHS in Eurasia and East Asia. Overall, we believe that our results provide evidence for selection on several complex traits that has caused changes in allele frequencies and/or elevated iHS scores at a number of associated loci. Since GWAS SNPs collectively exhibit elevated allele frequency measures and iHS scores, selection on complex traits may be quite widespread. Our findings are most consistent with this selection being either positive or negative, although the relative contributions of the two are difficult to discern. Our results also suggest that trait-SNP associations identified in Eurasian samples may not be present in Africa, Oceania, and the Americas, possibly due to differences in linkage disequilibrium patterns. This observation suggests that non-Eurasian and non-East Asian sample populations should be included in future GWAS.

    View details for DOI 10.1371/journal.pgen.1001266

    View details for Web of Science ID 000286653500005

    View details for PubMedID 21253569

    View details for PubMedCentralID PMC3017115

  • MARRIAGE SQUEEZE IN CHINA'S FUTURE ASIAN POPULATION STUDIES Jiang, Q., Sanchez-Barricarte, J. J., Li, S., Feldman, M. W. 2011; 7 (3): 177-193
  • A high-resolution human contact network for infectious disease transmission PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Salathe, M., Kazandjieva, M., Lee, J. W., Levis, P., Feldman, M. W., Jones, J. H. 2010; 107 (51): 22020-22025

    Abstract

    The most frequent infectious diseases in humans--and those with the highest potential for rapid pandemic spread--are usually transmitted via droplets during close proximity interactions (CPIs). Despite the importance of this transmission route, very little is known about the dynamic patterns of CPIs. Using wireless sensor network technology, we obtained high-resolution data of CPIs during a typical day at an American high school, permitting the reconstruction of the social network relevant for infectious disease transmission. At 94% coverage, we collected 762,868 CPIs at a maximal distance of 3 m among 788 individuals. The data revealed a high-density network with typical small-world properties and a relatively homogeneous distribution of both interaction time and interaction partners among subjects. Computer simulations of the spread of an influenza-like disease on the weighted contact graph are in good agreement with absentee data during the most recent influenza season. Analysis of targeted immunization strategies suggested that contact network data are required to design strategies that are significantly more effective than random immunization. Immunization strategies based on contact network data were most effective at high vaccination coverage.

    View details for DOI 10.1073/pnas.1009094108

    View details for Web of Science ID 000285521800019

    View details for PubMedID 21149721

    View details for PubMedCentralID PMC3009790

  • Co-evolution of learning complexity and social foraging strategies JOURNAL OF THEORETICAL BIOLOGY Arbilly, M., Motro, U., Feldman, M. W., Lotem, A. 2010; 267 (4): 573-581

    Abstract

    Variation in learning abilities within populations suggests that complex learning may not necessarily be more adaptive than simple learning. Yet, the high cost of complex learning cannot fully explain this variation without some understanding of why complex learning is too costly for some individuals but not for others. Here we propose that different social foraging strategies can favor different learning strategies (that learn the environment with high or low resolution), thereby maintaining variable learning abilities within populations. Using a genetic algorithm in an agent-based evolutionary simulation of a social foraging game (the producer-scrounger game) we demonstrate how an association evolves between a strategy based on independent search for food (playing a producer) and a complex (high resolution) learning rule, while a strategy that combines independent search and following others (playing a scrounger) evolves an association with a simple (low resolution) learning rule. The reason for these associations is that for complex learning to have an advantage, a large number of learning steps, normally not achieved by scroungers, are necessary. These results offer a general explanation for persistent variation in cognitive abilities that is based on co-evolution of learning rules and social foraging strategies.

    View details for DOI 10.1016/j.jtbi.2010.09.026

    View details for Web of Science ID 000284513700012

    View details for PubMedID 20858503

  • The Rate of Fitness-Valley Crossing in Sexual Populations GENETICS Weissman, D. B., Feldman, M. W., Fisher, D. S. 2010; 186 (4): 1389-1410

    Abstract

    Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a "fitness valley" to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population.

    View details for DOI 10.1534/genetics.110.123240

    View details for Web of Science ID 000285297000025

    View details for PubMedID 20923976

    View details for PubMedCentralID PMC2998319

  • Cumulative cultural dynamics and the coevolution of cultural innovation and transmission: an ESS model for panmictic and structured populations JOURNAL OF EVOLUTIONARY BIOLOGY Lehmann, L., Feldman, M. W., Kaeuffer, R. 2010; 23 (11): 2356-2369

    Abstract

    When individuals in a population can acquire traits through learning, each individual may express a certain number of distinct cultural traits. These traits may have been either invented by the individual himself or acquired from others in the population. Here, we develop a game theoretic model for the accumulation of cultural traits through individual and social learning. We explore how the rates of innovation, decay, and transmission of cultural traits affect the evolutionary stable (ES) levels of individual and social learning and the number of cultural traits expressed by an individual when cultural dynamics are at a steady-state. We explore the evolution of these phenotypes in both panmictic and structured population settings. Our results suggest that in panmictic populations, the ES level of learning and number of traits tend to be independent of the social transmission rate of cultural traits and is mainly affected by the innovation and decay rates. By contrast, in structured populations, where interactions occur between relatives, the ES level of learning and the number of traits per individual can be increased (relative to the panmictic case) and may then markedly depend on the transmission rate of cultural traits. This suggests that kin selection may be one additional solution to Rogers's paradox of nonadaptive culture.

    View details for DOI 10.1111/j.1420-9101.2010.02096.x

    View details for Web of Science ID 000283374200008

    View details for PubMedID 20825551

  • How Demography, Life History, and Kinship Shape the Evolution of Genomic Imprinting AMERICAN NATURALIST Van Cleve, J., Feldman, M. W., Lehmann, L. 2010; 176 (4): 440-455

    Abstract

    How phenomena like helping, dispersal, or the sex ratio evolve depends critically on demographic and life-history factors. One phenotype that is of particular interest to biologists is genomic imprinting, which results in parent-of-origin-specific gene expression and thus deviates from the predictions of Mendel's rules. The most prominent explanation for the evolution of genomic imprinting, the kinship theory, originally specified that multiple paternity can cause the evolution of imprinting when offspring affect maternal resource provisioning. Most models of the kinship theory do not detail how population subdivision, demography, and life history affect the evolution of imprinting. In this work, we embed the classic kinship theory within an island model of population structure and allow for diverse demographic and life-history features to affect the direction of selection on imprinting. We find that population structure does not change how multiple paternity affects the evolution of imprinting under the classic kinship theory. However, if the degree of multiple paternity is not too large, we find that sex-specific migration and survival and generation overlap are the primary factors determining which allele is silenced. This indicates that imprinting can evolve purely as a result of sex-related asymmetries in the demographic structure or life history of a species.

    View details for DOI 10.1086/656277

    View details for Web of Science ID 000282001800006

    View details for PubMedID 20738206

    View details for PubMedCentralID PMC2989731

  • Birth Registration in China: Practices, Problems and Policies POPULATION RESEARCH AND POLICY REVIEW Li, S., Zhang, Y., Feldman, M. W. 2010; 29 (3): 297-317
  • Visual recognition of shapes and textures: an fMRi study BRAIN STRUCTURE & FUNCTION Stylianou-Korsnes, M., Reiner, M., Magnussen, S. J., Feldman, M. W. 2010; 214 (4): 355-359

    Abstract

    Previous literature suggest that processing of visually presented shapes and textures starts in the early visual areas, but subsequently follow different pathways. The purpose of this experiment was to further investigate differential activation for shapes and textures in order elucidate the pathways involved in visual shape and texture matching. In the present study, brain areas involved in discrimination of shapes and textures are mapped, using the same set of stimuli for shape and texture decisions. Texture matching activates more prefrontal regions than shape matching, particularly regions in the left middle frontal gyrus and bilateral inferior frontal gyrus. Shape specific activation includes an occipital/temporal region which is associated with multimodal object matching. The pattern of results suggests that recognition of textures may be based upon different ordering conditions in memory, which involve a prefrontal network and require a great deal more workload than the holistic representation of shape.

    View details for DOI 10.1007/s00429-010-0241-5

    View details for Web of Science ID 000277283200004

    View details for PubMedID 20237799

  • Why Copy Others? Insights from the Social Learning Strategies Tournament SCIENCE Rendell, L., Boyd, R., Cownden, D., Enquist, M., Eriksson, K., Feldman, M. W., Fogarty, L., Ghirlanda, S., Lillicrap, T., Laland, K. N. 2010; 328 (5975): 208-213

    Abstract

    Social learning (learning through observation or interaction with other individuals) is widespread in nature and is central to the remarkable success of humanity, yet it remains unclear why copying is profitable and how to copy most effectively. To address these questions, we organized a computer tournament in which entrants submitted strategies specifying how to use social learning and its asocial alternative (for example, trial-and-error learning) to acquire adaptive behavior in a complex environment. Most current theory predicts the emergence of mixed strategies that rely on some combination of the two types of learning. In the tournament, however, strategies that relied heavily on social learning were found to be remarkably successful, even when asocial information was no more costly than social information. Social learning proved advantageous because individuals frequently demonstrated the highest-payoff behavior in their repertoire, inadvertently filtering information for copiers. The winning strategy (discountmachine) relied nearly exclusively on social learning and weighted information according to the time since acquisition.

    View details for DOI 10.1126/science.1184719

    View details for Web of Science ID 000276459600037

    View details for PubMedID 20378813

  • On the Classification of Epistatic Interactions GENETICS Gao, H., Granka, J. M., Feldman, M. W. 2010; 184 (3): 827-U351

    Abstract

    Modern genomewide association studies are characterized by the problem of "missing heritability." Epistasis, or genetic interaction, has been suggested as a possible explanation for the relatively small contribution of single significant associations to the fraction of variance explained. Of particular concern to investigators of genetic interactions is how to best represent and define epistasis. Previous studies have found that the use of different quantitative definitions for genetic interaction can lead to different conclusions when constructing genetic interaction networks and when addressing evolutionary questions. We suggest that instead, multiple representations of epistasis, or epistatic "subtypes," may be valid within a given system. Selecting among these epistatic subtypes may provide additional insight into the biological and functional relationships among pairs of genes. In this study, we propose maximum-likelihood and model selection methods in a hypothesis-testing framework to choose epistatic subtypes that best represent functional relationships for pairs of genes on the basis of fitness data from both single and double mutants in haploid systems. We gauge the performance of our method with extensive simulations under various interaction scenarios. Our approach performs reasonably well in detecting the most likely epistatic subtype for pairs of genes, as well as in reducing bias when estimating the epistatic parameter (epsilon). We apply our approach to two available data sets from yeast (Saccharomyces cerevisiae) and demonstrate through overlap of our identified epistatic pairs with experimentally verified interactions and functional links that our results are likely of biological significance in understanding interaction mechanisms. We anticipate that our method will improve detection of epistatic interactions and will help to unravel the mysteries of complex biological systems.

    View details for DOI 10.1534/genetics.109.111120

    View details for Web of Science ID 000281886300019

    View details for PubMedID 20026678

    View details for PubMedCentralID PMC2845349

  • Floating choices: a generational perspective on intentions of rural-urban migrants in China ENVIRONMENT AND PLANNING A Yue, Z., Li, S., Feldman, M. W., Du, H. 2010; 42 (3): 545-562

    View details for DOI 10.1068/a42161

    View details for Web of Science ID 000277374700004

  • A Genetic Algorithm with Local Search Strategy for Improved Detection of Community Structure COMPLEXITY Li, S., Chen, Y., Du, H., Feldman, M. W. 2010; 15 (4): 53-60

    View details for DOI 10.1002/cplx.20300

    View details for Web of Science ID 000275504200006

  • Bacterial Genetic Signatures of Human Social Phenomena among M-tuberculosis from an Aboriginal Canadian Population MOLECULAR BIOLOGY AND EVOLUTION Pepperell, C., Hoeppner, V. H., Lipatov, M., Wobeser, W., Schoolnik, G. K., Feldman, M. W. 2010; 27 (2): 427-440

    Abstract

    Despite a widespread global distribution and highly variable disease phenotype, there is little DNA sequence diversity among isolates of Mycobacterium tuberculosis. In addition, many regional population genetic surveys have revealed a stereotypical structure in which a single clone, lineage, or clade makes up the majority of the population. It is often assumed that dominant clones are highly adapted, that is, the overall structure of M. tuberculosis populations is the result of positive selection. In order to test this assumption, we analyzed genetic data from extant populations of bacteria circulating in Aboriginal communities in Saskatchewan, Canada. Demographic parameters of the bacterial population were estimated from archival epidemiological data collected over approximately 130 years since the onset of epidemic tuberculosis in the host communities. Bacterial genetic data were tested against neutral theory expectations and the local evolutionary history of M. tuberculosis investigated by phylogenetic analysis. Our findings are not consistent with positive selection on the bacterial population. Instead, we uncovered founder effects persisting over decades and barriers to gene flow within the bacterial population. Simulation experiments suggested that a combination of these neutral influences could result in the stereotypical structure of M. tuberculosis populations. Some aspects of population structure were suggestive of background selection, and data were on the whole consistent with combined effects of population bottlenecks, subdivision, and background selection. Neutral phenomena, namely, bottlenecks and partitions within populations, are prominent influences on the evolution of M. tuberculosis and likely contribute to restricted genetic diversity observed within this species. Given these influences, a complex evolutionary model will be required to define the relative fitness of different M. tuberculosis lineages and, ultimately, to uncover the genetic basis for its success as a pathogen.

    View details for DOI 10.1093/molbev/msp261

    View details for PubMedID 19861642

  • Sex, mixability, and modularity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Livnat, A., Papadimitriou, C., Pippenger, N., Feldman, M. W. 2010; 107 (4): 1452-1457

    Abstract

    The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the recombination rate between them, respectively. Implications for sex and evolution theory are discussed.

    View details for DOI 10.1073/pnas.0910734106

    View details for Web of Science ID 000273974600042

    View details for PubMedID 20080594

  • Characterization of X-Linked SNP genotypic variation in globally distributed human populations GENOME BIOLOGY Casto, A. M., Li, J. Z., Absher, D., Myers, R., Ramachandran, S., Feldman, M. W. 2010; 11 (1)

    Abstract

    The transmission pattern of the human X chromosome reduces its population size relative to the autosomes, subjects it to disproportionate influence by female demography, and leaves X-linked mutations exposed to selection in males. As a result, the analysis of X-linked genomic variation can provide insights into the influence of demography and selection on the human genome. Here we characterize the genomic variation represented by 16,297 X-linked SNPs genotyped in the CEPH human genome diversity project samples.We found that X chromosomes tend to be more differentiated between human populations than autosomes, with several notable exceptions. Comparisons between genetically distant populations also showed an excess of X-linked SNPs with large allele frequency differences. Combining information about these SNPs with results from tests designed to detect selective sweeps, we identified two regions that were clear outliers from the rest of the X chromosome for haplotype structure and allele frequency distribution. We were also able to more precisely define the geographical extent of some previously described X-linked selective sweeps.The relationship between male and female demographic histories is likely to be complex as evidence supporting different conclusions can be found in the same dataset. Although demography may have contributed to the excess of SNPs with large allele frequency differences observed on the X chromosome, we believe that selection is at least partially responsible. Finally, our results reveal the geographical complexities of selective sweeps on the X chromosome and argue for the use of diverse populations in studies of selection.

    View details for DOI 10.1186/gb-2010-11-1-r10

    View details for Web of Science ID 000276433600007

    View details for PubMedID 20109212

    View details for PubMedCentralID PMC2847713

  • Floating Choices: A Generational Perspective on Intentions of Rural-Urban Migrants in China. Environment & planning A Yue, Z., Li, S., Feldman, M. W., Du, H. 2010; 42 (3): 545-562

    Abstract

    Using data from a 2005 Survey of rural-urban migrants in Shenzhen, this paper investigates intentions of two groups of migrants. We use the birth years from 1970 to 1980 as a reasonable range of dividing lines to separate the two groups. For each year we divide the sample into those born before that year and those born in or after that year. These are referred to as the old and the new generation, respectively. Three possible development trajectories are considered: settling in cities, returning home to seek a nonagricultural job, and returning home to farm. We find that members of the new generation have stronger desires to do non-farm work, and returning to seek a nonagricultural job has become the most important planned trajectory for this generation. Sharp differences exist between the two generations in the reasons that underlie their intentions. For the old generation, conditions such as age, family responsibility, and type of job are important determinants of intentions, while other conditions such as initial migration motives, social capital, and socioeconomic conditions of origin areas are important for the intentions of the new generation. Thus the new generation is more likely to view migration as a form of investment with the accumulation of human capital and social capital. Those migrants from the old generation who have higher education levels also intend to seek non-farm jobs. However, because of the combined effects of life cycle and the market transition in China, these intentions are not as strong as those of the new generation. We discuss economic and policy implications of our findings.

    View details for DOI 10.1068/a42161

    View details for PubMedID 24151348

    View details for PubMedCentralID PMC3800544

  • Sociocultural epistasis and cultural exaptation in footbinding, marriage form, and religious practices in early 20th-century Taiwan PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Brown, M. J., Feldman, M. W. 2009; 106 (52): 22139-22144

    Abstract

    Social theorists have long recognized that changes in social order have cultural consequences but have not been able to provide an individual-level mechanism of such effects. Explanations of human behavior have only just begun to explore the different evolutionary dynamics of social and cultural inheritance. Here we provide ethnographic evidence of how cultural evolution, at the level of individuals, can be influenced by social evolution. Sociocultural epistasis--association of cultural ideas with the hierarchical structure of social roles--influences cultural change in unexpected ways. We document the existence of cultural exaptation, where a custom's origin was not due to acceptance of the later associated ideas. A cultural exaptation can develop in the absence of a cultural idea favoring it, or even in the presence of a cultural idea against it. Such associations indicate a potentially larger role for social evolutionary dynamics in explaining individual human behavior than previously anticipated.

    View details for DOI 10.1073/pnas.0907520106

    View details for Web of Science ID 000273178700021

    View details for PubMedID 20080786

    View details for PubMedCentralID PMC2796906

  • Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations BMC GENETICS Kopelman, N. M., Stone, L., Wang, C., Gefel, D., Feldman, M. W., Hillel, J., Rosenberg, N. A. 2009; 10

    Abstract

    Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations.We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations.These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.

    View details for DOI 10.1186/1471-2156-10-80

    View details for Web of Science ID 000273553900001

    View details for PubMedID 19995433

  • A theory for the evolution of other-regard integrating proximate and ultimate perspectives PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Akcay, E., Van Cleve, J., Feldman, M. W., Roughgarden, J. 2009; 106 (45): 19061-19066

    Abstract

    Although much previous work describes evolutionary mechanisms that promote or stabilize different social behaviors, we still have little understanding of the factors that drive animal behavior proximately. Here we present a modeling approach to answer this question. Our model rests on motivations to achieve objectives as the proximate determinants of behavior. We develop a two-tiered framework by first modeling the dynamics of a social interaction at the behavioral time scale and then find the evolutionarily stable objectives that result from the outcomes these dynamics produce. We use this framework to ask whether "other-regarding" motivations, which result from a kind of nonselfish objective, can evolve when individuals are engaged in a social interaction that entails a conflict between their material payoffs. We find that, at the evolutionarily stable state, individuals can be other-regarding in that they are motivated to increase their partners' payoff as well as their own. In contrast to previous theories, we find that such motivations can evolve because of their direct effect on fitness and do not require kin selection or a special group structure. We also derive general conditions for the evolutionary stability of other-regarding motivations. Our conditions indicate that other-regarding motivations are more likely to evolve when social interactions and behavioral objectives are both synergistic.

    View details for DOI 10.1073/pnas.0904357106

    View details for Web of Science ID 000271637500035

    View details for PubMedID 19858492

    View details for PubMedCentralID PMC2776409

  • Inferring population histories using cultural data PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Rogers, D. S., Feldman, M. W., Ehrlich, P. R. 2009; 276 (1674): 3835-3843

    Abstract

    The question as to whether cultures evolve in a manner analogous to that of genetic evolution can be addressed by attempting to reconstruct population histories using cultural data. As others have argued, this can only succeed if cultures are isolated enough to maintain and pass on a central core of traditions that can be modified over time. In this study we used a set of cultural data (canoe design traits from Polynesia) to look for the kinds of patterns and relationships normally found in population genetic studies. After developing new techniques to accommodate the peculiarities of cultural data, we were able to infer an ancestral region (Fiji) and a sequence of cultural origins for these Polynesian societies. In addition, we found evidence of cultural exchange, migration and a serial founder effect. Results were stronger when analyses were based on functional traits (presumably subject to natural selection and convergence) rather than symbolic or stylistic traits (probably subject to cultural selection for rapid divergence). These patterns strongly suggest that cultural evolution, while clearly affected by cultural exchange, is also subject to some of the same processes and constraints as genetic evolution.

    View details for DOI 10.1098/rspb.2009.1088

    View details for Web of Science ID 000270174800013

    View details for PubMedID 19675007

    View details for PubMedCentralID PMC2817289

  • Coevolution of adaptive technology, maladaptive culture and population size in a producer-scrounger game PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Lehmann, L., Feldman, M. W. 2009; 276 (1674): 3853-3862

    Abstract

    Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a 'producer-scrounger' game, which can also usefully be interpreted as an 'individual-social' learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction.

    View details for DOI 10.1098/rspb.2009.0724

    View details for Web of Science ID 000270174800015

    View details for PubMedID 19692409

    View details for PubMedCentralID PMC2817275

  • ON THE EVOLUTION OF HARMING AND RECOGNITION IN FINITE PANMICTIC AND INFINITE STRUCTURED POPULATIONS EVOLUTION Lehmann, L., Feldman, M. W., Rousset, F. 2009; 63 (11): 2896-2913

    Abstract

    Natural selection may favor two very different types of social behaviors that have costs in vital rates (fecundity and/or survival) to the actor: helping behaviors, which increase the vital rates of recipients, and harming behaviors, which reduce the vital rates of recipients. Although social evolutionary theory has mainly dealt with helping behaviors, competition for limited resources creates ecological conditions in which an actor may benefit from expressing behaviors that reduce the vital rates of neighbors. This may occur if the reduction in vital rates decreases the intensity of competition experienced by the actor or that experienced by its offspring. Here, we explore the joint evolution of neutral recognition markers and marker-based costly conditional harming whereby actors express harming, conditional on actor and recipient bearing different conspicuous markers. We do so for two complementary demographic scenarios: finite panmictic and infinite structured populations. We find that marker-based conditional harming can evolve under a large range of recombination rates and group sizes under both finite panmictic and infinite structured populations. A direct comparison with results for the evolution of marker-based conditional helping reveals that, if everything else is equal, marker-based conditional harming is often more likely to evolve than marker-based conditional helping.

    View details for DOI 10.1111/j.1558-5646.2009.00778.x

    View details for Web of Science ID 000271031900011

    View details for PubMedID 19624725

    View details for PubMedCentralID PMC2989735

  • Genetic structure of a wide-spectrum chicken gene pool ANIMAL GENETICS Granevitze, Z., Hillel, J., Feldman, M., Six, A., Eding, H., Weigend, S. 2009; 40 (5): 686-693

    Abstract

    The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as 'Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool.

    View details for DOI 10.1111/j.1365-2052.2009.01902.x

    View details for Web of Science ID 000269572800013

    View details for PubMedID 19496773

  • Evolution of Stochastic Switching Rates in Asymmetric Fitness Landscapes GENETICS Salathe, M., Van Cleve, J., Feldman, M. W. 2009; 182 (4): 1159-1164

    Abstract

    Uncertain environments pose a tremendous challenge to populations: The selective pressures imposed by the environment can change so rapidly that adaptation by mutation alone would be too slow. One solution to this problem is given by the phenomenon of stochastic phenotype switching, which causes genetically uniform populations to be phenotypically heterogenous. Stochastic phenotype switching has been observed in numerous microbial species and is generally assumed to be an adaptive bet-hedging strategy to anticipate future environmental change. We use an explicit population genetic model to investigate the evolutionary dynamics of phenotypic switching rates. We find that whether or not stochastic switching is an adaptive strategy is highly contingent upon the fitness landscape given by the changing environment. Unless selection is very strong, asymmetric fitness landscapes-where the cost of being maladapted is not identical in all environments-strongly select against stochastic switching. We further observe a threshold phenomenon that causes switching rates to be either relatively high or completely absent, but rarely intermediate. Our finding that marginal changes in selection pressures can cause fundamentally different evolutionary outcomes is important in a wide range of fields concerned with microbial bet hedging.

    View details for DOI 10.1534/genetics.109.103333

    View details for Web of Science ID 000270214000019

    View details for PubMedID 19474199

    View details for PubMedCentralID PMC2728856

  • Conceptual Barriers to Progress Within Evolutionary Biology FOUNDATIONS OF SCIENCE Laland, K. N., Odling-Smee, J., Feldman, M. W., Kendal, J. 2009; 14 (3): 195-216
  • The rate at which asexual populations cross fitness valleys THEORETICAL POPULATION BIOLOGY Weissman, D. B., Desai, M. M., Fisher, D. S., Feldman, M. W. 2009; 75 (4): 286-300

    Abstract

    Complex traits often involve interactions between different genetic loci. This can lead to sign epistasis, whereby mutations that are individually deleterious or neutral combine to confer a fitness benefit. In order to acquire the beneficial genotype, an asexual population must cross a fitness valley or plateau by first acquiring the deleterious or neutral intermediates. Here, we present a complete, intuitive theoretical description of the valley-crossing process across the full spectrum of possible parameter regimes. We calculate the rate at which a population crosses a fitness valley or plateau of arbitrary width, as a function of the mutation rates, the population size, and the fitnesses of the intermediates. We find that when intermediates are close to neutral, a large population can cross even wide fitness valleys remarkably quickly, so that valley-crossing dynamics may be common even when mutations that directly increase fitness are also possible. Thus the evolutionary dynamics of large populations can be sensitive to the structure of an extended region of the fitness landscape - the population may not take directly uphill paths in favor of paths across valleys and plateaus that lead eventually to fitter genotypes. In smaller populations, we find that below a threshold size, which depends on the width of the fitness valley and the strength of selection against intermediate genotypes, valley-crossing is much less likely and hence the evolutionary dynamics are less influenced by distant regions of the fitness landscape.

    View details for DOI 10.1016/j.tpb.2009.02.006

    View details for Web of Science ID 000266833500009

    View details for PubMedID 19285994

    View details for PubMedCentralID PMC2992471

  • Intergenerational support and subjective health of older people in rural China: A gender-based longitudinal study AUSTRALASIAN JOURNAL ON AGEING Li, S., Song, L., Feldman, M. W. 2009; 28 (2): 81-86

    Abstract

    To examine gender differences in the effect of intergenerational exchanges on subjective health of Chinese rural elderly.Using the data from three waves of the survey 'Well-being of Elderly in Anhui Province, China' conducted in 2001, 2003 and 2006, respectively, this study uses random effect logit models for men and women separately.While an increase in instrumental support from children to older people is associated with deterioration in the subjective health of older men, financial support from older people to children is associated with improvement in the formers' subjective health. Although an increase in instrumental support from older people to children, and mutual emotional support is associated with improved subjective health of older women, financial support from children to older women has a negative effect on the latter's subjective health.Reciprocal intergenerational transfers contribute to improvement in subjective health of older people, while increased support through demand-based transfers appears to result in deterioration of their health.

    View details for DOI 10.1111/j.1741-6612.2009.00364.x

    View details for Web of Science ID 000267314100006

    View details for PubMedID 19566802

  • The Role of Geography in Human Adaptation PLOS GENETICS Coop, G., Pickrell, J. K., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Myers, R. M., Cavalli-Sforza, L. L., Feldman, M. W., Pritchard, J. K. 2009; 5 (6)

    Abstract

    Various observations argue for a role of adaptation in recent human evolution, including results from genome-wide studies and analyses of selection signals at candidate genes. Here, we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme F(ST) values across the whole genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes -- especially population history, migration, and drift -- exert powerful influences over the fate and geographic distribution of selected alleles.

    View details for DOI 10.1371/journal.pgen.1000500

    View details for Web of Science ID 000268444600034

    View details for PubMedID 19503611

    View details for PubMedCentralID PMC2685456

  • Sam Karlin and multi-locus population genetics THEORETICAL POPULATION BIOLOGY Feldman, M. W. 2009; 75 (4): 233-235

    Abstract

    Between 1967 and 1982, Sam Karlin made fundamental contributions to many areas of deterministic population genetic theory. This remembrance focuses on his work in multi-locus population genetics, primarily on the interaction between genotypic selection and the rate of recombination.

    View details for DOI 10.1016/j.tpb.2009.01.002

    View details for Web of Science ID 000266833500003

    View details for PubMedID 19344629

  • Complementation and Epistasis in Viral Coinfection Dynamics GENETICS Gao, H., Feldman, M. W. 2009; 182 (1): 251-263

    Abstract

    Coinfection in RNA virus populations results in two important phenomena, complementation and recombination. Of the two, complementation has a strong effect on selection against deleterious mutations, as has been confirmed in earlier studies. As complementation delays the purging of less-fit mutations, coinfection may be detrimental to the evolution of a virus population. Here we employ both deterministic modeling and stochastic simulation to explore the mechanisms underlying the interactions between complementation and other evolutionary factors, namely, mutation, selection, and epistasis. We find that strong complementation reduces slightly the overall fitness of a virus population but substantially enhances its diversity and robustness, especially when interacting with selection and epistasis.

    View details for DOI 10.1534/genetics.108.099796

    View details for Web of Science ID 000270213800021

    View details for PubMedID 19270273

    View details for PubMedCentralID PMC2674821

  • Signals of recent positive selection in a worldwide sample of human populations GENOME RESEARCH Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W., Pritchard, J. K. 2009; 19 (5): 826-837

    Abstract

    Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number of populations. Here, we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel. We refine the geographic distributions of known selective sweeps, and find extensive overlap between these distributions for populations in the same continental region but limited overlap between populations outside these groupings. We present several examples of previously unrecognized candidate targets of selection, including signals at a number of genes in the NRG-ERBB4 developmental pathway in non-African populations. Analysis of recently identified genes involved in complex diseases suggests that there has been selection on loci involved in susceptibility to type II diabetes. Finally, we search for local adaptation between geographically close populations, and highlight several examples.

    View details for DOI 10.1101/gr.087577.108

    View details for Web of Science ID 000265668800016

    View details for PubMedID 19307593

    View details for PubMedCentralID PMC2675971

  • DYNAMICS OF HYBRID INCOMPATIBILITY IN GENE NETWORKS IN A CONSTANT ENVIRONMENT EVOLUTION Palmer, M. E., Feldman, M. W. 2009; 63 (2): 418-431

    Abstract

    After an ancestral population splits into two allopatric populations, different mutations may fix in each. When pairs of mutations are brought together in a hybrid offspring, epistasis may cause reduced fitness. Such pairs are known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. A well-known model of BDM incompatibility due to Orr suggests that the fitness load on hybrids should initially accelerate, and continue to increase as the number of potentially incompatible substitutions increases (the "snowball effect"). In the gene networks model, which violates a key assumption of Orr's model (independence of fixation probabilities), the snowball effect often does not occur. Instead, we describe three possible dynamics in a constant environment: (1) Stabilizing selection can constrain two allopatric populations to remain near-perfectly compatible. (2) Despite constancy of environment, punctuated evolution may obtain; populations may experience rare adaptations asynchronously, permitting incompatibility. (3) Despite stabilizing selection, developmental system drift may permit genetic change, allowing two populations to drift in and out of compatibility. We reinterpret Orr's model in terms of genetic distance. We extend Orr's model to the finite loci case, which can limit incompatibility. Finally, we suggest that neutral evolution of gene regulation in nature, to the point of speciation, is a distinct possibility.

    View details for DOI 10.1111/j.1558-5646.2008.00577.x

    View details for Web of Science ID 000263254000010

    View details for PubMedID 19215292

    View details for PubMedCentralID PMC2989730

  • Topological Signatures of Species Interactions in Metabolic Networks JOURNAL OF COMPUTATIONAL BIOLOGY Borenstein, E., Feldman, M. W. 2009; 16 (2): 191-200

    Abstract

    The topology of metabolic networks can provide insight not only into the metabolic processes that occur within each species, but also into interactions between different species. Here, we introduce a novel pair-wise, topology-based measure of biosynthetic support, reflecting the extent to which the nutritional requirements of one species could be satisfied by the biosynthetic capacity of another. To evaluate the biosynthetic support for a given pair of species, we use a graph-based algorithm to identify the set of exogenously acquired compounds in the metabolic network of the first species, and calculate the fraction of this set that occurs in the metabolic network of the second species. Reconstructing the metabolic network of 569 bacterial species and several eukaryotes, and calculating the biosynthetic support score for all bacterial-eukaryotic pairs, we show that this measure indeed reflects host-parasite interactions and facilitates a successful prediction of such interactions on a large-scale. Integrating this method with phylogenetic analysis and calculating the biosynthetic support of ancestral species in the Firmicutes division (as well as other bacterial divisions) further reveals a large-scale evolutionary trend of biosynthetic capacity loss in parasites. The inference of ecological features from genomic-based data presented here lays the foundations for an exciting "reverse ecology" framework for studying the complex web of interactions characterizing various ecosystems.

    View details for DOI 10.1089/cmb.2008.06TT

    View details for Web of Science ID 000263057400006

    View details for PubMedID 19178139

    View details for PubMedCentralID PMC3035845

  • A serial founder effect model for human settlement out of Africa PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Deshpande, O., Batzoglou, S., Feldman, M. W., Cavalli-Sforza, L. L. 2009; 276 (1655): 291-300

    Abstract

    The increasing abundance of human genetic data has shown that the geographical patterns of worldwide genetic diversity are best explained by human expansion out of Africa. This expansion is modelled well by prolonged migration from a single origin in Africa with multiple subsequent serial founding events. We discuss a new simulation model for the serial founder effect out of Africa and compare it with results from previous studies. Unlike previous models, we distinguish colonization events from the continued exchange of people between occupied territories as a result of mating. We conduct a search through parameter space to estimate the range of parameter values that best explain key statistics from published data on worldwide variation in microsatellites. The range of parameters we use is chosen to be compatible with an out-of-Africa migration at 50-60Kyr ago and archaeo-ethno-demographic information. In addition to a colonization rate of 0.09-0.18, for an acceptable fit to the published microsatellite data, incorporation into existing models of exchange between neighbouring populations is essential, but at a very low rate. A linear decay of genetic diversity with geographical distance from the origin of expansion could apply to any species, especially if it moved recently into new geographical niches.

    View details for DOI 10.1098/rspb.2008.0750

    View details for Web of Science ID 000262005200013

    View details for PubMedID 18796400

    View details for PubMedCentralID PMC2674957

  • Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates MOLECULAR BIOLOGY AND EVOLUTION Henn, B. M., Gignoux, C. R., Feldman, M. W., Mountain, J. L. 2009; 26 (1): 217-230

    Abstract

    Previous research has established a discrepancy of nearly an order of magnitude between pedigree-based and phylogeny-based (human vs. chimpanzee) estimates of the mitochondrial DNA (mtDNA) control region mutation rate. We characterize the time dependency of the human mitochondrial hypervariable region one mutation rate by generating 14 new phylogeny-based mutation rate estimates using within-human comparisons and archaeological dates. Rate estimates based on population events between 15,000 and 50,000 years ago are at least 2-fold lower than pedigree-based estimates. These within-human estimates are also higher than estimates generated from phylogeny-based human-chimpanzee comparisons. Our new estimates establish a rapid decay in evolutionary mutation rate between approximately 2,500 and 50,000 years ago and a slow decay from 50,000 to 6 Ma. We then extend this analysis to the mtDNA-coding region. Our within-human coding region mutation rate estimates display a similar, though less rapid, time-dependent decay. We explore the possibility that multiple hits explain the discrepancy between pedigree-based and phylogeny-based mutation rates. We conclude that whereas nucleotide substitution models incorporating multiple hits do provide a possible explanation for the discrepancy between pedigree-based and human-chimpanzee mutation rate estimates, they do not explain the rapid decline of within-human rate estimates. We propose that demographic processes such as serial bottlenecks prior to the Holocene could explain the difference between rates estimated before and after 15,000 years ago. Our findings suggest that human mtDNA estimates of dates of population and phylogenetic events should be adjusted in light of this time dependency of the mutation rate estimates.

    View details for DOI 10.1093/molbev/msn244

    View details for Web of Science ID 000261681900021

    View details for PubMedID 18984905

  • War and the evolution of belligerence and bravery PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Lehmann, L., Feldman, M. W. 2008; 275 (1653): 2877-2885

    Abstract

    Tribal war occurs when a coalition of individuals use force to seize reproduction-enhancing resources, and it may have affected human evolution. Here, we develop a population-genetic model for the coevolution of costly male belligerence and bravery when war occurs between groups of individuals in a spatially subdivided population. Belligerence is assumed to increase an actor's group probability of trying to conquer another group. An actor's bravery is assumed to increase his group's ability to conquer an attacked group. We show that the selective pressure on these two traits can be substantial even in groups of large size, and that they may be driven by two independent reproduction-enhancing resources: additional mates for males and additional territory (or material resources) for females. This has consequences for our understanding of the evolution of intertribal interactions, as hunter-gatherer societies are well known to have frequently raided neighbouring groups from whom they appropriated territory, goods and women.

    View details for DOI 10.1098/rspb.2008.0842

    View details for Web of Science ID 000260611200012

    View details for PubMedID 18755675

    View details for PubMedCentralID PMC2605837

  • A mixability theory for the role of sex in evolution PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Livnat, A., Papadimitriou, C., Dushoff, J., Feldman, M. W. 2008; 105 (50): 19803-19808

    Abstract

    The question of what role sex plays in evolution is still open despite decades of research. It has often been assumed that sex should facilitate the increase in fitness. Hence, the fact that it may break down highly favorable genetic combinations has been seen as a problem. Here, we consider an alternative approach. We define a measure that represents the ability of alleles to perform well across different combinations and, using numerical iterations within a classical population-genetic framework, show that selection in the presence of sex favors this ability in a highly robust manner. We also show that the mechanism responsible for this effect has been out of the purview of previous theory, because it operates during the evolutionary transient, and that the breaking down of favorable genetic combinations is an integral part of it. Implications of these results and more to evolutionary theory are discussed.

    View details for DOI 10.1073/pnas.0803596105

    View details for Web of Science ID 000261802300043

    View details for PubMedID 19073912

  • Economics, cultural transmission, and the dynamics of the sex ratio at birth in China PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lipatov, M., Li, S., Feldman, M. W. 2008; 105 (49): 19171-19176

    Abstract

    In rural China, the ratio of newborn boys to newborn girls [sex ratio at birth (SRB)] has been rising for several decades, to values significantly above its biological norm. This trend has a number of alarming societal consequences, and has attracted the attention of scholars and politicians. The root of the problem lies in a 2,500-year-old culture of son preference. This culture is intricately linked with the economic reality of each couple's life, so that there are financial and psychological repercussions to parents who have no sons. To bring greater clarity and understanding to this issue, we present a quantitative framework that describes the interaction between economics and cultural transmission. We start with an explicit mechanism by which economic incentives can change cultural beliefs of a given individual, and go on to include a mechanism of cultural inheritance from generation to generation. We then show how economic conditions can affect the dynamics of cultural change in an entire society, and may lead to a decrease in the country's sex ratio at birth.

    View details for DOI 10.1073/pnas.0806747105

    View details for Web of Science ID 000261706600029

    View details for PubMedID 19047641

    View details for PubMedCentralID PMC2614734

  • High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography PLOS BIOLOGY Hershberg, R., Lipatov, M., Small, P. M., Sheffer, H., Niemann, S., Homolka, S., Roach, J. C., Kremer, K., Petrov, D. A., Feldman, M. W., Gagneux, S. 2008; 6 (12): 2658-2671

    Abstract

    Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

    View details for DOI 10.1371/journal.pbio.0060311

    View details for Web of Science ID 000261913700009

    View details for PubMedID 19090620

    View details for PubMedCentralID PMC2602723

  • Population differentiation and migration: Coalescence times in a two-sex island model for autosomal and X-linked loci THEORETICAL POPULATION BIOLOGY Ramachandran, S., Rosenberg, N. A., Feldman, M. W., Wakeley, J. 2008; 74 (4): 291-301

    Abstract

    Evolutionists have debated whether population-genetic parameters, such as effective population size and migration rate, differ between males and females. In humans, most analyses of this problem have focused on the Y chromosome and the mitochondrial genome, while the X chromosome has largely been omitted from the discussion. Past studies have compared F(ST) values for the Y chromosome and mitochondrion under a model with migration rates that differ between the sexes but with equal male and female population sizes. In this study we investigate rates of coalescence for X-linked and autosomal lineages in an island model with different population sizes and migration rates for males and females, obtaining the mean time to coalescence for pairs of lineages from the same deme and for pairs of lineages from different demes. We apply our results to microsatellite data from the Human Genome Diversity Panel, and we examine the male and female migration rates implied by observed F(ST) values.

    View details for DOI 10.1016/j.tpb.2008.08.003

    View details for Web of Science ID 000261533200002

    View details for PubMedID 18817799

  • Social and individual learning of helping in humans and other species TRENDS IN ECOLOGY & EVOLUTION Lehmann, L., Foster, K. R., Borenstein, E., Feldman, M. W. 2008; 23 (12): 664-671

    Abstract

    Helping behaviors can be innate, learned by copying others (cultural transmission) or individually learned de novo. These three possibilities are often entangled in debates on the evolution of helping in humans. Here we discuss their similarities and differences, and argue that evolutionary biologists underestimate the role of individual learning in the expression of helping behaviors in humans.

    View details for DOI 10.1016/j.tree.2008.07.012

    View details for Web of Science ID 000261532300004

    View details for PubMedID 18951656

  • How can economic schemes curtail the increasing sex ratio at birth in China? DEMOGRAPHIC RESEARCH Bhattacharjya, D., Sudarshan, A., Tuljapurkar, S., Shachter, R., Feldman, M. 2008; 19: 1831-1850

    Abstract

    Fertility decline, driven by the one-child policy, and son preference have contributed to an alarming difference in the number of live male and female births in China. We present a quantitative model where people choose to sex-select because they perceive that married sons are more valuable than married daughters. Due to the predominant patrilocal kinship system in China, daughters-in-law provide valuable emotional and financial support, enhancing the perceived present value of married sons. We argue that inter-generational transfer data will help ascertain the extent to which economic schemes (such as pension plans for families with no sons) can curtail the increasing sex ratio at birth.

    View details for Web of Science ID 000259977900001

    View details for PubMedCentralID PMC2990196

  • How can economic schemes curtail the increasing sex ratio at birth in China? Demographic research Bhattacharjya, D., Sudarshan, A., Tuljapurkar, S., Shachter, R., Feldman, M. 2008; 19 (54): 1831-1850

    Abstract

    Fertility decline, driven by the one-child policy, and son preference have contributed to an alarming difference in the number of live male and female births in China. We present a quantitative model where people choose to sex-select because they perceive that married sons are more valuable than married daughters. Due to the predominant patrilocal kinship system in China, daughters-in-law provide valuable emotional and financial support, enhancing the perceived present value of married sons. We argue that inter-generational transfer data will help ascertain the extent to which economic schemes (such as pension plans for families with no sons) can curtail the increasing sex ratio at birth.

    View details for DOI 10.4054/DemRes.2008.19.54

    View details for PubMedID 21113272

    View details for PubMedCentralID PMC2990196

  • Large-scale reconstruction and phylogenetic analysis of metabolic environments PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Borenstein, E., Kupiec, M., Feldman, M. W., Ruppin, E. 2008; 105 (38): 14482-14487

    Abstract

    The topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. Here we introduce the concept of a metabolic network's "seed set"--the set of compounds that, based on the network topology, are exogenously acquired--and provide a methodological framework to computationally infer the seed set of a given network. Such seed sets form ecological "interfaces" between metabolic networks and their surroundings, approximating the effective biochemical environment of each species. Analyzing the metabolic networks of 478 species and identifying the seed set of each species, we present a comprehensive large-scale reconstruction of such predicted metabolic environments. The seed sets' composition significantly correlates with several basic properties characterizing the species' environments and agrees with biological observations concerning major adaptations. Species whose environments are highly predictable (e.g., obligate parasites) tend to have smaller seed sets than species living in variable environments. Phylogenetic analysis of the seed sets reveals the complex dynamics governing gain and loss of seeds across the phylogenetic tree and the process of transition between seed and non-seed compounds. Our findings suggest that the seed state is transient and that seeds tend either to be dropped completely from the network or to become non-seed compounds relatively fast. The seed sets also permit a successful reconstruction of a phylogenetic tree of life. The "reverse ecology" approach presented lays the foundations for studying the evolutionary interplay between organisms and their habitats on a large scale.

    View details for DOI 10.1073/pnas.0806162105

    View details for Web of Science ID 000259592400047

    View details for PubMedID 18787117

    View details for PubMedCentralID PMC2567166

  • QTLs detected in a multigenerational resource chicken population JOURNAL OF HEREDITY Atzmon, G., Blum, S., Feldman, M., Cahaner, A., Lavi, U., Hillel, J. 2008; 99 (5): 528-538

    Abstract

    The genetic structure of resource populations affects the power of tests to detect associations between DNA markers and complex traits. Following a chicken interline cross (White Plymouth Rock background), we produced a multigenerational resource population based on 4 pedigreed generations. In this large sibship, 265 parents have been genotyped, and their 3317 progenies have been phenotyped for BW21, BW42, breast meat weight, fat pad weight, and egg production. We developed an approach to increase test power by imposing several ways of validation including the minimization of false-positive associations. Some of our detected associations were in agreement with QTLs previously reported in the literature. A large fraction of the 81 screened markers was found to be associated with quantitative traits. We examined 729 associations, of which 150 (21%) were significant, and of these, 54 are supported by the literature. These 54 associations were identified by 42 markers (some of which are linked to each other). This finding not only supports the results obtained in our resource population but may also give some indication about their general properties.

    View details for DOI 10.1093/jhered/esn030

    View details for Web of Science ID 000258330500010

    View details for PubMedID 18492652

  • Stable long-period cycling and complex dynamics in a single-locus fertility model with genomic imprinting JOURNAL OF MATHEMATICAL BIOLOGY Van Cleve, J., Feldman, M. W. 2008; 57 (2): 243-264

    Abstract

    Although long-period population size cycles and chaotic fluctuations in abundance are common in ecological models, such dynamics are uncommon in simple population-genetic models where convergence to a fixed equilibrium is most typical. When genotype-frequency cycling does occur, it is most often due to frequency-dependent selection that results from individual or species interactions. In this paper, we demonstrate that fertility selection and genomic imprinting are sufficient to generate a Hopf bifurcation and complex genotype-frequency cycling in a single-locus population-genetic model. Previous studies have shown that on its own, fertility selection can yield stable two-cycles but not long-period cycling characteristic of a Hopf bifurcation. Genomic imprinting, a molecular mechanism by which the expression of an allele depends on the sex of the donating parent, allows fitness matrices to be nonsymmetric, and this additional flexibility is crucial to the complex dynamics we observe in this fertility selection model. Additionally, we find under certain conditions that stable oscillations and a stable equilibrium point can coexist. These dynamics are characteristic of a Chenciner (generalized Hopf) bifurcation. We believe this model to be the simplest population-genetic model with such dynamics.

    View details for DOI 10.1007/s00285-008-0156-4

    View details for Web of Science ID 000255863900005

    View details for PubMedID 18253736

  • Cultural transmission can inhibit the evolution of altruistic helping AMERICAN NATURALIST Lehmann, L., Feldman, M. W., Foster, K. R. 2008; 172 (1): 12-24

    Abstract

    The study of culturally inherited traits has led to the suggestion that the evolution of helping behaviors is more likely with cultural transmission than without. Here we evaluate this idea through a comparative analysis of selection on helping under both genetic and cultural inheritance. We develop two simple models for the evolution of helping through cultural group selection: one in which selection on the trait depends solely on Darwinian fitness effects and one in which selection is driven by nonreproductive factors, specifically imitation of strategies achieving higher payoffs. We show that when cultural variants affect Darwinian fitness, the selection pressure on helping can be markedly increased relative to that under genetic transmission. By contrast, when variants are driven by nonreproductive factors, the selection pressure on helping may be reduced relative to that under genetic inheritance. This occurs because, unlike biological offspring, the spread of cultural variants from one group to another through imitation does not reduce the number of these variants in the source group. As a consequence, there is increased within-group competition associated with traits increasing group productivity, which reduces the benefits of helping. In these cases, selection for harming behavior (decreasing the payoff to neighbors) may occur rather than selection for helping.

    View details for DOI 10.1086/587851

    View details for Web of Science ID 000256752600005

    View details for PubMedID 18500938

  • The co-evolution of culturally inherited altruistic helping and cultural transmission under random group formation THEORETICAL POPULATION BIOLOGY Lehmann, L., Feldman, M. W. 2008; 73 (4): 506-516

    Abstract

    Limited migration results in kin selective pressure on helping behaviors under a wide range of ecological, demographic and life-history situations. However, such genetically determined altruistic helping can evolve only when migration is not too strong and group size is not too large. Cultural inheritance of helping behaviors may allow altruistic helping to evolve in groups of larger size because cultural transmission has the potential to markedly decrease the variance within groups and augment the variance between groups. Here, we study the co-evolution of culturally inherited altruistic helping behaviors and two alternative cultural transmission rules for such behaviors. We find that conformist transmission, where individuals within groups tend to copy prevalent cultural variants (e.g., beliefs or values), has a strong adverse effect on the evolution of culturally inherited helping traits. This finding is at variance with the commonly held view that conformist transmission is a crucial factor favoring the evolution of altruistic helping in humans. By contrast, we find that under one-to-many transmission, where individuals within groups tend to copy a "leader" (or teacher), altruistic helping can evolve in groups of any size, although the cultural transmission rule itself hitchhikes rather weakly with a selected helping trait. Our results suggest that culturally determined helping behaviors are more likely to be driven by "leaders" than by popularity, but the emergence and stability of the cultural transmission rules themselves should be driven by some extrinsic factors.

    View details for DOI 10.1016/j.tpb.2008.02.004

    View details for Web of Science ID 000256996000006

    View details for PubMedID 18420241

  • The generational cycle of state spaces and adequate genetical representation PHILOSOPHY OF SCIENCE Lloyd, E. A., Lewontin, R. C., Feldman, M. W. 2008; 75 (2): 140-156
  • Early experience affects producer-scrounger foraging tendencies in the house sparrow ANIMAL BEHAVIOUR Katsnelson, E., Motro, U., Feldman, M. W., Lotem, A. 2008; 75: 1465-1472
  • Evolution of learning in fluctuating environments: When selection favors both social and exploratory individual learning EVOLUTION Borenstein, E., Feldman, M. W., Aoki, K. 2008; 62 (3): 586-602

    Abstract

    Cumulative cultural change requires organisms that are capable of both exploratory individual learning and faithful social learning. In our model, an organism's phenotype is initially determined innately (by its genotypic value) or by social learning (copying a phenotype from the parental generation), and then may or may not be modified by individual learning (exploration around the initial phenotype). The environment alternates periodically between two states, each defined as a certain range of phenotypes that can survive. These states may overlap, in which case the same phenotype can survive in both states, or they may not. We find that a joint social and exploratory individual learning strategy-the strategy that supports cumulative culture-is likely to spread when the environmental states do not overlap. In particular, when the environmental states are contiguous and mutation is allowed among the genotypic values, this strategy will spread in either moderately or highly stable environments, depending on the exact nature of the individual learning applied. On the other hand, natural selection often favors a social learning strategy without exploration when the environmental states overlap. We find only partial support for the "consensus" view, which holds that individual learning, social learning, and innate determination of behavior will evolve at short, intermediate, and long environmental periodicities, respectively.

    View details for DOI 10.1111/j.1558-5646.2007.00313.x

    View details for Web of Science ID 000253758600008

    View details for PubMedID 18182074

  • On the evolution of epistasis III: The haploid case with mutation THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. 2008; 73 (2): 307-316

    Abstract

    Whether interaction between genes is better represented by synergistic or antagonistic epistasis has been a focus of experimental research in bacterial population genetics. Our previous research on evolution of modifiers of epistasis in diploid systems has indicated that the strength of positive or negative epistasis should increase provided linkage disequilibrium is maintained. Here we study a modifier of epistasis in fitness between two loci in a haploid system. Epistasis is modified in the neighborhood of a mutation-selection balance. We show that when linkage in the three-locus system is tight, an increase in the frequency of a modifier allele that induces either more negative or more positive epistasis is possible. Epistasis here can be measured on either an additive or multiplicative scale.

    View details for DOI 10.1016/j.tpb.2007.11.010

    View details for Web of Science ID 000254492600013

    View details for PubMedID 18215408

  • Worldwide human relationships inferred from genome-wide patterns of variation SCIENCE Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M., Cavalli-Sforza, L. L., Myers, R. M. 2008; 319 (5866): 1100-1104

    Abstract

    Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.

    View details for DOI 10.1126/science.1153717

    View details for Web of Science ID 000253311700046

    View details for PubMedID 18292342

  • The ethics of characterizing difference: guiding principles on using racial categories in human genetics GENOME BIOLOGY Lee, S. S., Mountain, J., Koenig, B., Altman, R., Brown, M., Camarillo, A., Cavalli-Sforza, L., Cho, M., Eberhardt, J., Feldman, M., Ford, R., Greely, H., King, R., Markus, H., Satz, D., Snipp, M., Steele, C., Underhill, P. 2008; 9 (7)

    Abstract

    We are a multidisciplinary group of Stanford faculty who propose ten principles to guide the use of racial and ethnic categories when characterizing group differences in research into human genetic variation.

    View details for DOI 10.1186/gb-2008-9-7-404

    View details for Web of Science ID 000258773600005

    View details for PubMedID 18638359

    View details for PubMedCentralID PMC2530857

  • Genetic diversity within chicken populations from different continents and management histories ANIMAL GENETICS Granevitze, Z., Hillel, J., Chen, G. H., CUC, N. T., Feldman, M., Eding, H., Weigend, S. 2007; 38 (6): 576-583

    Abstract

    Intra-population variation was assessed in 1970 chickens from 64 populations using 29 autosomal microsatellites. On average, 95% of the loci were polymorphic across populations. In 1456 (c. 83%) of the 1763 combinations of populations and polymorphic loci, no departure from Hardy-Weinberg equilibrium was observed. On average, there were 11.4 alleles per locus and 3.6 alleles per population across loci. Within populations, the average observed heterozygote frequency was 0.46, with a range between 0.20 and 0.64. Dagu, a Chinese population, and the Red Jungle Fowl (Gallus gallus gallus) had the highest average heterozygote frequencies at 0.64 and 0.63 respectively. An inbred line used as a reference population for comparison showed the lowest average of observed heterozygote frequency (0.05), followed by the European population Hamburger Lackhuhn, whose average observed heterozygote frequency was 0.20. A total of 32 private alleles (alleles detected in only one population) for 20 loci were found in 18 populations. H'mong chickens, a Vietnamese population, carried the largest number of private alleles at five, followed by the Red Jungle Fowl with four private alleles. Genetic diversity within populations was low in the NW European fancy breeds and high in the non-commercial Asian populations, in agreement with population management history.

    View details for DOI 10.1111/j.1365-2052.2007.01650.x

    View details for Web of Science ID 000251327600005

    View details for PubMedID 17931400

  • Marriage form and son preference in rural China: An investigation in three counties RURAL SOCIOLOGY Jin, X., Li, S., Feldman, M. W. 2007; 72 (4): 511-536
  • Genetic variation and population structure in Native Americans PLOS GENETICS Wang, S., Lewis, C. M., Jakobsson, M., Ramachandran, S., Ray, N., Bedoya, G., Rojas, W., Parra, M. V., Molina, J. A., Gallo, C., Mazzotti, G., Poletti, G., Hill, K., Hurtado, A. M., Labuda, D., Klitz, W., Barrantes, R., Bortolini, M. C., Salzano, F. M., Petzl-Erler, M. L., Tsuneto, L. T., Llop, E., Rothhammer, F., Excoffier, L., Feldman, M. W., Rosenberg, N. A., Ruiz-Linares, A. 2007; 3 (11): 2049-2067

    Abstract

    We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

    View details for DOI 10.1371/journal.pgen.0030185

    View details for Web of Science ID 000251310200002

    View details for PubMedID 18039031

  • Evolution can favor antagonistic epistasis GENETICS Desai, M. M., Weissman, D., Feldman, M. W. 2007; 177 (2): 1001-1010

    Abstract

    The accumulation of deleterious mutations plays a major role in evolution, and key to this are the interactions between their fitness effects, known as epistasis. Whether mutations tend to interact synergistically (with multiple mutations being more deleterious than would be expected from their individual fitness effects) or antagonistically is important for a variety of evolutionary questions, particularly the evolution of sex. Unfortunately, the experimental evidence on the prevalence and strength of epistasis is mixed and inconclusive. Here we study theoretically whether synergistic or antagonistic epistasis is likely to be favored by evolution and by how much. We find that in the presence of recombination, evolution favors less synergistic or more antagonistic epistasis whenever mutations that change the epistasis in this direction are possible. This is because evolution favors increased buffering against the effects of deleterious mutations. This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely.

    View details for DOI 10.1534/genetics.107.075812

    View details for Web of Science ID 000250657800029

    View details for PubMedID 17720923

  • An exact nonparametric method for inferring mosaic structure in sequence triplets GENETICS Boni, M. F., Posada, D., Feldman, M. W. 2007; 176 (2): 1035-1047

    Abstract

    Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Delta(m,n,b). We present a method for rapidly calculating the distribution of Delta(m,n,b) and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.

    View details for DOI 10.1534/genetics.106.068874

    View details for Web of Science ID 000247870700027

    View details for PubMedID 17409078

  • Sex-specific viability, sex linkage and dominance in genomic imprinting GENETICS Van Cleve, J., Feldman, M. W. 2007; 176 (2): 1101-1118

    Abstract

    Genomic imprinting is a phenomenon by which the expression of an allele at a locus depends on the parent of origin. Two different two-locus evolutionary models are presented in which a second locus modifies the imprinting status of the primary locus, which is under differential selection in males and females. In the first model, a modifier allele that imprints the primary locus invades the population when the average dominance coefficient among females and males is >12 and selection is weak. The condition for invasion is always heavily contingent upon the extent of dominance. Imprinting is more likely in the sex experiencing weaker selection only under some parameter regimes, whereas imprinting by either sex is equally likely under other regimes. The second model shows that a modifier allele that induces imprinting will increase when imprinting has a direct selective advantage. The results are not qualitatively dependent on whether the modifier locus is autosomal or X linked.

    View details for DOI 10.1534/genetics.107.071555

    View details for Web of Science ID 000247870700031

    View details for PubMedID 17435253

    View details for PubMedCentralID PMC1894577

  • Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L. GENETICS SELECTION EVOLUTION David, L., Rosenberg, N. A., Lavi, U., Feldman, M. W., Hillel, J. 2007; 39 (3): 319-340

    Abstract

    Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, supported the genetic distinctiveness of aquacultured and ornamental carps, despite the recent divergence of the two groups. In contrast to what was observed for AFLP-based diversity, the frequency of heterozygotes based on microsatellites was comparable among all populations. This discrepancy can potentially be explained by duplication of some loci in Cyprinus carpio L., and a model that shows how duplication can increase heterozygosity estimates for microsatellites but not for AFLP loci is discussed. Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication.

    View details for DOI 10.1051/gse:2007006

    View details for Web of Science ID 000245686900006

    View details for PubMedID 17433244

  • Female-specific DNA sequences in the chicken genome JOURNAL OF HEREDITY Granevitze, Z., Blum, S., Cheng, H., Vignal, A., Morisson, M., Ben-Ari, G., David, L., Feldman, M. W., Weigend, S., Hillel, J. 2007; 98 (3): 238-242

    Abstract

    Eight in silico W-specific sequences from the WASHUC1 chicken genome assembly gave female-specific PCR products using chicken DNA. Some of these fragments gave female-specific products with turkey and peacock DNA. Sequence analysis of these 8 fragments (3077 bp total) failed to detect any polymorphisms among 10 divergent chickens. In contrast, comparison of the DNA sequences of chicken with those of turkey and peacock revealed a nucleotide difference every 25 and 28 bp, respectively. Radiation hybrid mapping verified that these amplicons exist only on chromosome W. The homology of 6 W-specific fragments with chromo-helicase-DNA-binding gene and expressed sequenced tags from chicken and other species indicate that these fragments may have or have had a biological function. These fragments may be used for early sexing in commercial chicken and turkey flocks.

    View details for DOI 10.1093/jhered/esm010

    View details for Web of Science ID 000247813500006

    View details for PubMedID 17395599

  • On the evolution of epistasis II: A generalized Wright-Kimura framework THEORETICAL POPULATION BIOLOGY Liberman, U., Puniyani, A., Feldman, M. W. 2007; 71 (2): 230-238

    Abstract

    The evolution of fitness interactions between genes at two major loci is studied where the alleles at a third locus modify the epistatic interaction between the two major loci. The epistasis is defined by a parameter epsilon and a matrix structure that specifies the nature of the interactions. When epsilon=0 the two major loci have additive fitnesses, and when these are symmetric the interaction matrices studied here produce symmetric viabilities of the Wright [1952. The genetics of quantitative variability. In: Reeve, E.C.R., Waddington, C.H. (Eds.), Quantitative Inheritance. Her Majesty's Stationary Office, London]-Kimura [1956. A model of a genetic system which leads to closer linkage by natural selection. Evolution 10, 278-281] form. Two such interaction matrices are studied, for one of which epistasis as measured by |epsilon| always increases, and for the other it increases when the linkage between the major loci is tight enough and there is initial linkage disequilibrium. Increase of epistasis does not necessarily coincide with increase in equilibrium mean fitness.

    View details for DOI 10.1016/j.tpb.2006.10.002

    View details for Web of Science ID 000244907800009

    View details for PubMedID 17141817

  • Molecular markers for the assessment of chicken biodiversity WORLDS POULTRY SCIENCE JOURNAL Hillel, J., Granevitze, Z., Twito, T., ben-Avraham, D., Blum, S., Lavi, U., David, L., Feldman, M. W., Cheng, H., Weigend, S. 2007; 63 (1): 33-45

    View details for DOI 10.1079/WPS2006125

    View details for Web of Science ID 000253473300002

  • Detection of agriculturally important QTLs in chickens and analysis of the factors affecting genotyping strategy CYTOGENETIC AND GENOME RESEARCH Atzmon, G., Blum, S., Feldman, M., Lavi, U., Hillel, J. 2007; 117 (1-4): 327-337

    Abstract

    Three single cross populations were generated in order to analyze factors affecting the ability to detect true linkage with minimum false positive or false negative associations, and to detect associations between markers and quantitative traits. The three populations are: (1) a broiler x broiler cross of a single sire and 34 dams, resulting in 266 progeny; (2) a broiler x broiler cross of a single sire and 41 dams resulting in 360 progeny; and (3) a broiler x layer cross of a single sire with 56 dams resulting in 1180 progeny. Based on these three resource populations we show that: a) gradient selective genotyping was more effective than the random selective genotyping; b) selective genotyping was significant at a selected proportion less than 62% of the cumulative truncation point; c) as few as 10% of selected individuals (5% of each of the two tails) were sufficient to show significant association between markers and phenotypes; d) a gradient slices approach was more powerful than using replicates of the extreme groups; and e) in resource populations resulting from crosses between lines of different backgrounds, most of the microsatellite markers used are polymorphic. We also used simulation to test factors affecting power to detect true associations between markers and traits that are hard to detect in experimental resource populations. Using defined populations in the simulation, we concluded that the following guidelines provide reliable detection of linked QTLs: 1) the resource population size should be larger than 100; 2) a QTL effect larger than 0.4 SD is detectable with a reasonable number of markers (>100) and resource population size (>200 subjects); 3) the DNA pool from each tail of the trait distribution should contain at least 10% of the resource family; 4) each of the two DNA pools should include more than 35 individuals. Some of these guidelines that were deduced from the simulation analysis have been confirmed in the experimental part of this study.

    View details for DOI 10.1159/000103195

    View details for Web of Science ID 000249980800038

    View details for PubMedID 17675875

  • An algorithm for detecting community structure of social networks based on prior knowledge and modularity COMPLEXITY Du, H., Feldman, M. W., Li, S., Jin, X. 2007; 12 (3): 53-60

    View details for DOI 10.1002/cplx.20166

    View details for Web of Science ID 000244051800007

  • Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions CYTOGENETIC AND GENOME RESEARCH Twito, T., Weigend, S., Blum, S., Granevitze, Z., Feldman, M. W., Perl-Treves, R., Lavi, U., Hillel, J. 2007; 117 (1-4): 319-326

    Abstract

    Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness.

    View details for DOI 10.1159/000103194

    View details for Web of Science ID 000249980800037

    View details for PubMedID 17675874

  • Evolutionary theory for modifiers of epistasis using a general symmetric model PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Liberman, U., Feldman, M. W. 2006; 103 (51): 19402-19406

    Abstract

    Genetic interactions in fitness are studied by using modifier theory. The effects on fitness of two linked genes are perturbed by alleles at a third linked locus that controls the extent of epistasis in fitness between the first two. This epistasis is determined by a symmetric interaction matrix, and it is shown that a modifier allele that increases epistasis will invade when the linkage between the other two genes is sufficiently tight and these genes are in linkage disequilibrium. With linkage equilibrium among the major loci, increased or decreased epistasis may evolve depending on the allele frequencies at these loci.

    View details for DOI 10.1073/pnas.0608569103

    View details for Web of Science ID 000243166600034

    View details for PubMedID 17167052

  • Difference between evolutionarily effective and germ line mutation rate due to stochastically varying haplogroup size MOLECULAR BIOLOGY AND EVOLUTION Zhivotovsky, L. A., Underhill, P. A., Feldman, M. W. 2006; 23 (12): 2268-2270

    Abstract

    Within a Y-chromosome haplogroup defined by unique event mutations, variation in microsatellites can accumulate due to their rapid mutation. Estimates based on pedigrees for the Y-chromosome microsatellite mutation rate are 3 or more times greater than the same estimates from evolutionary considerations. We show by simulation that the haplogroups that survive the stochastic processes of drift and extinction accumulate microsatellite variation at a lower rate than predicted from corresponding pedigree estimates; in particular, under constant total population size, the accumulated variance is on average 3-4 times smaller.

    View details for DOI 10.1093/molbev/msl1105

    View details for Web of Science ID 000241955400003

    View details for PubMedID 16956974

  • Cultural coevolution of norm adoption and enforcement when punishers are rewarded or non-punishers are punished THEORETICAL POPULATION BIOLOGY Kendal, J., Feldman, M. W., Aoki, K. 2006; 70 (1): 10-25

    Abstract

    A number of studies have shown that social norms can be maintained at a high frequency when norm-violators are punished. However, there remains the problem of how norm-adopters and punishers coevolve within a single group. We develop a recursive system to examine the coevolution of norm-adopters and punishers where the viability of punishers is enhanced by one of two "metanorms": (1) Norm-observers reward punishers for punishing norm-violators (Reward Model); (2) Punishers punish non-punishers (Punishment Model). Both models generate a bistable system and each is characterized in phenotype frequency space by a distinct region of attraction to the equilibrium consisting of only norm-adopting punishers. Using a Monte Carlo simulation, we find that cultural drift may allow norm-adopters and punishers to coevolve from invasion into this region of attraction, resulting in their fixation. This coevolution typically occurs across a wider range of conditions under the reward- than the punishment-based metanorm. We also show that, under appropriate conditions, a large negative statistical association between the two traits may evolve only under the Reward Model. Furthermore, for each metanorm, a population of norm-adopters who always observe the norm can be locally stable over a continuum of punishment frequencies.

    View details for DOI 10.1016/j.tpb.2006.01.003

    View details for Web of Science ID 000238628900002

    View details for PubMedID 16516942

  • Cultural Niche Construction in a metapopulation THEORETICAL POPULATION BIOLOGY Borenstein, E., Kendal, J., Feldman, M. 2006; 70 (1): 92-104

    Abstract

    Cultural niche construction is the process by which certain evolving cultural traits form a cultural niche that affects the evolution of other genetic and cultural traits [Laland, K., et al., 2001. Cultural niche construction and human evolution. J. Evol. Biol. 14, 22-33; Ihara, Y., Feldman, M., 2004. Cultural niche construction and the evolution of small family size. Theor. Popul. Biol. 65, 105-111]. In this study we focus on cultural niche construction in a metapopulation (a population of populations), where the frequency of one cultural trait (e.g. the level of education) determines the transmission rate of a second trait (e.g. the adoption of fertility reduction preferences) within and between populations. We formulate the Metapopulation Cultural Niche Construction (MPCNC) model by defining the cultural niche induced by the first trait as the construction of a social interaction network on which the second trait may percolate. Analysis of the model reveals dynamics that are markedly different from those observed in a single population, allowing, for example, different (or even opposing) dynamics in each population. In particular, this model can account for the puzzling phenomenon reported in previous studies [Bongaarts, J., Watkins, S., 1996. Social interactions and contemporary fertility transitions. Popul. Dev. Rev. 22 (4), 639-682] that the onset of the demographic transition in different countries occurred at ever lower levels of development.

    View details for DOI 10.1016/j.tpb.2005.10.003

    View details for Web of Science ID 000238628900009

    View details for PubMedID 16426653

  • Epidemic dynamics and antigenic evolution in a single season of influenza A PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Boni, M. F., Gog, J. R., Andreasen, V., Feldman, M. W. 2006; 273 (1592): 1307-1316

    Abstract

    We use a mathematical model to study the evolution of influenza A during the epidemic dynamics of a single season. Classifying strains by their distance from the epidemic-originating strain, we show that neutral mutation yields a constant rate of antigenic evolution, even in the presence of epidemic dynamics. We introduce host immunity and viral immune escape to construct a non-neutral model. Our population dynamics can then be framed naturally in the context of population genetics, and we show that departure from neutrality is governed by the covariance between a strain's fitness and its distance from the original epidemic strain. We quantify the amount of antigenic evolution that takes place in excess of what is expected under neutrality and find that this excess amount is largest under strong host immunity and long epidemics.

    View details for DOI 10.1098/rspb.2006.3466

    View details for Web of Science ID 000237780100001

    View details for PubMedID 16777717

    View details for PubMedCentralID PMC1560306

  • Why is stress so deadly? An evolutionary perspective PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Hadany, L., Beker, T., Eshel, I., Feldman, M. W. 2006; 273 (1588): 881-885

    Abstract

    The reaction of the body to prolonged stress has many harmful effects. Classical theory assumes that stress responses have evolved due to their short-term selective advantages ('flight or fight'), and despite their adverse long-term effects. In contrast, we demonstrate that the adverse effects of stress responses may have a selective advantage. Using an analytical model we show that a gene that causes the early death of a relatively unfit individual can increase in frequency in a structured population even if it has no positive effect on that individual. This result offers a new perspective on the relations between stress factors, stress responses and stress-related diseases.

    View details for DOI 10.1098/rspb.2005.3384

    View details for Web of Science ID 000236279800016

    View details for PubMedID 16618683

    View details for PubMedCentralID PMC1560227

  • Marriage form and fertility in rural China: an investigation in three counties POPULATION RESEARCH AND POLICY REVIEW Jin, X., Li, S., Feldman, M. W. 2006; 25 (2): 141-156
  • A semi-symmetric two-locus model THEORETICAL POPULATION BIOLOGY Puniyani, A., Feldman, M. W. 2006; 69 (2): 211-215

    Abstract

    The two-locus symmetric viability model characterized by its invariance with respect to the exchange of alleles at each locus, is a well-studied model of classical two-locus theory. The symmetric model introduced by Lewontin and Kojima is among the few multi-locus models with epistatic interactions between loci for which a polymorphism with linkage equilibrium can be stable and this happens when recombination is sufficiently large. We show that an analogous property holds true for a different model, in which symmetry need exist at only one locus. The properties of this new semi-symmetric model are compared with those of the classical symmetric model. For tight linkage, two classes of polymorphisms are possible, depending on the magnitude of additive epistasis. The recombination rate above which linkage equilibrium becomes stable is derived analytically. As in the symmetric model, intervals of recombination in which no polymorphism is stable are possible, and stable polymorphisms can coexist with stable fixations.

    View details for DOI 10.1016/j.tpb.2005.07.004

    View details for Web of Science ID 000235325500010

    View details for PubMedID 16256158

  • The role of selection in the evolution of human mitochondrial genomes GENETICS Kivisild, T., Shen, P. D., Wall, D. P., Do, B., Sung, R., Davis, K., Passarino, G., Underhill, P. A., Scharfe, C., Torroni, A., Scozzari, R., Modiano, D., Coppa, A., de Knijff, P., Feldman, M., Cavalli-Sforza, L. L., Oefner, P. J. 2006; 172 (1): 373-387

    Abstract

    High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.

    View details for DOI 10.1534/genetics.105.043901

    View details for Web of Science ID 000235197700033

    View details for PubMedID 16172508

    View details for PubMedCentralID PMC1456165

  • Clines, clusters, and the effect of study design on the inference of human population structure PLOS GENETICS Rosenberg, N. A., Mahajan, S., Ramachandran, S., Zhao, C. F., Pritchard, J. K., Feldman, M. W. 2005; 1 (6): 660-671

    Abstract

    Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables--sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample--on the "clusteredness" of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.

    View details for DOI 10.1371/journal.pgen.0010070

    View details for Web of Science ID 000234900800005

    View details for PubMedID 16355252

  • Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ramachandran, S., Deshpande, O., Roseman, C. C., Rosenberg, N. A., Feldman, M. W., Cavalli-Sforza, L. L. 2005; 102 (44): 15942-15947

    Abstract

    Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. Here we find a linear relationship between genetic and geographic distance in a worldwide sample of human populations, with major deviations from the fitted line explicable by admixture or extreme isolation. A close relationship is shown to exist between the correlation of geographic distance and genetic differentiation (as measured by F(ST)) and the geographic pattern of heterozygosity across populations. Considering a worldwide set of geographic locations as possible sources of the human expansion, we find that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity. Although the relationship between F(ST) and geographic distance has been interpreted in the past as the result of an equilibrium model of drift and dispersal, simulation shows that the geographic pattern of heterozygosities in this data set is consistent with a model of a serial founder effect starting at a single origin. Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation.

    View details for Web of Science ID 000233090900042

    View details for PubMedID 16243969

  • Evidence for a major gene affecting the transition from normoglycaemia to hyperglycaemia in Psammomys obesus HEREDITY Hillel, J., Gefel, D., Kalman, R., Ben-Ari, G., David, L., Orion, O., Feldman, M. W., Bar-On, H., Blum, S., Raz, I., Schaap, T., Shpirer, I., Lavi, U., Shafrir, E., Ziv, E. 2005; 95 (2): 158-165

    Abstract

    We investigated the mode of inheritance of nutritionally induced diabetes in the desert gerbil Psammomys obesus (sand rat), following transfer from low-energy (LE) to high-energy (HE) diet which induces hyperglycaemia. Psammomys selected for high or low blood glucose level were used as two parental lines. A first backcross generation (BC(1)) was formed by crossing F(1) males with females of the diabetes-prone line. The resulting 232 BC(1) progeny were assessed for blood glucose. All progeny were weaned at 3 weeks of age (week 0), and their weekly assessment of blood glucose levels proceeded until week 9 after weaning, with all progeny maintained on HE diet. At weeks 1 to 9 post weaning, a clear bimodal distribution statistically different from unimodal distribution of blood glucose was observed, normoglycaemic and hyperglycaemic at a 1:1 ratio. This ratio is expected at the first backcross generation for traits controlled by a single dominant gene. From week 0 (prior to the transfer to HE diet) till week 8, the hyperglycaemic individuals were significantly heavier (4--17%) than the normoglycaemic ones. The bimodal blood glucose distribution in BC(1) generation, with about equal frequencies in each mode, strongly suggests that a single major gene affects the transition from normo- to hyperglycaemia. The wide range of blood glucose values among the hyperglycaemic individuals (180 to 500 mg/dl) indicates that several genes and environmental factors influence the extent of hyperglycaemia. The diabetes-resistant allele appears to be dominant; the estimate for dominance ratio is 0.97.

    View details for DOI 10.1038/sj.hdy.6800701

    View details for Web of Science ID 000230817000010

    View details for PubMedID 15931239

  • On the evolution of epistasis I: diploids under selection THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. W. 2005; 67 (3): 141-160

    Abstract

    One interpretation of recent literature on the evolution of phenotypic modularity is that evolution should act to decrease the degree of interaction between genes that contribute to different phenotypes. This issue is addressed directly here using a fitness scheme determined by two genetic loci and a third locus which modifies a measure of statistical interaction between the fitnesses due to the first two. The equilibrium structure of such an epistasis-modifying locus is studied. It is shown that under well-specified conditions a modifying allele that increases epistasis succeeds. In other words, genetic interactions tend to become stronger. It is speculated that this occurs because the mean fitness in such models is locally increasing as a function of the degree of epistasis.

    View details for DOI 10.1016/j.tpb.2004.11.001

    View details for Web of Science ID 000228417600001

    View details for PubMedID 15808333

  • Functional genomic analysis of the rates of protein evolution PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wall, D. P., Hirsh, A. E., Fraser, H. B., Kumm, J., Giaever, G., Eisen, M. B., Feldman, M. W. 2005; 102 (15): 5483-5488

    Abstract

    The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from high-throughput functional genomic experiments can identify the factors that cause proteins to evolve at such dramatically different rates. To this end, we estimated the evolutionary rates of >3,000 proteins in four species of the yeast genus Saccharomyces and investigated their relationship with levels of expression and protein dispensability. Each protein's dispensability was estimated by the growth rate of mutants deficient for the protein. Our analyses of these improved evolutionary and functional genomic data sets yield three main results. First, dispensability and expression have independent, significant effects on the rate of protein evolution. Second, measurements of expression levels in the laboratory can be used to filter data sets of dispensability estimates, removing variates that are unlikely to reflect real biological effects. Third, structural equation models show that although we may reasonably infer that dispensability and expression have significant effects on protein evolutionary rate, we cannot yet accurately estimate the relative strengths of these effects.

    View details for DOI 10.1073/pnas.0501761102

    View details for Web of Science ID 000228376600036

    View details for PubMedID 15800036

    View details for PubMedCentralID PMC555735

  • The emergence of social learning in a temporally changing environment: A theoretical model CURRENT ANTHROPOLOGY Aoki, K., Wakano, J. Y., Feldman, M. W. 2005; 46 (2): 334-340
  • Marriage form and age at first marriage: A comparative study in three counties in contemporary rural China SOCIAL BIOLOGY Jin, X., Li, S., Feldman, M. W. 2005; 52 (1-2): 18-46

    Abstract

    Using data from two surveys in three counties in which the prevalence of uxorilocal marriage differs greatly, this article analyzes the effects of marriage form, individual, family, and social factors on age at first marriage and spousal age difference. The results show that, under the Chinese patrilineal joint family system, compared with the dominant virilocal marriage form, uxorilocal marriage significantly lowers women's age at first marriage, increases men's age at first marriage, and consequently increases spousal age difference. Education, number of brothers, adoption status, marriage arrangement, and marriage circle also significantly affect age at first marriage for both genders. Age at first marriage and spousal age difference vary greatly among the three counties. These findings address the process and consequences of change in rural family and marriage customs during the current demographic and social transition and may help to promote later marriage and later childbearing under the present low fertility conditions in rural China.

    View details for Web of Science ID 000247586200002

    View details for PubMedID 17619629

  • Evolution of antibiotic resistance by human and bacterial niche construction EVOLUTION Boni, M. F., Feldman, M. W. 2005; 59 (3): 477-491

    Abstract

    Antibiotic treatment by humans generates strong viability selection for antibiotic-resistant bacterial strains. The frequency of host antibiotic use often determines the strength of this selection, and changing patterns of antibiotic use can generate many types of behaviors in the population dynamics of resistant and sensitive bacterial populations. In this paper, we present a simple model of hosts dimorphic for their tendency to use/avoid antibiotics and bacterial pathogens dimorphic in their resistance/sensitivity to antibiotic treatment. When a constant fraction of hosts uses antibiotics, the two bacterial strain populations can coexist unless host use-frequency is above a critical value; this critical value is derived as the ratio of the fitness cost of resistance to the fitness cost of undergoing treatment. When strain frequencies can affect host behavior, the dynamics may be analyzed in the light of niche construction. We consider three models underlying changing host behavior: conformism, the avoidance of long infections, and adherence to the advice of public health officials. In the latter two, we find that the pathogen can have quite a strong effect on host behavior. In particular, if antibiotic use is discouraged when resistance levels are high, we observe a classic niche-construction phenomenon of maintaining strain polymorphism even in parameter regions where it would not be expected.

    View details for Web of Science ID 000227943400001

    View details for PubMedID 15856691

  • Evolutionary traction: the cost of adaptation and the evolution of sex JOURNAL OF EVOLUTIONARY BIOLOGY Hadany, L., Feldman, M. W. 2005; 18 (2): 309-314

    Abstract

    The advantage of sexual reproduction remains a puzzle for evolutionary biologists. Everything else being equal, asexual populations are expected to have twice the number of offspring produced by similar sexual populations. Yet, asexual species are uncommon among higher eukaryotes. In models assuming small populations, high mutation rates, or frequent environmental changes, sexual reproduction seems to have at least a two-fold advantage over asexuality. But the advantage of sex for large populations, low mutation rates, and rare or mild environmental changes remains a conundrum. Here we show that without recombination, rare advantageous mutations can result in increased accumulation of deleterious mutations ('evolutionary traction'), which explains the long-term advantage of sex under a wide parameter range.

    View details for DOI 10.1111/j.1420-9101.2004.00858.x

    View details for Web of Science ID 000227017400007

    View details for PubMedID 15715837

  • Second report on chicken genes and chromosomes 2005 CYTOGENETIC AND GENOME RESEARCH Schmid, M., Nanda, I., Hoehn, H., Schartl, M., Haaf, T., Buerstedde, J. M., Arakawa, H., Caldwell, R. B., Weigend, S., Burt, D. W., Smith, J., Griffin, D. K., Masabanda, J. S., Groenen, M. A., Crooijmans, R. P., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Vignoles, M., Garrigues, A., Gellin, J., Rodionov, A. V., Galkina, S. A., Lukina, N. A., Ben-Ari, G., Blum, S., Hillel, J., Twito, T., Lavi, U., David, L., Feldman, M. W., Delany, M. E., Conley, C. A., Fowler, V. M., Hedges, S. B., Godbout, R., Katyal, S., Smith, C., Hudson, Q., Sinclair, A., Mizuno, S. 2005; 109 (4): 415-479

    View details for DOI 10.1159/000084205

    View details for Web of Science ID 000228996500002

    View details for PubMedID 15905640

  • Marriage forrn and duration of postmarital co-residence with parents in rural China: Evidence from Songzi JOURNAL OF COMPARATIVE FAMILY STUDIES Li, S. Z., Feldman, M. W., Jin, X. Y. 2005; 36 (1): 121-?
  • Gender differences in activity of daily living of the elderly in rural China: Evidence from Chaohu JOURNAL OF WOMEN & AGING Zhang, W. J., Li, S. Z., Feldman, M. W. 2005; 17 (3): 73-89

    Abstract

    Using data from a sample survey, Well-being of the elderly in Anhui province, China, this paper studies the effects of health, economic and family factors on the activities of daily living (ADLs) as measures of disability for elderly men and women. The objective is to explore reasons for gender differences in ADLs in rural China. Our results suggest that higher incidence rates of chronic diseases, lower cognitive ability, as well as heavier household and daily care burdens of females, are the main factors leading to a higher prevalence of ADL disability for the female elderly.

    View details for DOI 10.1300/J074v17n03_06

    View details for Web of Science ID 000233687200006

    View details for PubMedID 16186096

  • On the meaning of non-epistatic selection THEORETICAL POPULATION BIOLOGY Puniyani, A., Liberman, U., Feldman, M. W. 2004; 66 (4): 317-321

    Abstract

    In population genetics, the additive and multiplicative viability models are often used for the quantitative description of models in which the genetic contributions of several different loci are independent; that is, there is no epistasis. Non-epistasis may also be quantitatively defined in terms of measures of interaction used widely in statistics. Setting these measures of epistasis to zero yields alternative definitions of non-epistasis. We show here that these two definitions of non-epistasis are equivalent; that is, in the most general case of a multilocus, multiallele system, the additive and multiplicative viability models are unique solutions of the additive and multiplicative conditions, respectively, for non-epistasis.

    View details for DOI 10.1016/j.tpb.2004.05.001

    View details for Web of Science ID 000225649600004

    View details for PubMedID 15560910

  • Evolution of social learning: a mathematical analysis THEORETICAL POPULATION BIOLOGY Wakano, J. Y., Aoki, K., Feldman, M. W. 2004; 66 (3): 249-258

    Abstract

    Social learning is an important ability seen in a wide range of animals including humans. It has been argued that individual learning, social learning, and innate determination of behavior are favored by natural selection when environmental changes occur at short, intermediate, and long intervals, respectively. Only recently, however, has the hypothesis been examined by means of mathematical models. In this paper, we construct a simple model in which each organism uses one of three genetically determined strategies--it is an individual learner, a social learner or an "innate"--and the three types of organisms are in direct competition with each other. A reduced model, involving only the individual learners and innates, is effectively linear, and we show that by solving the eigenvalue problem of this reduced system we arrive at a good approximation to the global dynamics of the full model. We also study the effect of stochastic environmental changes and reversible mutations among the three strategies. Our results are consistent with the predictions of previous studies. In addition, we identify a critical level of environmental constancy below which only individual and social learners are present.

    View details for DOI 10.1016/j.tpb.2004.06.005

    View details for Web of Science ID 000224597600008

    View details for PubMedID 15465125

  • Demographic estimates from Y chromosome microsatellite polymorphisms: analysis of a worldwide sample. Human genomics Macpherson, J. M., Ramachandran, S., Diamond, L., Feldman, M. W. 2004; 1 (5): 345-354

    Abstract

    Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions about the prior distributions and the evolutionary models themselves.

    View details for PubMedID 15588495

  • Children, marriage form, and family support for the elderly in contemporary rural China - The case of Songzi RESEARCH ON AGING Li, S. Z., Feldman, M. W., Jin, X. Y. 2004; 26 (3): 352-384
  • Stable association between strains of Mycobacterium tuberculosis and their human host populations PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hirsh, A. E., Tsolaki, A. G., DeRiemer, K., Feldman, M. W., Small, P. M. 2004; 101 (14): 4871-4876

    Abstract

    Mycobacterium tuberculosis is an important human pathogen in virtually every part of the world. Here we investigate whether distinct strains of M. tuberculosis infect different human populations and whether associations between host and pathogen populations are stable despite global traffic and the convergence of diverse strains of the pathogen in cosmopolitan urban centers. The recent global movement and transmission history of 100 M. tuberculosis isolates was inferred from a molecular epidemiologic study of tuberculosis that spans 12 years. Genetic relationships among these isolates were deduced from the distribution of large genomic deletions, which were identified by DNA microarray and confirmed by PCR and sequence analysis. Phylogenetic analysis of these deletions indicates that they are unique event polymorphisms and that horizontal gene transfer is extremely rare in M. tuberculosis. In conjunction with the epidemiological data, phylogenies reveal three large phylogeographic regions. A host's region of origin is predictive of the strain of tuberculosis he or she carries, and this association remains strong even when transmission takes place in a cosmopolitan urban center outside of the region of origin. Approximate dating of the time since divergence of East Asian and Philippine clades of M. tuberculosis suggests that these lineages diverged centuries ago. Thus, associations between host and pathogen populations appear to be highly stable.

    View details for DOI 10.1073/pnas.0305627101

    View details for Web of Science ID 000220761200029

    View details for PubMedID 15041743

    View details for PubMedCentralID PMC387341

  • What is altruism? TRENDS IN ECOLOGY & EVOLUTION Kerr, B., Godfrey-Smith, P., Feldman, M. W. 2004; 19 (3): 135-140

    Abstract

    Altruism is generally understood to be behavior that benefits others at a personal cost to the behaving individual. However, within evolutionary biology, different authors have interpreted the concept of altruism differently, leading to dissimilar predictions about the evolution of altruistic behavior. Generally, different interpretations diverge on which party receives the benefit from altruism and on how the cost of altruism is assessed. Using a simple trait-group framework, we delineate the assumptions underlying different interpretations and show how they relate to one another. We feel that a thorough examination of the connections between interpretations not only reveals why different authors have arrived at disparate conclusions about altruism, but also illuminates the conditions that are likely to favor the evolution of altruism.

    View details for DOI 10.1016/j.tree.2003.10.004

    View details for Web of Science ID 000220183800009

    View details for PubMedID 16701244

  • Cultural niche construction and the evolution of small family size THEORETICAL POPULATION BIOLOGY Ihara, Y., Feldman, M. W. 2004; 65 (1): 105-111

    Abstract

    A model of cultural niche construction with two culturally transmitted traits is examined. The frequency of individuals with a certain general predisposition, which is transmitted vertically, plays a role as the cultural background, or the cultural niche, of the population. The cultural background determines the rate of oblique, relative to vertical, transmission of another cultural trait that affects fertility of individuals. It is assumed that individuals with fewer offspring are more likely to achieve social roles that influence the succeeding generation and are therefore overrepresented as transmitters in the process of oblique transmission. Our model suggests that even a slight overrepresentation of those with fewer offspring can drive the evolution of small family size, provided that the rate of oblique transmission depends strongly on the cultural background. In addition, our model may help to explain the time lag between the decrease in death rates and the subsequent decrease in birth rates during the demographic transition of industrializing societies.

    View details for DOI 10.1016/j.tpb.2003.07.003

    View details for Web of Science ID 000187356600009

    View details for PubMedID 14642348

  • Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Human genomics Ramachandran, S., Rosenberg, N. A., Zhivotovsky, L. A., Feldman, M. W. 2004; 1 (2): 87-97

    Abstract

    In this paper, data on 20 X-chromosomal microsatellite polymorphisms from the HGDP-CEPH cell line panel are used to infer human population structure. Inferences from these data are compared to those obtained from autosomal microsatellites. Some of the major features of the structure seen with 377 autosomal markers are generally visible with the X-linked markers, although the latter provide less resolution. Differences between the X-chromosomal and autosomal results can be explained without requiring major differences in demographic parameters between males and females. The dependence of the partitioning on the number of individuals sampled from each region and on the number of markers used is discussed.

    View details for PubMedID 15601537

  • Gender differences in child survival in contemporary rural China: A county study JOURNAL OF BIOSOCIAL SCIENCE Li, S. Z., Zhu, C. Z., Feldman, M. W. 2004; 36 (1): 83-109

    Abstract

    Using data from a survey of deaths of children less than 5 years old conducted in 1997 in a county in Shaanxi Province, China, this paper examines gender differences in child survival in contemporary rural China. First, excess female child mortality in the county in 1994-96 is described, followed by an analysis of the mechanisms whereby the excess mortality takes place, and the underlying social, economic and cultural factors behind it. Excess female child mortality in this county is probably caused primarily by discrimination against girls in curative health care rather than in preventive health care or food and nutrition. Although discrimination occurs in all kinds of families and communities, discrimination itself is highly selective, and is primarily against girls with some specific characteristics. It is argued that the excess mortality of girls is caused fundamentally by the strong son preference in traditional Chinese culture, but exacerbated by the government-guided family planning programme and regulations. This suggests that it is crucial to raise the status of girls within the family and community so as to mitigate the pressures to discriminate against girls in China's low fertility regime. Finally, the possible policy options to improve female child survival in contemporary rural China are discussed.

    View details for DOI 10.1017/S0021932004006126

    View details for Web of Science ID 000189148800007

    View details for PubMedID 14989533

  • The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus GENETICS Spencer, H. G., Feldman, M. W., Clark, A. G., Weisstein, A. E. 2004; 166 (1): 565-579

    Abstract

    We examine how genomic imprinting may have evolved at an X-linked locus, using six diallelic models of selection in which one allele is imprintable and the other is not. Selection pressures are generated by genetic conflict between mothers and their offspring. The various models describe cases of maternal and paternal inactivation, in which females may be monogamous or bigamous. When inactivation is maternal, we examine the situations in which only female offspring exhibit imprinting as well as when both sexes do. We compare our results to those previously obtained for an autosomal locus and to four models in which a dominant modifier of biallelic expression is subjected to the same selection pressures. We find that, in accord with verbal predictions, maternal inactivation of growth enhancers and paternal inactivation of growth inhibitors are more likely than imprinting in the respective opposite directions, although these latter outcomes are possible for certain parameter combinations. The expected outcomes are easier to evolve than the same outcomes for autosomal loci, contradicting the available evidence concerning the direction of imprinting on mammalian sex chromosomes. In most of our models stable polymorphism of imprinting status is possible, a behavior not predicted by verbal accounts.

    View details for Web of Science ID 000220021800046

    View details for PubMedID 15020445

  • The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time AMERICAN JOURNAL OF HUMAN GENETICS Zhivotovsky, L. A., Underhill, P. A., Cinnioglu, C., Kayser, M., Morar, B., Kivisild, T., Scozzari, R., Cruciani, F., Destro-Bisol, G., Spedini, G., Chambers, G. K., Herrera, R. J., Yong, K. K., Gresham, D., Tournev, I., Feldman, M. W., Kalaydjieva, L. 2004; 74 (1): 50-61

    Abstract

    We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.

    View details for Web of Science ID 000187723500005

    View details for PubMedID 14691732

  • Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation HUMAN MUTATION Shen, P. D., Lavi, T., Kivisild, T., Chou, V., Sengun, D., Gefel, D., Shpirer, I., Woolf, E., Hillel, J., Feldman, M. W., Oefner, P. J. 2004; 24 (3): 248-260

    Abstract

    The Samaritan community, which numbered more than a million in late Roman times and only 146 in 1917, numbers today about 640 people representing four large families. They are culturally different from both Jewish and non-Jewish populations in the Middle East and their origin remains a question of great interest. Genetic differences between the Samaritans and neighboring Jewish and non-Jewish populations are corroborated in the present study of 7,280 bp of nonrecombining Y-chromosome and 5,622 bp of coding and hypervariable segment I (HVS-I) mitochondrial DNA (mtDNA) sequences. Comparative sequence analysis was carried out on 12 Samaritan Y-chromosome, and mtDNA samples from nine male and seven female Samaritans separated by at least two generations. In addition, 18-20 male individuals were analyzed, each representing Ethiopian, Ashkenazi, Iraqi, Libyan, Moroccan, and Yemenite Jews, as well as Druze and Palestinians, all currently living in Israel. The four Samaritan families clustered to four distinct Y-chromosome haplogroups according to their patrilineal identity. Of the 16 Samaritan mtDNA samples, 14 carry either of two mitochondrial haplotypes that are rare or absent among other worldwide ethnic groups. Principal component analysis suggests a common ancestry of Samaritan and Jewish patrilineages. Most of the former may be traced back to a common ancestor in the paternally-inherited Jewish high priesthood (Cohanim) at the time of the Assyrian conquest of the kingdom of Israel.

    View details for DOI 10.1002/humu.20077

    View details for Web of Science ID 000223304800008

    View details for PubMedID 15300852

  • Evolution of disassortative and assortative mating preferences based on imprinting THEORETICAL POPULATION BIOLOGY Ihara, Y., Feldman, M. W. 2003; 64 (2): 193-200

    Abstract

    A two-locus haploid model of sexual selection is investigated to explore evolution of disassortative and assortative mating preferences based on imprinting. In this model, individuals imprint on a genetically transmitted trait during early ontogeny and choosy females later use those parental images as a criterion of mate choice. It is assumed that the presence or absence of the female preference is determined by a genetic locus. In order to incorporate such mechanisms as inbreeding depression and heterozygous advantage into our haploid framework, we assume that same-type matings are less fertile than different-type mating. The model suggests that: if all the females have a disassortative mating preference a viability-reducing trait may be maintained even without the fertility cost of same-type matings; a disassortative mating preference can be established even if it is initially rare, when there is a fertility cost of same-type matings. Further, an assortative mating preference is less likely to evolve than a disassortative mating preference. The model may be applicable to the evolution of MHC-disassortative mating preferences documented in house mice and humans.

    View details for DOI 10.1016/S0040-5809(03)00099-6

    View details for Web of Science ID 000185265500006

    View details for PubMedID 12948680

  • Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools GENETICS SELECTION EVOLUTION Hillel, J., Groenen, M. A., Tixier-Boichard, M., Korol, A. B., David, L., Kirzhner, V. M., Burke, T., Dirie, A. B., Crooijmans, R. P., Elo, K., Feldman, M., Freidlin, P. J., Maki-Tanila, A., Oortwijn, M., Thomson, P., Vignal, A., Wimmers, K., Weigend, S. 2003; 35 (5): 533-557

    Abstract

    In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.

    View details for DOI 10.1051/gse:2003038

    View details for Web of Science ID 000185007500005

    View details for PubMedID 12939204

    View details for PubMedCentralID PMC2697980

  • Rates of DNA duplication and mitochondrial DNA insertion in the human genome JOURNAL OF MOLECULAR EVOLUTION Bensasson, D., Feldman, M. W., Petrov, D. A. 2003; 57 (3): 343-354

    Abstract

    The hundreds of mitochondrial pseudogenes in the human nuclear genome sequence (numts) constitute an excellent system for studying and dating DNA duplications and insertions. These pseudogenes are associated with many complete mitochondrial genome sequences and through those with a good fossil record. By comparing individual numts with primate and other mammalian mitochondrial genome sequences, we estimate that these numts arose continuously over the last 58 million years. Our pairwise comparisons between numts suggest that most human numts arose from different mitochondrial insertion events and not by DNA duplication within the nuclear genome. The nuclear genome appears to accumulate mtDNA insertions at a rate high enough to predict within-population polymorphism for the presence/absence of many recent mtDNA insertions. Pairwise analysis of numts and their flanking DNA produces an estimate for the DNA duplication rate in humans of 2.2 x 10(-9) per numt per year. Thus, a nucleotide site is about as likely to be involved in a duplication event as it is to change by point substitution. This estimate of the rate of DNA duplication of noncoding DNA is based on sequences that are not in duplication hotspots, and is close to the rate reported for functional genes in other species.

    View details for DOI 10.1007/s00239-003-2485-7

    View details for Web of Science ID 000184992800012

    View details for PubMedID 14629044

  • Recent duplication of the, common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci MOLECULAR BIOLOGY AND EVOLUTION David, L., Blum, S., Feldman, M. W., Lavi, U., Hillel, J. 2003; 20 (9): 1425-1434

    Abstract

    Genome duplications may have played a role in the early stages of vertebrate evolution, near the time of divergence of the lamprey lineage. Additional genome duplication, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The common carp (Cyprinus carpio) has been considered tetraploid because of its chromosome number (2n = 100) and its high DNA content. We studied variation using 59 microsatellite primer pairs to better understand the ploidy level of the common carp. Based on the number of PCR amplicons per individual, about 60% of these primer pairs are estimated to amplify duplicates. Segregation patterns in families suggested a partially duplicated genome structure and disomic inheritance. This could suggest that the common carp is tetraploid and that polyploidy occurred by hybridization (allotetraploidy). From sequences of microsatellite flanking regions, we estimated the difference per base between pairs of alleles and between pairs of paralogs. The distribution of differences between paralogs had two distinct modes suggesting one whole-genome duplication and a more recent wave of segmental duplications. The genome duplication was estimated to have occurred about 12 MYA, with the segmental duplications occurring between 2.3 and 6.8 MYA. At 12 MYA, this would be one of the most recent genome duplications among vertebrates. Phylogenetic analysis of several cyprinid species suggests an evolutionary model for this tetraploidization, with a role for polyploidization in speciation and diversification.

    View details for DOI 10.1093/molbev/msg173

    View details for PubMedID 12832638

  • A genetic melting-pot NATURE Feldman, M. W., Lewontin, R. C., KING, M. C. 2003; 424 (6947): 374-374

    View details for DOI 10.1038/424374a

    View details for Web of Science ID 000184318400020

    View details for PubMedID 12879045

  • Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers AMERICAN JOURNAL OF HUMAN GENETICS Zhivotovsky, L. A., Rosenberg, N. A., Feldman, M. W. 2003; 72 (5): 1171-1186

    Abstract

    We study data on variation in 52 worldwide populations at 377 autosomal short tandem repeat loci, to infer a demographic history of human populations. Variation at di-, tri-, and tetranucleotide repeat loci is distributed differently, although each class of markers exhibits a decrease of within-population genetic variation in the following order: sub-Saharan Africa, Eurasia, East Asia, Oceania, and America. There is a similar decrease in the frequency of private alleles. With multidimensional scaling, populations belonging to the same major geographic region cluster together, and some regions permit a finer resolution of populations. When a stepwise mutation model is used, a population tree based on TD estimates of divergence time suggests that the branches leading to the present sub-Saharan African populations of hunter-gatherers were the first to diverge from a common ancestral population (approximately 71-142 thousand years ago). The branches corresponding to sub-Saharan African farming populations and those that left Africa diverge next, with subsequent splits of branches for Eurasia, Oceania, East Asia, and America. African hunter-gatherer populations and populations of Oceania and America exhibit no statistically significant signature of growth. The features of population subdivision and growth are discussed in the context of the ancient expansion of modern humans.

    View details for Web of Science ID 000182474400010

    View details for PubMedID 12690579

  • Acceptance of two types of uxorilocal marriage in contemporary rural China: The case of Lueyang JOURNAL OF FAMILY HISTORY Li, S. Z., Feldman, M. W., Li, N. 2003; 28 (2): 314-333
  • The application of molecular genetic approaches to the study of human evolution NATURE GENETICS Cavalli-Sforza, L. L., Feldman, M. W. 2003; 33: 266-275

    Abstract

    The past decade of advances in molecular genetic technology has heralded a new era for all evolutionary studies, but especially the science of human evolution. Data on various kinds of DNA variation in human populations have rapidly accumulated. There is increasing recognition of the importance of this variation for medicine and developmental biology and for understanding the history of our species. Haploid markers from mitochondrial DNA and the Y chromosome have proven invaluable for generating a standard model for evolution of modern humans. Conclusions from earlier research on protein polymorphisms have been generally supported by more sophisticated DNA analysis. Co-evolution of genes with language and some slowly evolving cultural traits, together with the genetic evolution of commensals and parasites that have accompanied modern humans in their expansion from Africa to the other continents, supports and supplements the standard model of genetic evolution. The advances in our understanding of the evolutionary history of humans attests to the advantages of multidisciplinary research.

    View details for DOI 10.1038/ng1113

    View details for Web of Science ID 000181390900007

    View details for PubMedID 12610536

  • Marriage form and family division in three villages in rural China POPULATION STUDIES-A JOURNAL OF DEMOGRAPHY Li, S. Z., Feldman, M. W., Jin, X. Y. 2003; 57 (1): 95-108
  • Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster AMERICAN JOURNAL OF HUMAN GENETICS Noonan, J. P., Li, J., Nguyen, L., Caoile, C., Dickson, M., Grimwood, J., Schmutz, J., Feldman, M. W., Myers, R. M. 2003; 72 (3): 621-635

    Abstract

    Regions of extensive linkage disequilibrium (LD) appear to be a common feature of the human genome. However, the mechanisms that maintain these regions are unknown. In an effort to understand whether gene density contributes to LD, we determined the degree of promoter sequence variation in a large tandem-arrayed gene family, the human protocadherin alpha cluster, on chromosome 5. These genes are expressed at synaptic junctions in the developing brain and the adult brain and may be involved in the determination of synaptic complexity. We sequenced the promoters of all 13 alpha protocadherin genes in 96 European Americans and identified polymorphisms in the promoters alpha 1, alpha 3, alpha 4, alpha 5, alpha 7, alpha 9, alpha 11, and alpha 13. In these promoters, 11 common SNPs are in extensive LD, forming two 48-kb haplotypes of equal frequency, in this population, that extend from the alpha1 through alpha 7 genes. We sequenced these promoters in East Asians and African Americans, and we estimated haplotype frequencies and calculated LD statistics for all three populations. Our results indicate that, although extensive LD is an ancient feature of the alpha cluster, it has eroded over time. SNPs 3' of alpha 7 are involved in ancestral recombination events in all populations, and overall alpha-cluster LD is reduced in African Americans. We obtained significant positive values for Tajima's D test for all alpha promoter SNPs in Europeans (D=3.03) and East Asians (D=2.64), indicating an excess of intermediate-frequency variants, which is a signature of balancing selection. We also discovered a 16.7-kb deletion that truncates the alpha 8 gene and completely removes the alpha 9 and alpha 10 genes. This deletion appears in unaffected individuals from multiple populations, suggesting that a reduction in protocadherin gene number is not obviously deleterious.

    View details for PubMedID 12577201

  • Runaway sexual selection with paternal transmission of the male trait and gene-culture determination of the female preference THEORETICAL POPULATION BIOLOGY Ihara, Y., Aoki, K., Feldman, M. W. 2003; 63 (1): 53-62

    Abstract

    Sexual selection is modeled with a male viability-reducing trait and a female mating preference for that trait both of which are culturally transmitted. Both the male trait and the female preference are transmitted only between same-sex individuals, so that non-random association between the trait and the preference, which would give rise to a Fisherian runaway process, cannot arise. Inclusion of an autosomal gene that confers a female predisposition to acquire a certain preference is shown to allow the coevolution of the male trait and the female preference by a Fisherian process. This holds true even when the female preference has a slight viability cost, provided the male cultural transmission is not perfect. It is also suggested that a Fisherian process can be more easily initiated in these models than in the conventional genetic models. Furthermore, a Fisherian process may cause cultural transmission of female preference to evolve. Additionally, polymorphism can be maintained at the predisposition locus if heterozygous females have a stronger predisposition to acquire the preference than homozygotes. Our models may be applicable to the case when the male trait is a Y-linked genetic or environmentally determined trait.

    View details for Web of Science ID 000180151400005

    View details for PubMedID 12464495

  • Genes and cultures - What creates our behavioral phenome? CURRENT ANTHROPOLOGY Ehrlich, P., Feldman, M. 2003; 44 (1): 87-107
  • Carving the cognitive niche: Optimal learning strategies in homogeneous and heterogeneous environments JOURNAL OF THEORETICAL BIOLOGY Kerr, B., Feldman, M. W. 2003; 220 (2): 169-188

    Abstract

    A model learning system is constructed, in which an organism samples behaviors from a behavioral repertoire in response to a stimulus and selects the behavior with the highest payoff. The stimulus and most rewarding behavior may be kept in the organism's long-term memory and reused if the stimulus is encountered again. The value of the memory depends on the reliability of the stimulus, that is, how the corresponding payoffs of behaviors change over time. We describe how the inclusion of memory can increase the optimal sampling size in environments with some stimulus reliability. In addition to using memory to guide behavior, our organism may use information in its memory to choose the stimulus to which it reacts. This choice is influenced by both the organism's memory state and how many stimuli the organism can observe (its sensory capability). The number of sampled behaviors, memory length, and sensory capability are the variables that define the learning strategy. When all stimuli have the same reliability, there appears to be only a single optimal learning strategy. However, when there is heterogeneity in stimulus reliability, multiple locally optimal strategies may exist.

    View details for DOI 10.1006/jtbi.2003.3146

    View details for Web of Science ID 000181037600003

    View details for PubMedID 12468290

  • Genetic structure of human populations SCIENCE Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kidd, K. K., Zhivotovsky, L. A., Feldman, M. W. 2002; 298 (5602): 2381-2385

    Abstract

    We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.

    View details for Web of Science ID 000179915900054

    View details for PubMedID 12493913

  • Coevolution of pathogens and cultural practices: A new look at behavioral heterogeneity in epidemics THEORETICAL POPULATION BIOLOGY Tanaka, M. M., Kumm, J., Feldman, M. W. 2002; 62 (2): 111-119

    Abstract

    The effect of heterogeneity within populations on the spread of infectious diseases has been a recent focus of research. Such heterogeneity may be, for example, spatial, temporal or behavioral in form. Generally, models that include population subdivision have assumed that individuals are permanently assigned to given behavioral states represented by the subpopulations. We consider a simple epidemic model in which a behavioral trait affects disease transmission, and this trait may be transferred among hosts as a consequence of social interaction. This creates a situation where the frequencies of different behavioral traits and disease states as well as their associations may change over time. We consider the impact of the culturally transmitted trait on the criterion for initial spread of the disease. We also explore the evolution of cultural traits in response to pathogen dynamics and show some conditions under which behavioral traits that reduce transmission evolve. We find that behaviors increasing the risk of infection can also evolve when they are inherently favored or when there is sufficient clustering of contacts between like behaviors.

    View details for DOI 10.1006/tpbi.2002.1585

    View details for Web of Science ID 000177739700002

    View details for PubMedID 12167351

  • Evolutionary genetic models of the ovarian time bomb hypothesis for the evolution of genomic imprinting GENETICS Weisstein, A. E., Feldman, M. W., Spencer, H. G. 2002; 162 (1): 425-439

    Abstract

    At a small number of loci in eutherian mammals, only one of the two copies of a gene is expressed; the other is silenced. Such loci are said to be "imprinted," with some having the maternally inherited allele inactivated and others showing paternal inactivation. Several hypotheses have been proposed to explain how such a genetic system could evolve in the face of the selective advantages of diploidy. In this study, we examine the "ovarian time bomb" hypothesis, which proposes that imprinting arose through selection for reduced risk of ovarian trophoblastic disease in females. We present three evolutionary genetic models that incorporate both this selection pressure and the effect of deleterious mutations to elucidate the conditions under which imprinting could evolve. Our findings suggest that the ovarian time bomb hypothesis can explain why some growth-enhancing genes active in early embryogenesis [e.g., mouse insulin-like growth factor 2 (Igf2)] have evolved to be maternally rather than paternally inactive and why the opposite imprinting status has evolved at some growth-inhibiting loci [e.g., mouse insulin-like growth factor 2 receptor (Igf2r)].

    View details for Web of Science ID 000178363400034

    View details for PubMedID 12242251

  • Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors NATURE Kerr, B., Riley, M. A., Feldman, M. W., Bohannan, B. J. 2002; 418 (6894): 171-174

    Abstract

    One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for non-transitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children's game rock-paper-scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.

    View details for DOI 10.1038/nature00823

    View details for Web of Science ID 000176710400037

    View details for PubMedID 12110887

  • Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition GENETICS Tang, H., Siegmund, D. O., Shen, P. D., Oefner, P. J., Feldman, M. W. 2002; 161 (1): 447-459

    Abstract

    This article proposes a method of estimating the time to the most recent common ancestor (TMRCA) of a sample of DNA sequences. The method is based on the molecular clock hypothesis, but avoids assumptions about population structure. Simulations show that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability. We discuss conditions that can lead to biased estimates. Performance of this estimator is compared with existing methods based on the coalescence theory. The method is applied to sequences of Y chromosomes and mtDNAs to estimate the coalescent times of human male and female populations.

    View details for Web of Science ID 000175814900040

    View details for PubMedID 12019257

  • Evolutionary rate in the protein interaction network SCIENCE Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C., Feldman, M. W. 2002; 296 (5568): 750-752

    Abstract

    High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution. Proteins with more interactors evolve more slowly not because they are more important to the organism, but because a greater proportion of the protein is directly involved in its function. At sites important for interaction between proteins, evolutionary changes may occur largely by coevolution, in which substitutions in one protein result in selection pressure for reciprocal changes in interacting partners. We confirm one predicted outcome of this process-namely, that interacting proteins evolve at similar rates.

    View details for Web of Science ID 000175281700060

    View details for PubMedID 11976460

  • A human genome diversity cell line panel SCIENCE Cann, H. M., de Toma, C., Cazes, L., Legrand, M. F., Morel, V., Piouffre, L., Bodmer, J., Bodmer, W. F., Bonne-Tamir, B., Cambon-Thomsen, A., Chen, Z., Chu, J. Y., Carcassi, C., Contu, L., Du, R. F., Excoffier, L., Ferrara, G. B., Friedlaender, J. S., Groot, H., Gurwitz, D., Jenkins, T., Herrera, R. J., Huang, X. Y., Kidd, J., Kidd, K. K., Langaney, A., Lin, A. A., Mehdi, S. Q., Parham, P., Piazza, A., Pistillo, M. P., Qian, Y. P., Shu, Q. F., Xu, J. J., Zhu, S., Weber, J. L., Greely, H. T., Feldman, M. W., Thomas, G., Dausset, J., Cavalli-Sforza, L. L. 2002; 296 (5566): 261-262

    View details for Web of Science ID 000175000300018

    View details for PubMedID 11954565

  • Genetic sampling error of distance (delta mu)(2) and variation in mutation rate among microsatellite loci MOLECULAR BIOLOGY AND EVOLUTION Zhivotovsky, L. A., Goldstein, D. B., Feldman, M. W. 2001; 18 (12): 2141-2145

    Abstract

    An expression is obtained for the time-dependent variance of the microsatellite genetic distance (delta(mu))2 when the mutation rate is allowed to vary randomly among loci. An estimator is presented for the coefficient of variation, C(w), in the mutation rate. Estimated values of C(w) from genetic distances between African and non-African populations were less than 100%. Caveats to this conclusion are discussed.

    View details for Web of Science ID 000172657900001

    View details for PubMedID 11719562

  • Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds GENETICS Rosenberg, N. A., Burke, T., Elo, K., Feldmann, M. W., Freidlin, P. J., Groenen, M. A., Hillel, J., Maki-Tanila, A., Tixier-Boichard, M., Vignal, A., Wimmers, K., Weigend, S. 2001; 159 (2): 699-713

    Abstract

    We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently approximately 98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95% clustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.

    View details for Web of Science ID 000171744900023

    View details for PubMedID 11606545

    View details for PubMedCentralID PMC1461842

  • Parallels and contrasts in female and male human evolutionary history. Shen, P., Tang, H., Passarino, P., Do, B., Sung, R., Davis, K., Sharfe, C., Cavalli-Sforza, L. L., Feldman, M. W., Oefner, P. J. CELL PRESS. 2001: 423–23
  • A comparative study of determinants of uxorilocal marriage in two counties of China SOCIAL BIOLOGY Li, S. Z., Feldman, M. W., Li, N. 2001; 48 (1-2): 125-150

    Abstract

    A strictly maintained patrilineal family system makes virilocal marriage almost universal and uxorilocal marriage rare in the history of rural China. Uxorilocal marriage can be divided into two types that may be termed, respectively, contingent and institutional. The former preserves family lineages in families without a son and occurs when uxorilocal marriage is uncommon. The latter serves practical economic purposes in families with sons and occurs when uxorilocal marriage is relatively prevalent. Using data from a survey in two counties of Shaanxi--Lueyang, where both kinds of uxorilocal marriage are prevalent, and Sanyuan, where uxorilocal marriage is rare and usually contingent--this paper employs logistic regression models in a quantitative comparative study of determinants of uxorilocal marriage in rural China. We show that the purposes and prevalence of the two types of uxorilocal marriage differ and that their determinants are also different in the two counties. In Sanyuan, the determinants are only a couple's sibling composition, membership in a large family clan, and educational level. In Lueyang, in addition to those determinants in Sanyuan, important contributions to the type of uxorilocal marriage include a couple's parental marriage type, age at marriage, adoption status, marriage arrangement, and their attitudes toward uxorilocal marriage. The results indicate the potential importance of encouraging uxorilocal marriage in rural areas as a means of mitigating demographic and social problems related to son preference, such as high sex ratio at birth and lack of old-age security, which are projected for China's future.

    View details for Web of Science ID 000177128600007

    View details for PubMedID 12194444

  • Distinctive genetic signatures in the Libyan Jews PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Rosenberg, N. A., Woolf, E., Pritchard, J. K., Schaap, T., Gefel, D., Shpirer, I., Lavi, U., Bonne-Tamir, B., Hillel, J., Feldman, M. W. 2001; 98 (3): 858-863

    Abstract

    Unlinked autosomal microsatellites in six Jewish and two non-Jewish populations were genotyped, and the relationships among these populations were explored. Based on considerations of clustering, pairwise population differentiation, and genetic distance, we found that the Libyan Jewish group retains genetic signatures distinguishable from those of the other populations, in agreement with some historical records on the relative isolation of this community. Our methods also identified evidence of some similarity between Ethiopian and Yemenite Jews, reflecting possible migration in the Red Sea region. We suggest that high-resolution statistical methods that use individual multilocus genotypes may make it practical to distinguish related populations of extremely recent common ancestry.

    View details for Web of Science ID 000166807300021

    View details for PubMedID 11158561

  • Cultural niche construction and human evolution JOURNAL OF EVOLUTIONARY BIOLOGY Laland, K. N., Odling-Smee, J., Feldman, M. W. 2001; 14 (1): 22-33
  • Models of sexual selection on a quantitative genetic trait when preference is acquired by sexual imprinting EVOLUTION Aoki, K., Feldman, M. W., Kerr, B. 2001; 55 (1): 25-32

    Abstract

    The evolution of a quantitative genetic trait under stabilizing viability selection and sexual selection is modeled for a polygynous species in which female mating preferences are acquired by sexual imprinting on the parents and by exposure to the surviving population at large. Stabilizing viability selection acts equally on both sexes in the case of a sexually monomorphic trait and on males only in the case of a dimorphic trait. A genetically fixed sensory or perceptual bias defines the origin of the scale on which the trait is measured, and the possibility is incorporated that female preferences may deviate asymmetrically from the familiar-either toward or away from this origin. When viability selection is strong relative to sexual selection, the models predict that the mean trait value will evolve to the viability optimum. With intermediate ratios of the strength of viability to sexual selection, a stable equilibrium can occur on either side of this viability optimum, depending on the direction of asymmetry in female preferences. When viability selection is relatively weak and certain other conditions are also satisfied, runaway selection is predicted.

    View details for Web of Science ID 000167167000002

    View details for PubMedID 11263743

  • Y chromosome sequence variation and the history of human populations NATURE GENETICS Underhill, P. A., Shen, P. D., Lin, A. A., Jin, L., Passarino, G., Yang, W. H., Kauffman, E., Bonne-Tamir, B., Bertranpetit, J., Francalacci, P., Ibrahim, M., Jenkins, T., Kidd, J. R., Mehdi, S. Q., Seielstad, M. T., WELLS, R. S., Piazza, A., Davis, R. W., Feldman, M. W., Cavalli-Sforza, L. L., Oefner, P. J. 2000; 26 (3): 358-361

    Abstract

    Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.

    View details for Web of Science ID 000165176500029

    View details for PubMedID 11062480

  • Cultural transmission in a demographic study of sex ratio at birth in China's future THEORETICAL POPULATION BIOLOGY Li, N., Feldman, M. W., Li, S. Z. 2000; 58 (2): 161-172

    Abstract

    A decline in fertility causes an increase in the sex ratio at birth (SRB) in countries with strong son preference. What happens to the SRB if fertility is maintained at a low level depends on the evolution of son preference. In this paper, we analyze trends in son preference and its effect on China's future SRB.

    View details for Web of Science ID 000090097500006

    View details for PubMedID 11042106

  • Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Thomson, R., Pritchard, J. K., Shen, P. D., Oefner, P. J., Feldman, M. W. 2000; 97 (13): 7360-7365

    Abstract

    We consider a data set of DNA sequence variation at three Y chromosome genes (SMCY, DBY, and DFFRY) in a worldwide sample of human Y chromosomes. Between 53 and 70 chromosomes were fully screened for sequence variation at each locus by using the method of denaturing high-performance liquid chromatography. The sum of the lengths of the three genes is 64,120 bp. We have used these data to study the ancestral genealogy of human Y chromosomes. In particular, we focused on estimating the expected time to the most recent common ancestor and the expected ages of certain mutations with interesting geographic distributions. Although the geographic structure of the inferred haplotype tree is reminiscent of that obtained for other loci (the root is in Africa, and most of the oldest non-African lineages are Asian), the expected time to the most recent common ancestor is remarkably short, on the order of 50,000 years. Thus, although previous studies have noted that Y chromosome variation shows extreme geographic structure, we estimate that the spread of Y chromosomes out of Africa is much more recent than previously was thought. We also show that our data indicate substantial population growth in the effective number of human Y chromosomes.

    View details for Web of Science ID 000087811600078

    View details for PubMedID 10861004

  • Human population expansion and microsatellite variation MOLECULAR BIOLOGY AND EVOLUTION Zhivotovsky, L. A., Bennett, L., Bowcock, A. M., Feldman, M. W. 2000; 17 (5): 757-767

    Abstract

    Polymorphisms at di-, tri-, and tetranucleotide microsatellite loci have been analyzed in 14 worldwide populations. A statistical index of population expansion, denoted S(k), is introduced to detect historical changes in population size using the variation at the microsatellites. The index takes the value 0 at equilibrium with constant population size and is positive or negative according to whether the population is expanding or contracting, respectively. The use of S(k) requires estimation of properties of the mutation distribution for which we use both family data of Dib et al. for dinucleotide loci and our population data on tri- and tetranucleotide loci. Statistical estimates of the expansion index, as well as their confidence intervals from bootstrap resampling, are provided. In addition, a dynamical analysis of S(k) is presented under various assumptions on population growth or decline. The studied populations are classified as having high, intermediate, or low values of S(k) and genetic variation, and we use these to interpret the data in terms of possible population dynamics. Observed values of S(k) for samples of di-, tri-, and tetranucleotide data are compatible with population expansion earlier than 60,000 years ago in Africa, Asia, and Europe if the initial population size before the expansion was on the order of 500. Larger initial population sizes force the lower bound for the time since expansion to be much earlier. We find it unlikely that bottlenecks occurred in Central African, East Asian, or European populations, and the estimated expansion times are rather similar for all of these populations. This analysis presented here suggests that modern human populations departed from Africa long before they began to expand in size. Subsequently, the major groups (the African, East Asian, and European groups) started to grow at approximately same time. Populations of South America and Oceania show almost no growth. The Mbuti population from Zaire appears to have experienced a bottleneck during its expansion.

    View details for Web of Science ID 000086875300009

    View details for PubMedID 10779536

  • On the product mean fitness and population growth in sexual and asexual populations EVOLUTIONARY ECOLOGY RESEARCH Manos, H., Liberman, U., Feldman, M. W. 2000; 2 (4): 525-545
  • Cultural transmission of uxorilocal marriage in Lueyang, China JOURNAL OF FAMILY HISTORY Li, S. Z., Feldman, M. W., Li, N. 2000; 25 (2): 158-177
  • The dynamics of repeated elements: Applications to the epidemiology of tuberculosis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Tanaka, M. M., Small, P. M., Salamon, H., Feldman, M. W. 2000; 97 (7): 3532-3537

    Abstract

    We propose a stepwise mutation model to describe the dynamics of DNA fingerprint variation in Mycobacterium tuberculosis. The genome of M. tuberculosis carries insertion sequences (IS6110) that are relatively stable over time periods of months but have an observable transposition rate over longer time scales. Variability in copy number and genomic location of (IS6110) can be harnessed to generate a DNA fingerprint for each strain, by digesting the genome with a restriction enzyme and using a portion of the element as a probe for Southern blots. The number of bands found for a given genome approximates the number of copies of IS6110 it carries. A large data set of such fingerprints from tuberculosis (TB) cases in San Francisco provides an observed distribution of IS6110 copy number. Implementation of the model through deterministic and stochastic simulation indicates some general features of IS/TB dynamics. By comparing observations with outcomes of the model, we conclude that the IS/TB system is very heterogeneous and far from equilibrium. We find that the transposition parameters have a much stronger effect than the epidemic parameters on copy number distribution.

    View details for Web of Science ID 000086195200103

    View details for PubMedID 10716736

  • Microsatellite evolution in modern humans: a comparison of two data sets from the same populations ANNALS OF HUMAN GENETICS Jin, L., Baskett, M. L., Cavalli-Sforza, L. L., Zhivotovsky, L. A., Feldman, M. W., Rosenberg, N. A. 2000; 64: 117-134

    Abstract

    We genotyped 64 dinucleotide microsatellite repeats in individuals from populations that represent all inhabited continents. Microsatellite summary statistics are reported for these data, as well as for a data set that includes 28 out of 30 loci studied by Bowcock et al. (1994) in the same individuals. For both data sets, diversity statistics such as heterozygosity, number of alleles per locus, and number of private alleles per locus produced the highest values in Africans, intermediate values in Europeans and Asians, and low values in Americans. Evolutionary trees of populations based on genetic distances separated groups from different continents. Corresponding trees were topologically similar for the two data sets, with the exception that the (deltamu)2 genetic distance reliably distinguished groups from different continents for the larger data set, but not for the smaller one. Consistent with our results from diversity statistics and from evolutionary trees, population growth statistics S k and beta, which seem particularly useful for indicating recent and ancient population size changes, confirm a model of human evolution in which human populations expand in size and through space following the departure of a small group from Africa.

    View details for Web of Science ID 000088739600003

    View details for PubMedID 11246466

  • Niche construction, biological evolution, and cultural change BEHAVIORAL AND BRAIN SCIENCES Laland, K. N., Odling-Smee, J., Feldman, M. W. 2000; 23 (1): 131-?

    Abstract

    We propose a conceptual model that maps the causal pathways relating biological evolution to cultural change. It builds on conventional evolutionary theory by placing emphasis on the capacity of organisms to modify sources of natural selection in their environment (niche construction) and by broadening the evolutionary dynamic to incorporate ontogenetic and cultural processes. In this model, phenotypes have a much more active role in evolution than generally conceived. This sheds light on hominid evolution, on the evolution of culture, and on altruism and cooperation. Culture amplifies the capacity of human beings to modify sources of natural selection in their environments to the point where that capacity raises some new questions about the processes of human adaptation.

    View details for Web of Science ID 000088647900069

    View details for PubMedID 11303338

  • Niche construction and gene-culture coevolution: An evolutionary basis for the human sciences 5th Biannual Symposium on the Science of Behavior Odling-Smee, F. J., Laland, K. N., Feldman, M. W. KLUWER ACADEMIC/PLENUM PUBL. 2000: 89–111
  • Group selection: A niche construction perspective JOURNAL OF CONSCIOUSNESS STUDIES Laland, K. N., Odling-Smee, F. J., Feldman, M. W. 2000; 7 (1-2): 221-225
  • Population growth of human Y chromosomes: A study of Y chromosome microsatellites MOLECULAR BIOLOGY AND EVOLUTION Pritchard, J. K., Seielstad, M. T., Perez-Lezaun, A., Feldman, M. W. 1999; 16 (12): 1791-1798

    Abstract

    We use variation at a set of eight human Y chromosome microsatellite loci to investigate the demographic history of the Y chromosome. Instead of assuming a population of constant size, as in most of the previous work on the Y chromosome, we consider a model which permits a period of recent population growth. We show that for most of the populations in our sample this model fits the data far better than a model with no growth. We estimate the demographic parameters of this model for each population and also the time to the most recent common ancestor. Since there is some uncertainty about the details of the microsatellite mutation process, we consider several plausible mutation schemes and estimate the variance in mutation size simultaneously with the demographic parameters of interest. Our finding of a recent common ancestor (probably in the last 120,000 years), coupled with a strong signal of demographic expansion in all populations, suggests either a recent human expansion from a small ancestral population, or natural selection acting on the Y chromosome.

    View details for Web of Science ID 000084147700014

    View details for PubMedID 10605120

  • Rekindling an old flame: A haploid model for the evolution and impact of flammability in resprouting plants EVOLUTIONARY ECOLOGY RESEARCH Kerr, B., Schwilk, D. W., Bergman, A., Feldman, M. W. 1999; 1 (7): 807-833
  • Theoretical considerations of cross-immunity, recombination and the evolution of new parasitic strains JOURNAL OF THEORETICAL BIOLOGY Tanaka, M. M., Feldman, M. W. 1999; 198 (2): 145-163

    Abstract

    We explore the dynamics of multiple strains of a parasite in order to assess the conditions under which a novel strain, perhaps a mutant or migrant, may invade a population that already carries an endemic strain. Multiple strain dynamics can be modeled through coinfection or complete cross-immunity. We examine these three modes to discuss the relationships among cross-immunity, the basic reproductive rates of each strain, and the invasion of the new strain. Superinfection is more restrictive than coinfection in the proportion of parameters that allows invasion. The coinfection model is extended to allow haploid strains to undergo recombination within the host. We investigate the effects of recombination and cross-immunity on the invasion of new strains. Interestingly, although recombination is understood to generate diversity, it is not always advantageous.

    View details for Web of Science ID 000080543300001

    View details for PubMedID 10339390

  • Genetic conflicts and the evolutionary origin of genomic imprinting TRENDS IN ECOLOGY & EVOLUTION Spencer, H. G., Clark, A. G., Feldman, M. W. 1999; 14 (5): 197-201
  • Statistical properties of two tests that use multilocus data sets to detect population expansions MOLECULAR BIOLOGY AND EVOLUTION Reich, D. E., Feldman, M. W., Goldstein, D. B. 1999; 16 (4): 453-466
  • Migration versus mutation in the evolution of recombination under multilocus selection GENETICS RESEARCH Pylkov, K. V., Zhivotovsky, L. A., Feldman, M. W. 1998; 71 (3): 247-256

    Abstract

    We use modifier theory to compare the evolution of recombination under mutation-selection and migration-selection balance models. Recombination between loosely linked loci subject to weak multilocus selection is controlled by the genotype at a selectively neutral modifier locus. We show that the success of a new modifier depends on the sign and amount of epistasis as well as on the linkage of the modifier locus to the loci under selection. With both migration and mutation, for recombination to increase requires negative (synergistic) epistasis. When epistasis is sufficiently weak, increased recombination is always favoured under mutation-selection balance and never under migration-selection balance. With stronger negative epistasis, there exists a critical recombination value. In this case, a recombination-increasing allele invades the population under mutation-selection balance if its recombination rate with the major loci is less than the critical recombination value, whereas with weak migration it must be above this value. These results are the same for haploid and diploid populations.

    View details for Web of Science ID 000075333300006

    View details for PubMedID 9717440

  • Waiting with and without recombination: The time to production of a double mutant THEORETICAL POPULATION BIOLOGY Christiansen, F. B., Otto, S. P., Bergman, A., Feldman, M. W. 1998; 53 (3): 199-215

    Abstract

    R.A. Fisher and H.J. Muller argued in the 1930s that a major evolutionary advantage of recombination is that it allows favorable mutations to be combined within an individual even when they first appear in different individuals. This effect is evaluated in a two-locus, two-allele model by calculating the average waiting time until a new genotypic combination first appears in a haploid population. Three approximations are developed and compared with Monte Carlo simulations of the Wright-Fisher process of random genetic drift in a finite population. First, a crude method, based on the deterministic accumulation of single mutants, produces a waiting time of 1/square root of N mu(2) with no recombination and [formula: see text] with recombination between the two loci, where mu is the mutation rate, N is the haploid population size, and R is the recombination rate. Second, the waiting time is calculated as the expected value of a heterogeneous geometric distribution obtained from a branching process approximation. This gives accurate estimates for small values of N mu large. The estimates for small values of N mu are considerably lower than the simulated values. Finally, diffusion analysis of the Wright-Fisher process provides accurate estimates for N mu small, and the time scales of the diffusion process show a difference between R = 0 and for R > 0 of the same order of magnitude as seen in the deterministic analysis. In the absence of recombination, accurate approximations to the waiting time are obtained by using the branching process for high N mu and the diffusion approximation for low N mu. For low N mu the waiting time is well approximated by 1/the square root of 8N2 mu(3). With R > 0, the following dependence on N mu is observed: For N mu > 1 the waiting time is virtually independent of recombination and is well described by the branching process approximation. For N mu approximately equal to 1 the waiting time is well described by a simplified diffusion approximation that assumes symmetry in the frequencies of single mutants. For N mu < 1 the waiting time is well described by the diffusion approximation allowing asymmetry in the frequencies of single mutants. Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small compared to that of the mutation rate and population size. For large N mu, recombination has a negligible effect, and its effect is strongest for small N mu, in which case the waiting time approaches a fixed fraction of the waiting time for R = 0. Free recombination lowers the waiting time to about 45% of the waiting time for absolute linkage for small N mu. Selection has little effect on the importance of recombination in general.

    View details for Web of Science ID 000074831600003

    View details for PubMedID 9679320

  • Microsatellite behavior with range constraints: Parameter estimation and improved distances for use in phylogenetic reconstruction THEORETICAL POPULATION BIOLOGY Pollock, D. D., Bergman, A., Feldman, M. W., Goldstein, D. B. 1998; 53 (3): 256-271

    Abstract

    A symmetric stepwise mutation model with reflecting boundaries is employed to evaluate microsatellite evolution under range constraints. Methods of estimating range constraints and mutation rates under the assumptions of the model are developed. Least squares procedures are employed to improve molecular distance estimation for use in phylogenetic reconstruction in the case where range constraints and mutation rates vary across loci. The bias and accuracy of these methods are evaluated using computer simulations, and they are compared to previously existing methods which do not assume range constraints. Range constraints are seen to have a substantial impact on phylogenetic conclusions based on molecular distances, particularly for more divergent taxa. Results indicate that if range constraints are in effect, the methods developed here should be used in both the preliminary planning and final analysis of phylogenetic studies employing microsatellites. It is also seen that in order to make accurate phylogenetic inferences under range constraints, a larger number of loci are required than in their absence.

    View details for Web of Science ID 000074831600006

    View details for PubMedID 9679321

  • Long-term evolution, short-term evolution, and population genetic theory JOURNAL OF THEORETICAL BIOLOGY Eshel, I., Feldman, M. W., Bergman, A. 1998; 191 (4): 391-396
  • Genetic conflicts, multiple paternity and the evolution of genomic imprinting GENETICS Spencer, H. G., Feldman, M. W., Clark, A. G. 1998; 148 (2): 893-904

    Abstract

    We present nine diallelic models of genetic conflict in which one allele is imprintable and the other is not to examine how genomic imprinting may have evolved. Imprinting is presumed to be either maternal (i.e., the maternally derived gene is inactivated) or paternal. Females are assumed to be either completely monogamous or always bigamous, so that we may see any effect of multiple paternity. In contrast to previous verbal and quantitative genetic models, we find that genetic conflicts need not lead to paternal imprinting of growth inhibitors and maternal imprinting of growth enhancers. Indeed, in some of our models--those with strict monogamy--the dynamics of maternal and paternal imprinting are identical. Multiple paternity is not necessary for the evolution of imprinting, and in our models of maternal imprinting, multiple paternity has no effect at all. Nevertheless, multiple paternity favors the evolution of paternal imprinting of growth inhibitors and hinders that of growth enhancers. Hence, any degree of multiple paternity means that growth inhibitors are more likely to be paternally imprinted, and growth enhancers maternally so. In all of our models, stable polymorphism of imprinting status is possible and mean fitness can decrease over time. Neither of these behaviors have been predicted by previous models.

    View details for Web of Science ID 000072187500032

    View details for PubMedID 9504935

  • A gene-culture coevolutionary model for brother-sister mating PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Aoki, K., Feldman, M. W. 1997; 94 (24): 13046-13050

    Abstract

    We present a gene-culture coevolutionary model for brother-sister mating in the human. It is shown that cultural--as opposed to innate--determination of mate preference may evolve, provided the inbreeding depression is sufficiently high. At this coevolutionary equilibrium, sib mating is avoided because of cultural pressures.

    View details for Web of Science ID A1997YJ45600064

    View details for PubMedID 9371797

  • Biased mutations and microsatellite variation MOLECULAR BIOLOGY AND EVOLUTION Zhivotovsky, L. A., Feldman, M. W., GRISHECHKIN, S. A. 1997; 14 (9): 926-933

    Abstract

    Mutation bias is one of the forces that may constrain the variation at microsatellite loci. Here, we study the dynamics of population statistics and the genetic distance between two populations under multiple stepwise mutations with linear bias and random drift. Expressions are derived for these statistics as functions of time, as well as at mutation-drift equilibrium. Applying these expressions to published data on humans and chimpanzees, the regression coefficient of mutation bias on allele size was estimated to be at least between -0.0064 and -0.013. The assumption of mutational bias produces larger estimates of divergence times than are obtained in its absence; in particular, the time of split between African and non-African human populations is estimated to be between 183,000 and 222,000 years, assuming one-step mutations and no selection. With multistep mutations, the divergence time is estimated to be lower.

    View details for Web of Science ID A1997XT79200004

    View details for PubMedID 9287425

  • Gene-culture coevolution and sex ratios .2. Sex-chromosomal distorters and cultural preferences for offspring sex THEORETICAL POPULATION BIOLOGY Kumm, J., Feldman, M. W. 1997; 52 (1): 1-15

    Abstract

    Cultural preferences for the sex of offspring may produce behavior, such as female infanticide, sex-selective abortion and sex-selective parental investment, which alter the sex ratio in a population. Empirical evidence suggests that some genetic sex-ratio distorters are located on the sex chromosomes. Interactions between cultural preferences and sex-linked sex-ratio distorters are examined. Criteria for the spread of cultural preferences and sex-chromosomal distorter alleles are derived analytically, and the coevolution of preferences and distorters is examined through numerical iteration. Evolutionary equilibria and trajectories of gene-culture interactions involving sex-chromosomal distorter alleles may produce severely male- or female-biased primary sex ratios and adult sex ratios in populations. Adult sex ratios, primary sex ratios, allele frequencies and the prevalence of cultural preferences in the population are sensitive to initial conditions and cultural transmission parameters. During the coevolutionary process phenoallelic association is observed in many cases and is associated with unusual dynamics.

    View details for Web of Science ID A1997YA85000001

    View details for PubMedID 9345791

  • Gene-Culture Coevolution and Sex Ratios: II. Sex-Chromosomal Distorters and Cultural Preferences for Offspring Sex Theoretical population biology KUMM, Feldman 1997; 7 (1): 1-15

    Abstract

    Cultural preferences for the sex of offspring may produce behavior, such as female infanticide, sex-selective abortion and sex-selective parental investment, which alter the sex ratio in a population. Empirical evidence suggests that some genetic sex-ratio distorters are located on the sex chromosomes. Interactions between cultural preferences and sex-linked sex-ratio distorters are examined. Criteria for the spread of cultural preferences and sex-chromosomal distorter alleles are derived analytically, and the coevolution of preferences and distorters is examined through numerical iteration. Evolutionary equilibria and trajectories of gene-culture interactions involving sex-chromosomal distorter alleles may produce severely male- or female-biased primary sex ratios and adult sex ratios in populations. Adult sex ratios, primary sex ratios, allele frequencies and the prevalence of cultural preferences in the population are sensitive to initial conditions and cultural transmission parameters. During the coevolutionary process phenoallelic association is observed in many cases and is associated with unusual dynamics. Copyright 1997 Academic Press

    View details for PubMedID 9356319

  • Deleterious mutations, variable epistatic interactions, and the evolution of recombination THEORETICAL POPULATION BIOLOGY Otto, S. P., Feldman, M. W. 1997; 51 (2): 134-147

    Abstract

    In this paper, we examine the conditions that allow increased recombination to evolve in the presence of recurrent deleterious mutation. We focus on a three-locus model first studied by Feldman et al. (1980), which follows the dynamics of a modifier locus that alters the recombination rate between two loci subject to deleterious mutation. Although Feldman et al. (1980) indicated that increased recombination might be favored if there is diminishing-returns epistasis, we show that alleles that increase the recombination rate can only invade if there is synergistic epistasis between the loci under selection. Even with synergistic epistasis, evolution at the modifier locus will lead to decreased recombination if the modifier locus is loosely linked and epistasis is strong. Using the multi-locus analysis of Barton (1995), we show that variability among loci in the sign and strength of epistasis further decreases the parameter space over which increased recombination may evolve. We conclude that, even with negative epistasis, increased recombination may only be favored when linkage is tight, especially if, as seems likely, epistatic interactions are highly variable among loci.

    View details for Web of Science ID A1997WW85300005

    View details for PubMedID 9169238

  • Microsatellite genetic distances with range constraints: Analytic description and problems of estimation GENETICS Feldman, M. W., Bergman, A., Pollock, D. D., Goldstein, D. B. 1997; 145 (1): 207-216

    Abstract

    Statistical properties of the symmetric stepwise-mutation model for microsatellite evolution are studied under the assumption that the number of repeats is strictly bounded above and below. An exact analytic expression is found for the expected products of the frequencies of alleles separated by k repeats. This permits characterization of the asymptotic behavior of our distances D1 and (delta mu)2 under range constraints. Based on this characterization we develop transformations that partially restore linearity when allele size is restricted. We show that the appropriate transformation cannot be applied in the case of varying mutation rates (beta) and range constraints (R) because of statistical difficulties. In the special case of no variation in beta and R across loci, however, the transformation simplifies to a usable form and results in a distance much more linear with time than distances developed for an infinite range. Although analytically incorrect in the case of variation in beta and R, the simpler transformation is surprisingly insensitive to variation in these parameters, suggesting that it may have considerable utility in phylogenetic studies.

    View details for Web of Science ID A1997WC86800021

    View details for PubMedID 9017402

  • Proposed model ethical protocol for collecting DNA samples. Houston law review Weiss, K. M., Cavalli-Sforza, L. L., Dunston, G. M., Feldman, M., Greely, H. T., Kidd, K. K., King, M., Moore, J. A., Szathmary, E., Twinn, C. M. 1997; 33 (5): 1431-1474

    View details for PubMedID 12627556

  • Statistics for microsatellite variation based on coalescence THEORETICAL POPULATION BIOLOGY Pritchard, J. K., Feldman, M. W. 1996; 50 (3): 325-344

    Abstract

    The stepwise mutation model, which was at one time chiefly of interest in studying the evolution of protein charge-states, has recently undergone a resurgence of interest with the new popularity of microsatellites as phylogenetic markers. In this paper we describe a method which makes it possible to transfer many population genetics results from the standard infinite sites model to the stepwise mutation model. We study in detail the properties of pairwise differences in microsatellite repeat number between randomly chosen alleles. We show that the problem of finding the expected squared distance between two individuals and finding the variance of the squared distance can be reduced for a wide range of population models to finding the mean and mean square coalescence times. In many cases the distributions of coalescence times have already been studied for infinite site problems. In this study we show how to calculate these quantities for several population models. We also calculate the variance in mean squared pairwise distance (an estimator of mutation rate x population size) for samples of arbitrary size and show that this variance does not approach zero as the sample size increases. We can also use our method to study alleles at linked microsatellite loci. We suggest a metric which quantifies the level of association between loci-effectively a measure of linkage disequilibrium. It is shown that there can be linkage disequilibrium between partially linked loci at mutation-drift equilibrium.

    View details for Web of Science ID A1996WA54400006

    View details for PubMedID 9000493

  • Fitness patterns and phenotypic plasticity in a spatially heterogeneous environment GENETICAL RESEARCH Zhivotovsky, L. A., Feldman, M. W., Bergman, A. 1996; 68 (3): 241-248

    Abstract

    We analyse patterns of the means and variances of genotypic fitnesses across different niches in a randomly mating haploid population. The population inhabits a spatially heterogeneous environment where it is subject to mutation and weak multilocus additive selection, with different election coefficients in different niches. Approximate analytical expressions are derived for the stationary mean and variance of genotypic fitnesses among the niches in terms of environmental and genetic parameters. As a special case, we analyse an environment described by a variable t, distributed among the niches with mean t(star) and variance D(star) and quadratic decrease in correlation between environments as a function of the difference in values of t. If the niches have the same qualities, the mean and variance of genotypic fitnesses evolve to be quadratic functions of t that achieve their maximum and minimum, respectively, at t(star). With unequal niche qualities, these are non-polynomial functions that attain their extrema at different, usually intermediate values of t, although the coefficient of variation of the genotypic fitnesses still attains its minimum near t(star). The functions involve the total mutation rate, the combination of the loci to genotypic fitnesses, and the frequency and quality distributions of the niches. Thus, for this relatively simple model the norms of reaction may be calculated in terms of the detailed properties of the environmental heterogeneity, and the genetic system.

    View details for Web of Science ID A1996WN32200006

    View details for PubMedID 9062081

  • Genetic data and the African origin of humans SCIENCE Pritchard, J. K., Feldman, M. W. 1996; 274 (5292): 1548-1548

    View details for Web of Science ID A1996VV77500054

    View details for PubMedID 8966621

  • Statistical properties of the variation at linked microsatellite loci: Implications for the history of human Y chromosomes MOLECULAR BIOLOGY AND EVOLUTION Goldstein, D. B., Zhivotovsky, L. A., Nayar, K., Linares, A. R., CAVALLISFORZA, L. L., Feldman, M. W. 1996; 13 (9): 1213-1218

    Abstract

    It has recently been suggested that observed levels of variation at microsatellite loci can be used to infer patterns of selection in genomes and to assess demographic history. In order to evaluate the feasibility of these suggestions it is necessary to know something about how levels of variation at microsatellite loci are expected to fluctuate due simply to stochasticity in the processes of mutation and inheritance (genetic sampling). Here we use recently derived properties of the stepwise mutation model to place confidence intervals around the variance in repeat score that is expected at mutation-drift equilibrium and outline a statistical test for whether an observed value differs significantly from expectation. We also develop confidence intervals for the time course of the buildup of variation following a complete elimination of variation, such as might be caused by a selective sweep or an extreme population bottleneck. We apply these methods to the variation observed at human Y-specific microsatellites. Although a number of authors have suggested the possibility of a very recent sweep, our analyses suggest that a sweep or extreme bottleneck is unlikely to have occurred anytime during the last approximately 74,000 years. To generate this result we use a recently estimated mutation rate for microsatellite loci of 5.6 x 10(-4) along with the variation observed at autosomal microsatellite loci to estimate the human effective population size. This estimate is 18,000, implying an effective number of 4,500 Y chromosomes. One important general conclusion to emerge from this study is that in order to reject mutation-drift equilibrium at a set of linked microsatellite loci it is necessary to have an unreasonably large number of loci unless the observed variance is far below that expected at mutation-drift equilibrium.

    View details for Web of Science ID A1996VR29900007

    View details for PubMedID 8896373

  • Gene-culture coevolutionary theory TRENDS IN ECOLOGY & EVOLUTION Feldman, M. W., Laland, K. N. 1996; 11 (11): 453-457

    Abstract

    Gene-culture coevolutionary theory is a branch of theoretical population genetics that models the transmission of genes and cultural traits from one generation to the next, exploring how they interact. These models have been employed to examine the adaptive advantages of learning and culture, to investigate the forces of cultural change, to partition the variance in complex human behavioral and personality traits, and to address specific cases in human evolution in which there is an interaction between genes and culture.

    View details for Web of Science ID A1996VN15900006

    View details for PubMedID 21237920

  • Geographic clustering of human Y-chromosome haplotypes. Annals of human genetics Ruiz Linares, A., Nayar, K., Goldstein, D. B., Hebert, J. M., Seielstad, M. T., Underhill, P. A., Lin, A. A., Feldman, M. W., Cavalli Sforza, L. L. 1996; 60: 401-408

    Abstract

    Five polymorphic markers on the Y-chromosome (mostly microsatellites) were typed in 121 individuals from 13 populations around the world. With these markers 78 different haplotypes were detected. Haplotypes present more than once tend to be shared by individuals from the same population or continent. A reconstruction of haplotype phylogeny also indicates significant geographic structure in the data. Based on the similarity of the haplotypes, population relationships were examined and found to be largely concordant with those obtained with other markers. Even though the sample size and the number of markers are small, there is very signficant clustering of the haplotypes by continent of origin.

    View details for PubMedID 8912793

  • Individual versus social learning: Evolutionary analysis in a fluctuating environment ANTHROPOLOGICAL SCIENCE Feldman, M. W., Aoki, K., Kumm, J. 1996; 104 (3): 209-231
  • The evolutionary consequences of niche construction: A theoretical investigation using two-locus theory JOURNAL OF EVOLUTIONARY BIOLOGY Laland, K. N., ODLINGSMEE, F. J., Feldman, M. W. 1996; 9 (3): 293-316
  • On the evolution of phenotypic plasticity in a spatially heterogeneous environment EVOLUTION Zhivotovsky, L. A., Feldman, M. W., Bergman, A. 1996; 50 (2): 547-558
  • ON THE EVOLUTION OF PHENOTYPIC PLASTICITY IN A SPATIALLY HETEROGENEOUS ENVIRONMENT. Evolution; international journal of organic evolution Zhivotovsky, L. A., Feldman, M. W., Bergman, A. 1996; 50 (2): 547-558

    Abstract

    A genetic model for the dynamics of a quantitative trait is analyzed in terms of gene frequencies, linkage disequilibria, and environmental effects on the trait. In a randomly mating population, at each generation progeny move to niches where they are subject to weak Gaussian selection on the trait, with different fitness levels in the different niches. Initially, the variability of the trait is due to additive loci with heterozygous homeostasis. The evolution of plasticity is then described in terms of the invasion of the population by genetic modifiers that may epistatically affect the trait, its optimum in each niche, the strengths of selection, and other parameters characteristic of the niches. We show that the evolution of trait means within niches depends on the overall evolution in the whole system, and in general, optimum phenotypic values are not attained. The reaction norm and genotype-environment interaction may evolve even if the only effects of the modifier are on individual rates of dispersal, or on fitness effects resulting from the different environments in the different niches; this evolution does not require that the modifier affect parameters that influence the values of the trait. It is conjectured that in the least frequently reached niches with low fitness levels, the deviations from the trait optima should be larger than those in more commonly experienced and less stringent niches. Our analysis makes explicit the different contribution of between- and within-niche effects on the evolutionary dynamics of phenotypic plasticity in heterogeneous environments.

    View details for DOI 10.1111/j.1558-5646.1996.tb03867.x

    View details for PubMedID 28568922

  • Niche construction. AMERICAN NATURALIST ODLINGSMEE, F. J., Laland, K. N., Feldman, M. W. 1996; 147 (4): 641-648
  • On the modification of recombination with sex-dependent fitnesses and linkage JOURNAL OF MATHEMATICAL BIOLOGY Liberman, U., Feldman, M. W. 1996; 34 (3): 239-252
  • Population genetic perspectives on the evolution of recombination ANNUAL REVIEW OF GENETICS Feldman, M. W., Otto, S. P., Christiansen, F. B. 1996; 30: 261-295

    Abstract

    Optimality arguments and modifier theory are reviewed as paradigms for the study of the evolution of recombination. Optimality criteria (such as maximization of mean fitness) may agree with results from models developed in terms of the evolution of recombination at modifier loci. Modifier models demonstrate, however, that equilibrium mean fitness can decrease during the evolution of recombination rates and is not always maximized. Therefore, optimality arguments do not successfully predict the conditions under which increased or decreased recombination will evolve. The results from modifier models indicate that decreased recombination rates are usually favored when the population is initially near a polymorphic equilibrium with linkage disequilibrium. When the population is subject to directional selection or to deleterious mutations, increased recombination may be favored under certain conditions, provided that there is negative epistasis among alleles.

    View details for Web of Science ID A1996WA81200011

    View details for PubMedID 8982456

  • On the modification of recombination with sex-dependent fitnesses and linkage. Journal of mathematical biology Liberman, U., Feldman, M. W. 1996; 34 (3): 230-252

    Abstract

    According to the Reduction Principle, when a recombination-reducing allele is introduced near an equilibrium that depends on recombination, that allele will increase in frequency. If the allele increases the recombination rate, it will be expelled from the population. There are known cases where this principle fails. In this respect, an interesting question is what kind of two-sex viability regimes support a general Reduction Principle. In this paper, we construct a model of viabilities, due to two autosomal linked genes, which differ between the sexes, such that recombination is different in the sexes. A complete analysis is provided for the case where recombination is absent in one sex. It is proved that the Reduction Principle is still valid for recombination in the other sex.

    View details for PubMedID 8819815

  • MICROSATELLITE VARIABILITY AND GENETIC DISTANCES PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Zhivotovsky, L. A., Feldman, M. W. 1995; 92 (25): 11549-11552

    Abstract

    We analyze the within- and between-population dynamics of the distribution of the number of repeats at multiple microsatellite DNA loci subject to stepwise mutation. Analytical expressions for moments up to the fourth order within a locus and the variance of between-locus variance at mutation-drift equilibrium have been obtained. These statistics may be used to test the appropriateness of the one-step mutation model and to detect between-locus variation in the mutation rate. Published data are compatible with the one-step mutation model, although they do not reject the two-step model. Using both multinomial sampling and diffusion approximations for the analysis of the genetic distance introduced by Goldstein et al. [Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727], we show that this distance follows a chi 2 distribution with degrees of freedom equal to the number of loci when there is no variation in mutation rates among the loci. In the presence of such variation, the variance of the distance is obtained. We conclude that the number of microsatellite loci required for the construction of phylogenetic trees with reliable branch lengths may be several hundred. Also, mutations that change repeat scores by several units, even though extremely rare, may dramatically influence estimates of population parameters.

    View details for Web of Science ID A1995TJ22200048

    View details for PubMedID 8524801

  • On the evolution of learning: Representation of a stochastic environment THEORETICAL POPULATION BIOLOGY Bergman, A., Feldman, M. W. 1995; 48 (3): 251-276
  • A GENE-CULTURE MODEL OF HUMAN HANDEDNESS BEHAVIOR GENETICS Laland, K. N., Kumm, J., VanHorn, J. D., Feldman, M. W. 1995; 25 (5): 433-445

    Abstract

    A model of handedness incorporating both genetic and cultural processes is proposed, based on an evolutionary analysis, and maximum-likelihood estimates of its parameters are generated. This model has the characteristics that (i) no genetic variation underlies variation in handedness, and (ii) variation in handedness among humans is the result of a combination of cultural and developmental factors, but (iii) a genetic influence remains since handedness is a facultative trait. The model fits the data from 17 studies of handedness in families and 14 studies of handedness in monozygotic and dizygotic twins. This model has the additional advantages that it can explain why monozygotic and dizygotic twins and siblings have similar concordance rates, and no hypothetical selection regimes are required to explain the persistence of left handedness.

    View details for Web of Science ID A1995RW36200003

    View details for PubMedID 7487840

  • POPULATION-STRUCTURE, FITNESS SURFACES, AND LINKAGE IN THE SHIFTING BALANCE PROCESS GENETICAL RESEARCH Bergman, A., Goldstein, D. B., Holsinger, K. E., Feldman, M. W. 1995; 66 (1): 85-92

    Abstract

    Wright first introduced the idea that random genetic drift and classical mass-action selection might combine in such a way as to allow populations to find the highest peak in complicated adaptive surfaces. His theory assumes large but structured populations, in which mating is spatially local. If gene flow is sufficiently low, and the subpopulations (demes) are small enough, they will be subject to genetic drift. Distant demes drift independently, allowing many independent searches of the adaptive surface to take place. A deme that has shifted to a higher peak can, by emigration, cause the rest of the demes to shift to the higher peak. The probability of this shift depends on the migration rate. Previous studies have concluded that very little migration is necessary to effect the shift in adaptive peaks that characterizes the last phase of Wright's Shifting Balance Process (SBP). Here we present the results of a computer study that investigates the roles of dispersal distance, the degree of epistasis in the fitness surface, and recombination on the shifting balance process. In particular, we measure their effect on the population's mean fitness. We show that over a range of dispersal distances the advantage of the SBP is a monotonically increasing function of the amount of epistasis. Our results show that the extent of dispersal that results in the greatest effect of the SBP in increasing mean fitness depends on the extent of epistasis. Finally, for low levels of epistasis, higher recombination performs better, while for intermediate levels, lower recombination results in a greater advantage of the SBP.

    View details for Web of Science ID A1995RU68400009

    View details for PubMedID 8575671

  • GENETIC ABSOLUTE DATING BASED ON MICROSATELLITES AND THE ORIGIN OF MODERN HUMANS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Goldstein, D. B., Linares, A. R., CAVALLISFORZA, L. L., Feldman, M. W. 1995; 92 (15): 6723-6727

    Abstract

    We introduce a new genetic distance for microsatellite loci, incorporating features of the stepwise mutation model, and test its performance on microsatellite polymorphisms in humans, chimpanzees, and gorillas. We find that it performs well in determining the relations among the primates, but less well than other distance measures (not based on the stepwise mutation model) in determining the relations among closely related human populations. However, the deepest split in the human phylogeny seems to be accurately reconstructed by the new distance and separates African and non-African populations. The new distance is independent of population size and therefore allows direct estimation of divergence times if the mutation rate is known. Based on 30 microsatellite polymorphisms and a recently reported average mutation rate of 5.6 x 10(-4) at 15 dinucleotide microsatellites, we estimate that the deepest split in the human phylogeny occurred about 156,000 years ago. Unlike most previous estimates, ours requires no external calibration of the rate of molecular evolution. We can use such calibrations, however, to test our estimate.

    View details for Web of Science ID A1995RJ89200012

    View details for PubMedID 7624310

  • EFFECTS OF CIS-TRANS VIABILITY SELECTION ON SOME 2-LOCUS MODELS THEORETICAL POPULATION BIOLOGY Nordborg, M., Franklin, I. R., Feldman, M. W. 1995; 47 (3): 365-392

    Abstract

    Most analyses of two-locus viability models have assumed that the fitness of double heterozygotes are the same whether in the cis or trans configuration. This assumption is unlikely to hold for polymorphic sites within the same locus. We examine the quantitative and qualitative effects of incorporating cis-trans viability differences into a number of deterministic two-locus models. A new result is the finding that two asymmetric equilibria with similar levels of linkage disequilibrium, but different gene frequencies, may arise in quite realistic biological models. The general, and most important, conclusion is that high levels of linkage disequilibrium may be generated by very small selective differences in cis and trans. Polymorphic sites that interact selectively are expected to show high levels of linkage disequilibrium. Conversely, if two polymorphic sites within a gene are found to be in linkage equilibrium, it is likely that one or both are selectively neutral.

    View details for Web of Science ID A1995RL20900007

    View details for PubMedID 7667795

  • THE REDUCTION PRINCIPLE FOR RECOMBINATION UNDER DENSITY-DEPENDENT SELECTION THEORETICAL POPULATION BIOLOGY Zhivotovsky, L. A., Feldman, M. W. 1995; 47 (2): 244-256

    Abstract

    In diploid random mating populations with constant viability selection, genetic modifiers of recombination, introduced near equilibria that exhibit genetic association, invade if they reduce recombination. In this study we combine ecological and standard populations genetics in a haploid multilocus model that includes density-dependent regulation of population size and weak density-dependent differential selection among the multilocus genotypes. An allele that affects recombination among the genes contributing to the ecological selection, introduced near a stable equilibrium of the ecological-genetic system, invades if it reduces a weighted average of the recombination rates among pairs of loci under selection. This generalizes the Reduction Principle for the evolution of recombination (M. W. Feldman and U. Liberman, Proc. Nat. Acad. Sci. USA 83, 4824-4827, 1986; L. A. Zhivotovsky, W. M. Feldman, and F. B. Christiansen, Theor. Popul. Biol. 44, 225-245, 1993). It is also shown that the stronger the extent of density-dependence, the weaker the selection for reduced recombination.

    View details for Web of Science ID A1995QR83000005

    View details for PubMedID 7740441

  • HIGH SEX-RATIOS IN CHINA FUTURE SCIENCE Tuljapurkar, S., Li, N., Feldman, M. W. 1995; 267 (5199): 874-876

    Abstract

    In China in recent years, male live births have exceeded those of females by amounts far greater than those that occur naturally in human populations, a trend with significant demographic consequences. The resulting imbalance in the first-marriage market is estimated to be about 1 million males per year after 2010. These "excess" males were not easily accommodated in models with substantial changes in first-marriage patterns. The current sex ratio at birth has little effect on a couple's probability of having at least one son, so future increases in the sex ratio may well occur, especially given increasing access to sex-selective abortion.

    View details for Web of Science ID A1995QG20700055

    View details for PubMedID 7846529

  • GENE-CULTURE COEVOLUTIONARY THEORY - A TEST-CASE CURRENT ANTHROPOLOGY Laland, K. N., Kumm, J., Feldman, M. W. 1995; 36 (1): 131-156
  • SEX DETERMINATION IN A SYMMETRICAL AUTOSOMAL MULTILOCUS MODEL THEORETICAL POPULATION BIOLOGY Christiansen, F. B., Feldman, M. W. 1995; 47 (1): 107-127

    Abstract

    A model of determination of sex by an individual's genotype at n loci is discussed. The parameters that determine the probability that an individual is male (or female) depend only on the loci at which the individual is heterozygous, extending the two-gene theory of Feldman et al. (1991, Genetics 129, 297-312). The analysis uses a set indexation technique that allows a compact expression of the recombination process, and a transformation of the chromosome frequencies that induces a natural subgroup structure on hyperplanes in the frequency simplex. It is shown that the polymorphic equilibria correspond to these subgroups. Conditions are determined under which equilibria that exhibit the even sex ratio are stable. How recombination affects the stability of other equilibria, including those with linkage disequilibrium, are also explored.

    View details for Web of Science ID A1995QL09500005

    View details for PubMedID 7709367

  • AN EVALUATION OF GENETIC DISTANCES FOR USE WITH MICROSATELLITE LOCI GENETICS Goldstein, D. B., Linares, A. R., CAVALLISFORZA, L. L., Feldman, M. W. 1995; 139 (1): 463-471

    Abstract

    Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

    View details for Web of Science ID A1995PZ24800040

    View details for PubMedID 7705647

  • High sex ratio at birth and its consequences. Chinese journal of population science Li, N., Tuljapurkar, S., Feldman, M. 1995; 7 (3): 213-221

    View details for PubMedID 12290857

  • GENE-CULTURE COEVOLUTION AND SEX-RATIOS - THE EFFECTS OF INFANTICIDE, SEX-SELECTIVE ABORTION, SEX SELECTION, AND SEX-BIASED PARENTAL INVESTMENT ON THE EVOLUTION OF SEX-RATIOS THEORETICAL POPULATION BIOLOGY Kumm, J., Laland, K. N., Feldman, M. W. 1994; 46 (3): 249-278

    Abstract

    The evolutionary consequences of culturally transmitted practices that cause differential mortality between the sexes, thereby distorting the sex ratio (e.g., female infanticide and sex-selective abortion), are explored using dynamic models of gene-culture coevolution. We investigate how a preference for the sex of offspring may affect the selection of genes distorting the primary sex ratio. Sex-dependent differences in mortality have been predicted to select for a male- or female-biased primary sex ratio, to have no effect, or to favor either under different circumstances. We find that when a mating pair's behavior modifies mortality rates in favor of one sex, but does not change the number of offspring produced in the mating, the primary sex ratio will evolve a bias against the favored sex. However, when the total number of offspring of a mating pair is significantly reduced as a consequence of their prejudice, the primary sex ratio will evolve to favor the preferred sex. These results hold irrespective of whether the sex ratio is distorted by the mother's, the father's or the individual's own autosomal genes. The use of dynamic models of gene-culture coevolution allows us to explore the evolution of alleles which distort the sex ratio, as well as the final equilibrium states of the system. Gene-culture interactions can provide equilibria different from those in purely genetic systems, slow the approach to these equilibria by orders of magnitude, and move the primary (PSR) and the adult sex ratio (ASR) away from any stable equilibrium for hundreds of generations.

    View details for Web of Science ID A1994PX20800001

    View details for PubMedID 7846643

  • EVOLUTION OF RECOMBINATION AMONG MULTIPLE SELECTED LOCI - A GENERALIZED REDUCTION PRINCIPLE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Zhivotovsky, L. A., Feldman, M. W., Christiansen, F. B. 1994; 91 (3): 1079-1083

    Abstract

    Conditions for invasion by a new allele that controls the recombination pattern among an arbitrary number of genes under viability selection are studied. The recombination pattern may include interference. The new allele increases if its appropriately averaged marginal fitness is greater than the mean fitness prior to its introduction. Under weak additive-by-additive epistatic selection, this condition involves a weighted average of the changes in pairwise recombination rates relative to those prior to the introduction of the modifier. The weights here are positive functions of the epistatic selection components. In particular, the modifier allele may succeed even if it increases recombination among some pairs of loci, provided the overall average effect is one of reduction.

    View details for Web of Science ID A1994MV27800053

    View details for PubMedID 8302835

  • CULTURAL TRANSMISSION OF A SIGN LANGUAGE WHEN DEAFNESS IS CAUSED BY RECESSIVE ALLELES AT 2 INDEPENDENT LOCI THEORETICAL POPULATION BIOLOGY Aoki, K., Feldman, M. W. 1994; 45 (1): 101-120

    Abstract

    Two unlinked autosomal loci are assumed to affect the ability to hear in such a way that homozygosity for the recessive allele at either locus causes deafness. The five deaf genotypes are subject to the same negative selection due to a lower likelihood of marriage, but unmarried deaf persons remain socially active and participate in the cultural transmission of sign languages. Marriages are assortative for deafness or for hearing, and mutation occurs irreversibly from the dominant to recessive allele at each locus at the same rate. At mutation-selection balance, the fully polymorphic equilibrium is symmetrical. Based on this genetic model, we consider the relative importance of various forms of cultural transmission as they affect the persistence of sign languages. Horizontal transmission is shown to be effective when deaf children are able to interact with many peers. This observation is especially pertinent if assortative meeting of deaf children occurs, for example, at schools for the deaf. Oblique transmission can also be effective, but the literature suggests that this kind of transmission plays only a minor role. It is necessary, however, that some form of cultural transmission occur between generations. Thus, vertical transmission is a critical factor, despite the fact that parent-child transmission is often interrupted due to the recessive inheritance of deafness. In particular, the contribution of vertical transmission is enhanced by assortative mating for deafness.

    View details for Web of Science ID A1994NG50500006

    View details for PubMedID 8023314

  • ON THE COMPLEXITY OF CULTURAL TRANSMISSION AND EVOLUTION Workshop on Complexity: Metaphors, Models, and Reality Feldman, M. W., CAVALLISFORZA, L. L., Zhivotovsky, L. A. ADDISON-WESLEY PUBL CO. 1994: 47–64
  • THE EVOLUTION OF INTERFERENCE - REDUCTION OF RECOMBINATION AMONG 3 LOCI THEORETICAL POPULATION BIOLOGY Goldstein, D. B., Bergman, A., Feldman, M. W. 1993; 44 (2): 246-259

    Abstract

    Crossover events along chromosomes do not occur independently, but influence the probability of other nearby events. The most common interaction between nearby crossover events is inhibitory: a crossover event tends to reduce the probability of other such events nearby, and this is called positive interference. A crossover event may increase the probability of events nearby, and this rare phenomenon is called negative interference. In this paper, we use numerical methods to investigate how interference among three loci would evolve if it were under the genetic control of a fourth, selectively neutral locus. We first discuss the effect of interference on the overall rate of recombination among the three loci, and then show that, under a variety of conditions, interference evolves in the same way as would be predicted based upon its effect on the overall rate of recombination. That is, the overall rate evolves in the same direction as would the rate at a locus that controls recombination between two loci directly. We then check for the existence of viability-analogous Hardy-Weinberg equilibria in the four-locus model of interference modification.

    View details for Web of Science ID A1993MB63300007

    View details for PubMedID 8248888

  • RECOMBINATION MODIFICATION WITH X-LINKED CHARACTERS THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. W. 1993; 44 (2): 225-245

    View details for Web of Science ID A1993MB63300006

    View details for PubMedID 8248887

  • HETEROGENEOUS SELECTION IN SUBDIVIDED POPULATIONS JOURNAL OF MATHEMATICAL BIOLOGY Zhivotovsky, L. A., Feldman, M. W. 1993; 31 (7): 747-759

    Abstract

    The dynamics of allele frequencies changing under migration and heterogeneous selection in a subdivided population are investigated. Using perturbation techniques, a stationary state is obtained when migration and selection are both small. Heterogeneous selection leads to a positive correlation between values of F-statistics and heterozygosities when these are compared among sets of subdivided populations. This contrast with a negative value of the correlation obtained under Wright's classical model of homogeneous selection, and with the absence of correlation in the completely neutral situation.

    View details for Web of Science ID A1993LY30200006

    View details for PubMedID 8245733

  • THE EFFECTS OF THE MATING SYSTEM ON THE EVOLUTION OF MIGRATION IN A SPATIALLY HETEROGENEOUS POPULATION EVOLUTIONARY ECOLOGY Wiener, P., Feldman, M. W. 1993; 7 (3): 251-269
  • ON THE PROBABILITY OF LOSS OF NEW MUTATIONS IN THE PRESENCE OF LINKAGE DISEQUILIBRIUM JOURNAL OF MATHEMATICAL BIOLOGY Zhivotovsky, L. A., Feldman, M. W. 1993; 31 (2): 177-188

    Abstract

    A new selectively neutral mutation occurs in a multilocus genetic background that has achieved a stable equilibrium at which there is a linkage disequilibrium. Perturbation techniques are applied to an extension of the branching process formulation of Fisher in order to address the question of extinction probabilities. We show that under appropriate conditions the probability of extinction of the new mutant is increased by the existence of linkage disequilibrium in the genetic background.

    View details for Web of Science ID A1993KH93600006

    View details for PubMedID 8445349

  • GENE CULTURE COEVOLUTION - TOWARD A GENERAL-THEORY OF VERTICAL TRANSMISSION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Feldman, M. W., Zhivotovsky, L. A. 1992; 89 (24): 11935-11938

    Abstract

    A general formulation of cultural and genetic transmission is developed. The cultural transmission is vertical and the genetics may involve multiple loci. Each individual is represented by a phenogenotype, and conditions are given under which the evolutionary dynamics of phenogenotype frequencies are reducible to phenogametic or phenoallelic frequencies. The interaction between genes and culture is specified by an association measure, and results on the order of magnitude of this association at equilibrium are presented.

    View details for Web of Science ID A1992KC84400061

    View details for PubMedID 1465422

  • ASSORTATIVE MATING AND GRANDPARENTAL TRANSMISSION FACILITATE THE PERSISTENCE OF A SIGN LANGUAGE THEORETICAL POPULATION BIOLOGY Feldman, M. W., Aoki, K. 1992; 42 (2): 107-116

    Abstract

    Conditions for the persistence (i.e., protection from loss) of a sign language are investigated assuming monogenic recessive inheritance of deafness, assortative mating for deafness or hearing, and cultural transmission of the sign language to deaf individuals from their deaf parents and deaf maternal grandparents. A new method is introduced to deal with the problem of grandparental transmission in which the basic variables are the frequencies of triplets comprising a mother, a father, and their daughter of permissible phenogenotypes. Usual stability analysis is then done on the system of linear recursions in the frequencies of these triplets, derived on the assumption that signers (users of the sign language) are rare. It is shown that assortative mating is the most important factor contributing to persistence, but that grandparental transmission can also have a significant effect when assortment is as strong as observed in England and the United States.

    View details for Web of Science ID A1992JZ81400001

    View details for PubMedID 1481169

  • ON THE DIFFERENCE BETWEEN MEAN AND OPTIMUM OF QUANTITATIVE CHARACTERS UNDER SELECTION. Evolution; international journal of organic evolution Zhivotovsky, L. A., Feldman, M. W. 1992; 46 (5): 1574-1578

    View details for DOI 10.1111/j.1558-5646.1992.tb01149.x

    View details for PubMedID 28569008

  • ON GENETIC SEGREGATION AND THE EVOLUTION OF SEX EVOLUTION Wiener, P., Feldman, M. W., Otto, S. P. 1992; 46 (3): 775-782
  • ON GENETIC SEGREGATION AND THE EVOLUTION OF SEX. Evolution; international journal of organic evolution Wiener, P., Feldman, M. W., Otto, S. P. 1992; 46 (3): 775-782

    Abstract

    It has recently been argued that because the genetic load borne by an asexual species resulting from segregation, relative to a comparable sexual population, is greater than two, sex can overcome its twofold disadvantage and succeed. We evaluate some of the assumptions underlying this argument and discuss alternative assumptions. Further, we simulate the dynamics of competition between sexual and asexual types. We find that for populations of size 100 and 500 the advantages of segregation do not outweigh the cost of producing males. We conclude that, at least for small populations, drift and the cost of sex govern the evolution of sexuality, not selection or segregation. We believe, however, that if sexual and asexual populations were isolated for a sufficiently long period, segregation might impart a fitness advantage upon sexuals that could compensate for the cost of sex and allow sexuals to outcompete asexuals upon their reunion.

    View details for DOI 10.1111/j.1558-5646.1992.tb02083.x

    View details for PubMedID 28568655

  • ON MODELS OF QUANTITATIVE GENETIC-VARIABILITY - A STABILIZING SELECTION-BALANCE MODEL GENETICS Zhivotovsky, L. A., Feldman, M. W. 1992; 130 (4): 947-955

    Abstract

    A model of stabilizing selection on a multilocus character is proposed that allows the maintenance of stable allelic polymorphism and linkage disequilibrium. The model is a generalization of Lerner's model of homeostasis in which heterozygotes are less susceptible to environmental variation and hence are superior to homozygotes under phenotypic stabilizing selection. The analysis is carried out for weak selection with a quadratic-deviation model for the stabilizing selection. The stationary state is characterized by unequal allele frequencies, unequal proportions of complementary gametes, and a reduction of the genetic (and phenotypic) variance by the linkage disequilibrium. The model is compared with Mather's polygenic balance theory, with models that include mutation-selection balance, and others that have been proposed to study the role of linkage disequilibrium in quantitative inheritance.

    View details for Web of Science ID A1992HL49000023

    View details for PubMedID 1582569

  • RECOMBINATION DYNAMICS AND THE FITNESS LANDSCAPE PHYSICA D Bergman, A., Feldman, M. W. 1992; 56 (1): 57-67
  • THE EVOLUTION OF DISPERSAL IN A MODEL OF MIXED SELFING AND RANDOM MATING. Evolution; international journal of organic evolution Wiener, P., Feldman, M. W. 1991; 45 (7): 1717-1726

    View details for DOI 10.1111/j.1558-5646.1991.tb02679.x

    View details for PubMedID 28564132

  • LEWONTIN AND KOJIMA MEET FISHER - LINKAGE IN A SYMMETRICAL MODEL OF SEX DETERMINATION GENETICS Feldman, M. W., Christiansen, F. B., Otto, S. P. 1991; 129 (1): 297-312

    Abstract

    The effect of linkage and epistasis on the evolution of the sex-ratio is studied in a symmetric two-locus model of autosomal sex determination closely related to the symmetric viability model of R. C. Lewontin and K. Kojima. R. A. Fisher's expectation of an even sex ratio for autosomal sex determination by a single gene governs the dynamics when the loci are tightly linked. However, recombination may preclude optimization of the sex ratio just as occurs in viability selection models. Many of the evolutionary phenomena known for the symmetric viability model also occur here. In addition, we exhibit a series of new phenomena related to the presence of surfaces of even sex ratio.

    View details for Web of Science ID A1991GD51200028

    View details for PubMedID 1936963

  • RECESSIVE HEREDITARY DEAFNESS, ASSORTATIVE MATING, AND PERSISTENCE OF A SIGN LANGUAGE THEORETICAL POPULATION BIOLOGY Aoki, K., Feldman, M. W. 1991; 39 (3): 358-372

    Abstract

    We model the cultural transmission of sign language when there is one-locus genetic variation for deafness and hearing. Our premises are that the deaf are more motivated to learn sign language than the hearing, and that a vertically transmitted sign language, unlike recessive hereditary deafness, cannot "jump a generation." Conditions are obtained for persistence (i.e. protection from loss) of signers. These conditions are more easily satisfied the greater the fraction of the hearing who also learn sign language and as the frequency of the recessive gene for deafness increases. Persistence is also facilitated by assortative mating for deafness, but not by assortment for signing. With vertical transmission only, it is necessary that one signer parent be able to transmit sign language with greater than one-half the efficiency of two. Under the assumption that the hearing do not learn sign language, the following additional results are obtained. Persistence is more likely with dominant as opposed to recessive inheritance. When recessive hereditary and acquired deafness co-occur, increasing the frequency of the latter has opposite effects depending on the degree of assortment. Opportunities for the deaf to learn sign language outside the family seem not to affect the conditions for persistence.

    View details for Web of Science ID A1991FX07800008

    View details for PubMedID 1896949

  • A COMPARATIVE APPROACH TO THE POPULATION-GENETICS THEORY OF SEGREGATION DISTORTION AMERICAN NATURALIST Feldman, M. W., Otto, S. P. 1991; 137 (3): 443-456
  • THE HANDICAP PRINCIPLE IN PARENT-OFFSPRING CONFLICT - COMPARISON OF OPTIMALITY AND POPULATION GENETIC ANALYSES AMERICAN NATURALIST Eshel, I., Feldman, M. W. 1991; 137 (2): 167-185
  • MORE ON SELECTION FOR AND AGAINST RECOMBINATION THEORETICAL POPULATION BIOLOGY Bergman, A., Feldman, M. W. 1990; 38 (1): 68-92

    View details for Web of Science ID A1990DU51300003

    View details for PubMedID 2205018

  • MUTATION MODIFICATION WITH MULTIPLICATIVE FERTILITY SELECTION THEORETICAL POPULATION BIOLOGY TWOMEY, M. J., Feldman, M. W. 1990; 37 (2): 320-342

    Abstract

    Two diallelic loci in an infinite panmictic population of diploid individuals are modelled. The A/a locus is subject to unidirectional mutation and either multiplicative fertility selection or, equivalently, sex-asymmetric viability selection. The M/m locus acts as a selectively neutral modifier of the mutation rate at A/a. The loci recombine at rate R. If the M/m locus is initially monomorphic, and the A/a locus has reached equilibrium, the fate of a new modifier allele is found to depend not just on its relative effect on mutation but also upon the linkage, R. Each initial equilibrium may be characterized by a critical value of the recombination rate, R*. If 0 less than R* less than 0.5, a sufficiently small "down" modifier of the mutation rate will invade the population when R less than R* whereas a sufficiently small "up" modifier will succeed when R greater than R*. If R* less than 0 or R* greater than 0.5, only mutation reduction may occur. Numerical analysis of 56,000 sample equilibria indicates that mutation rates may be increased, but only when the selection regime is such that the A/a locus would remain polymorphic in the absence of mutation.

    View details for Web of Science ID A1990DA37800003

    View details for PubMedID 2336642

  • 2-LOCUS AUTOSOMAL SEX DETERMINATION - ON THE EVOLUTIONARY GENETIC STABILITY OF THE EVEN SEX-RATIO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Liberman, U., Feldman, M. W., Eshel, I., Otto, S. P. 1990; 87 (5): 2013-2017

    Abstract

    In two-locus models of sex determination, there are two kinds of interior (polymorphic) equilibria. One class has the even sex ratio, and the other has equal allele frequencies in the two sexes. Equilibria of the second class may exhibit linkage disequilibrium. The condition for external stability of these second-class equilibria to invasion by a new allele is that the appropriately averaged sex ratio near the equilibrium be moved closer to the even sex ratio than the average among the resident genotypes. However, invasion by a new chromosome depends on the recombination fraction in a way that appears to preclude general results about the evolutionary genetic stability of the even sex ratio in this situation.

    View details for Web of Science ID A1990CR82000081

    View details for PubMedID 2308959

  • SPATIAL SUBDIVISION OF POPULATIONS AND ESTIMATES OF GENETIC-VARIATION THEORETICAL POPULATION BIOLOGY CAVALLISFORZA, L. L., Feldman, M. W. 1990; 37 (1): 3-25

    Abstract

    Measures of variation in space are strongly affected by correlations between subdivisions used for sampling. Here we consider variation in gene frequencies across populations. Usually the variance of gene frequencies is standardized by dividing it by the mean gene frequency times one minus the mean (FST). Under the model of isolation by distance (usually called the "stepping stone" model), at the stationary state the correlation between the gene frequencies of two populations falls exponentially with the geographic distance between them. Using this model, we derive formulas for variances of blocks of populations of different sizes in one- and two-dimensional space and suggest that the theoretical results may be useful for understanding real observations, some examples of which are presented. We demonstrate how FST increases with the degree of subdivision among populations. We also show the effect of gaps between the sampled populations. Our results are valid, however, for traits other than gene frequencies, as long as their correlation with geographic distance falls exponentially. In the extension to 2-dimensional spaces, we present in closed form the distributions of distances between nodes of a lattice or of two lattices. These distributions might have applications in ecology.

    View details for Web of Science ID A1990CU08800001

    View details for PubMedID 2326767

  • MORE ON RECOMBINATION AND SELECTION IN THE MODIFIER THEORY OF SEX-RATIO DISTORTION THEORETICAL POPULATION BIOLOGY Feldman, M. W., Otto, S. P. 1989; 35 (2): 207-225

    Abstract

    G. Maffi and S.D. Jayakar suggested a model for the two-locus control of sex determination in the mosquito Aedes aegypti (1981, Theor. Pop. Biol. 19, 19-36). This model was extended to multiple alleles and analyzed in mathematical detail by S. Lessard (1987, Theor. Pop. Biol. 31, 339-358). The model supposes that males are "Mm" and females "mm" but the transmission from males is controlled by a second gene with alleles Ai. We show that in addition to the equilibrium in which mAi in females, MAi from males and mAi from males all have the same frequencies, a second class of polymorphic equilibria exists and can be stable. The former class was shown by Lessard to be stable for intermediate and/or loose linkage. The new class of equilibria may be stable for tight linkage under the conditions that preclude stability of the former. We also develop the theory of linkage modification from the neighborhood of the new equilibrium. Successful modifiers of recombination may either reduce or increase the recombination fraction with the outcome depending on the linkage of the modifier to the major genes.

    View details for Web of Science ID A1989U629800006

    View details for PubMedID 2727954

  • PLEIOTROPY AND PREADAPTATION IN THE EVOLUTION OF HUMAN LANGUAGE CAPACITY THEORETICAL POPULATION BIOLOGY Aoki, K., Feldman, M. W. 1989; 35 (2): 181-194

    Abstract

    The capacity for spoken language in the human is a genetic trait, but the information communicated by this means is to a large extent culturally determined. Using a gene-culture coevolutionary approach, we model the hypothesis that speech evolved as a channel for the communication of adaptive cultural traits from parent to offspring. The motivation for this paper is a condition obtained previously that initial increase of communication would require at least a two-fold advantage for the transmitted trait. Here, we show that under reasonable assumptions the invasion condition becomes less stringent. In Model 1, we assume that two adaptive cultural traits can be transmitted. A gene which permits communication of the second adaptive trait. In Model 2, we assume that a related function such as greater memory capacity is a prerequisite for speech, and that this function confers an advantage independent of its association with speech. In both models we assume haploid sexual genetics and a simple scheme of vertical transmission. The stability properties of all corner and edge equilibria of the models are analyzed. The two models taken together suggest a possible scenario for the initial stages of the evolution of speech.

    View details for Web of Science ID A1989U629800004

    View details for PubMedID 2727952

  • BEHAVIOR-DEPENDENT CONTEXTS FOR REPEATED PLAYS OF THE PRISONERS-DILEMMA JOURNAL OF CONFLICT RESOLUTION THOMAS, E. A., Feldman, M. W. 1988; 32 (4): 699-726
  • A GENERAL ASYMPTOTIC PROPERTY OF 2-LOCUS SELECTION MODELS THEORETICAL POPULATION BIOLOGY Lewontin, R. C., Feldman, M. W. 1988; 34 (2): 177-193

    Abstract

    It is shown that any two-locus, two-allele model of selection with constant fitnesses has at least one polymorphic equilibrium for which the linkage association measure, D, is arbitrarily close to zero for large enough recombination, R. As R----+/- infinity, D----0 in such a way that the product l = RD----a non-zero finite constant. There may be 1, 3, or 5 distinct asymptotic equilibria, depending upon fitness parameters.

    View details for Web of Science ID A1988Q567400006

    View details for PubMedID 3232120

  • THE EVOLUTION OF ALTRUISM BY KIN SELECTION - NEW PHENOMENA WITH STRONG SELECTION ETHOLOGY AND SOCIOBIOLOGY Mueller, L. D., Feldman, M. W. 1988; 9 (2-4): 223-239
  • KIN SELECTION AND THE EVOLUTION OF MONOGAMY SCIENCE Peck, J. R., Feldman, M. W. 1988; 240 (4859): 1672-1674

    Abstract

    A two-locus genetic model is studied in which one locus controls the tendency of individuals to act altruistically toward siblings and the other locus controls the mating habits of females. It is demonstrated that genetic variation at the altruism locus is often sufficient to induce an increase in the frequency of genes that cause females to produce all of their offspring with a single mate. This occurs because of nonrandom associations that develop between genes that cause altruism and those that affect female mating behavior. The results provide a new explanation for the evolution of monogamy, and they suggest a previously unexplored mechanism for the evolution of a variety of other behavioral traits as well.

    View details for Web of Science ID A1988N833700036

    View details for PubMedID 3381088

  • BEHAVIOR-DEPENDENT CONTEXTS FOR REPEATED PLAYS OF THE PRISONERS-DILEMMA .2. DYNAMIC ASPECTS OF THE EVOLUTION OF COOPERATION JOURNAL OF THEORETICAL BIOLOGY Feldman, M. W., THOMAS, E. A. 1987; 128 (3): 297-315

    Abstract

    Iterated Prisoner's Dilemma models are proposed in which, at any trial, the probability of staying in the game depends on the outcome of the previous trial. If a player's choice depends on its own play (cooperate or defect) at the previous trial, it becomes possible for cooperative strategies to increase when rare in a population of egoists. A dynamic analysis is used to demonstrate that stable polymorphisms may result, and may involve more strategies than just Tit-for-Tat and all-Defect. The tendency for clustering among like strategists to enhance their initial increase when rare is also explored dynamically.

    View details for PubMedID 3444341

  • TOWARD A THEORY FOR THE EVOLUTION OF CULTURAL COMMUNICATION - COEVOLUTION OF SIGNAL TRANSMISSION AND RECEPTION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Aoki, K., Feldman, M. W. 1987; 84 (20): 7164-7168

    Abstract

    A haploid sexual two-locus model of gene-culture coevolution is examined, in which a dichotomous phenotype subject to natural selection is transmitted vertically with probabilities dependent on the chosen parent's genotype and phenotype and the offspring's genotype. Stability conditions for the genetically monomorphic corner equilibria are obtained. In a specialization of this general model, one locus controls the transmission and the other controls the reception of adaptive information. The corner and edge equilibria of this doubly coevolutionary model are fully analyzed, and conditions for transmission and reception to coevolve are derived in terms of the efficiency of vertical transmission, the selective advantage gained from possessing the information, the costs of transmission and reception, and the recombination fraction between the two loci. Possible applications of the model are to the evolution of semantic alarm calls in vervet monkeys and the phonetic aspects of human language. In a third model with diploid genetics, we consider the initial increase of cultural transmission from a mutation-selection balance in which the adaptive phenotype is the consequence of a dominant gene at one locus. A second gene controls the transmission of the phenotype in such a way that a new mutant at this second locus permits learning of the adaptive phenotype from a parent who has it. This new mutant cannot increase when rare.

    View details for Web of Science ID A1987K504900043

    View details for PubMedID 3478689

  • A GENERAL REDUCTION PRINCIPLE FOR GENETIC MODIFIERS OF RECOMBINATION THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. W. 1986; 30 (3): 341-371

    View details for Web of Science ID A1986F274800003

    View details for PubMedID 3810506

  • MODIFIERS OF MUTATION-RATE - A GENERAL REDUCTION PRINCIPLE THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. W. 1986; 30 (1): 125-142

    Abstract

    A deterministic two-locus population genetic model with random mating is studied. The first locus, with two alleles, is subject to mutation and arbitrary viability selection. The second locus, with an arbitrary number of alleles, controls the mutation at the first locus. A class of viability-analogous Hardy-Weinberg equilibria is analyzed in which the selected gene and the modifier locus are in linkage equilibrium. It is shown that at these equilibria a reduction principle for the success of new mutation-modifying alleles is valid. A new allele at the modifier locus succeeds if its marginal average mutation rate is less than the mean mutation rate of the resident modifier allele evaluated at the equilibrium. Internal stability properties of these equilibria are also described.

    View details for Web of Science ID A1986D376900008

    View details for PubMedID 3750215

  • AN EVOLUTIONARY REDUCTION PRINCIPLE FOR GENETIC MODIFIERS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Feldman, M. W., Liberman, U. 1986; 83 (13): 4824-4827

    Abstract

    The joint evolution of major genes under viability selection and a modifier locus that controls recombination between the major genes, mutation at the major gene, or migration between two demes is studied. The modifying locus is selectively neutral and may have an arbitrary number of alleles. For each case a class of polymorphic equilibria exists in which the frequencies of the modifying alleles are those computed by assuming that the recombination, mutation, or migration rates were viabilities and in which the major and modifier loci are not statistically associated. These are called viability-analogous Hardy-Weinberg (VAHW) equilibria. A new allele introduced near these equilibria will enter the population if its marginal average rate of recombination, mutation, or migration (whichever applies) is less than the population average prior to its introduction. Stability properties of these VAHW equilibria are also reported.

    View details for Web of Science ID A1986C992000051

    View details for PubMedID 3460074

  • A NUMERICAL-SIMULATION OF THE ONE-LOCUS, MULTIPLE-ALLELE FERTILITY MODEL GENETICS Clark, A. G., Feldman, M. W. 1986; 113 (1): 161-176

    Abstract

    Numerical simulations were performed to determine the equilibrium behavior of the one-locus fertility model in which fitness is considered as a property of a pair of mating diploids. A series of patterns of "fertility matrices" were considered for a single locus with two to six alleles. From these simulations, 19 different statistics were collected that characterize, at equilibrium, the heterozygosity, the mean fitness and the fate of populations begun at the allele-frequency centroid. For more than one-half of the trajectories produced by random fertility matrices, there was a decrease in the mean fitness at some time on the way to equilibrium. The mean number of alleles maintained at equilibrium increased only slightly with matrix dimension. Despite the potential for fertility models to display multiple stable equilibria, random fertility models maintain fewer distinct stable points than do random one-locus viability models. Pleiotropic models were also considered with fertility and viability selection operating sequentially within each generation. Most of the equilibrium statistics (with the exception of mean fertility) for the pleiotropic model were intermediate between the corresponding random viability and fertility models.

    View details for Web of Science ID A1986C220200013

    View details for PubMedID 3710142

  • SELECTION FOR INCREASED MUTATION-RATES WITH FERTILITY DIFFERENCES BETWEEN MATINGS GENETICS Holsinger, K. E., Feldman, M. W., Altenberg, L. 1986; 112 (4): 909-922

    Abstract

    Previous studies of mutation modification have considered models in which selection is a result of viability differences that are sex symmetric. The results of a numerical study of a model in which selection is a result of fertility differences between mated pairs demonstrate that the type of selection to which a population is subject can have a significant impact on the evolution of various parameters of the genetic system. When the fertility of matings between individuals with different genotypes exceeds the fertility of at least some of the matings between individuals with the same genotype, selection may favor increased rates of mutation, in contrast to the results from all existing constant viability models with random mating and infinite population size. Increased mutation rates are most frequently favored when forward and back mutation occur at approximately equal rates and when the modifying locus is loosely linked to the selected locus. We present one example in which selection favors increased rates of mutation even though the selection scheme is reducible to one of differential viability between the sexes.

    View details for Web of Science ID A1986A549800013

    View details for PubMedID 3957011

    View details for PubMedCentralID PMC1202785

  • THE EVOLUTION OF HELPING-BEHAVIOR IN LARGE, RANDOMLY MIXED POPULATIONS AMERICAN NATURALIST Peck, J. R., Feldman, M. W. 1986; 127 (2): 209-221
  • GENE CULTURE COEVOLUTION - MODELS FOR THE EVOLUTION OF ALTRUISM WITH CULTURAL TRANSMISSION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Feldman, M. W., CAVALLISFORZA, L. L., Peck, J. R. 1985; 82 (17): 5814-5818

    Abstract

    Models of sexual haploids under kin selection are constructed. The trait of altruism is transmitted vertically from parent to child, but not in a strictly genetic manner. Two systems of altruism are considered: parent-to-offspring and sib-to-sib. In the former case it is shown that even when Hamilton's conditions for the success of genetically determined altruism are met, genes that increase the transmission of altruism may not invade the population. With sib-to-sib altruism, such genes will always increase initially.

    View details for Web of Science ID A1985AQM9400051

    View details for PubMedID 3862097

  • SELECTION IN COMPLEX GENETIC SYSTEMS .6. EQUILIBRIUM PROPERTIES OF 2 LOCUS SELECTION MODELS WITH PARTIAL SELFING THEORETICAL POPULATION BIOLOGY Holsinger, K. E., Feldman, M. W. 1985; 28 (1): 117-132

    Abstract

    The results of a combined analytical and numerical study of two locus selection models with partial selfing indicate that several commonly held opinions about the effects of partial self-fertilization do not hold in general. For example, the heterozygosity of a population may actually increase as the selfing rate is increased. Similarly, selection strong enough to guarantee a two locus polymorphism with complete selfing does not necessarily guarantee a two locus polymorphism with intermediate amounts of self-fertilization. The results presented here and a brief review of previously existing results indicate that the predictions of population genetic models based on the assumption of random mating will not be greatly altered by a small amount of self-fertilization, unless the loci involved are tightly linked. On the other hand, the results presented indicate that a very small amount of outcrossing may lead to marked differences from the expectation based on complete self-fertilization.

    View details for Web of Science ID A1985ARQ7900006

    View details for PubMedID 4060083

  • POPULATION GENETIC THEORY OF KIN SELECTION - A 2-LOCUS MODEL AMERICAN NATURALIST Mueller, L. D., Feldman, M. W. 1985; 125 (4): 535-549
  • A SYMMETRIC 2-LOCUS FERTILITY MODEL GENETICS Feldman, M. W., Liberman, U. 1985; 109 (1): 229-253

    Abstract

    A model in which selection is mediated by differential fertilities among the genotypes at two diallelic loci is proposed. Fertility depends only on the number of heterozygous loci participating in the mating. Classes analogous to symmetric equilibria in symmetric viability models are determined explicitly and shown to exhibit stability behavior very different from the viability results. Linkage equilibrium is shown to occur in a relatively asymmetric fashion and to overlap in stability with linkage disequilibrium. In many cases single-locus or two-locus polymorphism is shown to be stable simultaneously with chromosome fixation even under very tight linkage. It is suggested that historical effects may be of great significance in the evolution of systems in which fertility is the primary agent of natural selection.

    View details for Web of Science ID A1985TX92000015

    View details for PubMedID 3967817

  • A SYMMETRIC 2 LOCUS MODEL WITH VIABILITY AND FERTILITY SELECTION JOURNAL OF MATHEMATICAL BIOLOGY Liberman, U., Feldman, M. W. 1985; 22 (1): 31-60

    Abstract

    A two locus deterministic population genetic model is analysed. One locus is under viability selection, the other under fertility selection with both forms of selection completely symmetric. It is shown that linkage equilibrium may occur at two different equilibrium points. For a two-locus polymorphism to be stable, it is necessary that the viability locus be overdominant but not necessary that the fertility locus, considered separately, be able to support a stable polymorphism. The overlaps in stability are not as complex as under two locus symmetric fertilities, but considerably more complex than with symmetric viabilities. Extensions of the analysis for the central linkage equilibrium point with multiple viability and fertility loci are indicated.

    View details for Web of Science ID A1985AKY2000004

    View details for PubMedID 4020304

  • CULTURAL AND BIOLOGICAL EVOLUTIONARY PROCESSES - GENE CULTURE DISEQUILIBRIUM PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES Feldman, M. W., CAVALLISFORZA, L. L. 1984; 81 (5): 1604-1607

    Abstract

    The dynamics of the interaction between genetic and cultural transmission are studied by using a simple two-phenotype diallelic haploid genetic system. The value of an individual's phenotype is determined by cultural transmission from its parent or by a randomly chosen member of the parental population. In the absence of phenotypic selection, polymorphic equilibria of the gene and trait frequencies are obtained. The correlation between genotype and phenotype within or between populations depends on a quantity formally similar to linkage disequilibrium and is determined by a relationship among transmission coefficients analogous to a coefficient of epistasis. With natural selection on the phenotype and no mutation, only degenerate transmission rules allow polymorphic equilibria to be attained, and, in general, the genotype allowing the strongest transmission of the favored phenotype is successful.

    View details for Web of Science ID A1984SJ69300069

    View details for PubMedID 6584896

  • POPULATION GENETIC THEORY OF THE COST OF INBREEDING AMERICAN NATURALIST Feldman, M. W., Christiansen, F. B. 1984; 123 (5): 642-653
  • INITIAL INCREASE OF NEW MUTANTS AND SOME CONTINUITY PROPERTIES OF ESS IN 2-LOCUS SYSTEMS AMERICAN NATURALIST Eshel, I., Feldman, M. W. 1984; 124 (5): 631-640
  • Cultural evolution. Anthropology and cultural transmission. Nature Cavalli-Sforza, L., Feldman, M., DORNBUSCH, S., Chen, K. H. 1983; 304 (5922): 124-?

    View details for PubMedID 6866108

  • PARADOX OF THE EVOLUTION OF COMMUNICATION AND OF SOCIAL INTERACTIVITY PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES CAVALLISFORZA, L. L., Feldman, M. W. 1983; 80 (7): 2017-2021

    Abstract

    Communication between individuals of a species is likely to increase the capacity to acquire skills useful for survival and propagation and thus may confer important selective advantages. Since interaction occurs between two or more individuals, the selective process is frequency dependent, and the analysis shows that communication cannot initially increase at a reasonable rate when it is limited to random unrelated individuals, so that it is likely to abort for stochastic reasons. However, this bottleneck is removed if the communication process takes place in the nuclear family or among close relatives or if aggregation of communicators occurs because of assortative mating or meeting. Use of the individual conditional fitnesses we have introduced earlier permits an exact analysis. We show that, in general, the initial rate of increase can be geometric if and only if, in the class of selective models considered, the conditional probability of a communicator interacting with another contains a positive constant term. In our discussion of communication, cost factors for the act of communication have been omitted. However, the model has been generalized to include cooperativeness, and also altruism, or competition, by introducing costs. There is a close relationship among these situations, and the same considerations about the initial bottleneck and its resolution also extend to them. The models given here are for haploids but they extend to diploids and the conclusions are similar.

    View details for Web of Science ID A1983QJ91900050

    View details for PubMedID 6572958

  • LINKAGE MODIFICATION WITH MIXED RANDOM MATING AND SELFING - A NUMERICAL STUDY GENETICS Holsinger, K. E., Feldman, M. W. 1983; 103 (2): 323-333

    Abstract

    Although recombination cannot increase under conditions of random mating or complete selfing in regimes of constant selection, with mixed random mating and selfing, selection for increased recombination can occur. For some fitness regimes there may be selection for reduced recombination with both low and high degrees of selfing but selection for increased recombination with moderate degrees of selfing. With some fitness regimes there is a historical effect: depending on which equilibrium a population starts from, there may be selection for either increased or decreased recombination. In other cases the direction of selection may be determined by the present state of individuals within the population. If recombination is already fairly limited, there may be selection for further reduction. If recombination is already fairly frequent, there may be selection for increased recombination. For certain symmetric viability systems there may be an intermediate value of the recombination fraction between 0 and 0.5 toward which the population will evolve. Although it is not yet possible to classify precisely those fitness matrices that can exhibit selection for increased recombination, it does appear that selection for increased recombination can occur only if at least two of the double homozygotes are less fit than would be expected on the basis of a comparison of the fitnesses of the single and double heterozygotes on an additive scale.

    View details for Web of Science ID A1983PY84900012

    View details for PubMedID 6832583

    View details for PubMedCentralID PMC1219982

  • MODIFIERS OF MUTATION-RATE - EVOLUTIONARY OPTIMUM WITH COMPLETE SELFING PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES Holsinger, K. E., Feldman, M. W. 1983; 80 (21): 6732-6734

    Abstract

    It often has been assumed that, for infinite random mating populations in a constant environment, natural selection will favor genotypes at a neutral modifier locus that minimize the mutation rate. Mathematical modeling of this process confirms this assertion, independent of the selection regime. The same model under conditions of complete selfing can produce, under certain nondegenerate overdominance conditions, an optimum mutation rate below which increased mutation is favored and above which decreased mutation is favored. This occurs with unidirectional mutation models and a class of reversible mutation models with fitness overdominance. This is the first time that such a modifier optimum has been produced analytically for an infinite population in a constant environment.

    View details for Web of Science ID A1983RP12500064

    View details for PubMedID 16593388

    View details for PubMedCentralID PMC391245

  • PHYSIOLOGICAL-EFFECTS OF AN ALLOZYME POLYMORPHISM - GLUTAMATE PYRUVATE TRANSAMINASE AND RESPONSE TO HYPEROSMOTIC STRESS IN THE COPEPOD TIGRIOPUS-CALIFORNICUS BIOCHEMICAL GENETICS Burton, R. S., Feldman, M. W. 1983; 21 (3-4): 239-251

    Abstract

    In order to regulate cell volume during hyperosmotic stress, the intertidal copepod Tigriopus californicus, like other aquatic crustaceans, rapidly accumulates high levels of intracellular alanine, proline, and glycine. Glutamate-pyruvate transaminase (GPT; EC 2.6.1.2), which catalyzes the final step of alanine synthesis, is genetically polymorphic in T. californicus populations at Santa Cruz, California. Spectrophotometric studies of homogenates derived from a homozygous isofemale line of each of the two common GPT alleles indicated that the GPTF allozyme has a significantly higher specific activity than the GPTS allozyme. Under conditions of hyperosmotic stress, individual adult copepods of GPTF and GPTF/S genotypes accumulated alanine, but not glycine or proline, more rapidly than GPTS homozygotes. When young larvae were subjected to the same hyperosmotic conditions, GPTS larvae suffered a significantly higher mortality than GPTF or GPTF/S larvae. These results suggest that the biochemical differences among GPT allozymes result in specific physiological variation among GPT genotypes and that this physiological variation is manifested in differential genotypic survivorships under some naturally occurring environmental conditions.

    View details for Web of Science ID A1983QJ90200003

    View details for PubMedID 6860293

  • SELECTION IN COMPLEX GENETIC SYSTEMS .5. SOME PROPERTIES OF MIXED SELFING AND RANDOM MATING WITH 2 LOCI THEORETICAL POPULATION BIOLOGY Christiansen, F. B., Feldman, M. W. 1983; 23 (2): 257-272

    View details for Web of Science ID A1983QU75700008

    View details for PubMedID 6612635

  • CULTURAL VERSUS GENETIC ADAPTATION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES CAVALLISFORZA, L. L., Feldman, M. W. 1983; 80 (16): 4993-4996

    Abstract

    We analyze the problem of the competition between genetic and cultural adaptation, testing various types of cultural transmission models versus a genetic (haploid) transmission model. With a vertical (parent-to-child) plus an infectious (oblique) cultural transmission, genetic adaptation always prevails, although its relative increase may be slow and polymorphism may persist for some time. Only under very special conditions of cultural transmission may a permanent polymorphism in which the two types of adaptation are represented be reached. There may, however, be an overall evolutionary advantage to a flexible mechanism of cultural transmission that allows adaptation to new situations for which no genetic mutants are available.

    View details for Web of Science ID A1983RD40300026

    View details for PubMedID 6576371

  • ON SOME MODELS OF FERTILITY SELECTION GENETICS Feldman, M. W., Christiansen, F. B., Liberman, U. 1983; 105 (4): 1003-1010

    Abstract

    Additive, multiplicative and symmetric models of fertility controlled by one diallelic gene are studied. For the completely symmetric fertility system a complete equilibrium and local stability analysis is possible. Contrary to previous conjectures, asymmetric equilibria can be stable. Conditions are derived under which a multiplicative model can be regarded as equivalent to a symmetric fertility system.

    View details for Web of Science ID A1983RR69400015

    View details for PubMedID 17246176

  • ON THE EVOLUTION OF SEX DETERMINATION AND THE SEX-RATIO IN HAPLODIPLOID POPULATIONS THEORETICAL POPULATION BIOLOGY Eshel, I., Feldman, M. W. 1982; 21 (3): 440-450
  • THE EVOLUTION OF RECOMBINATION IN PERMANENT TRANSLOCATION HETEROZYGOTES THEORETICAL POPULATION BIOLOGY Holsinger, K. E., Feldman, M. W. 1982; 22 (2): 278-297
  • ON THE EVOLUTION OF FLUCTUATING SEGREGATION DISTORTION THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. W. 1982; 21 (3): 301-317
  • CHANGES IN FREE AMINO-ACID-CONCENTRATIONS DURING OSMOTIC RESPONSE IN THE INTER-TIDAL COPEPOD TIGRIOPUS-CALIFORNICUS COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY Burton, R. S., Feldman, M. W. 1982; 73 (3): 441-445
  • POPULATION GENETIC THEORY OF KIN SELECTION .2. THE MULTIPLICATIVE MODEL AMERICAN NATURALIST Uyenoyama, M. K., Feldman, M. 1982; 120 (5): 614-627
  • THEORY AND OBSERVATION IN CULTURAL TRANSMISSION SCIENCE CAVALLISFORZA, L. L., Feldman, M. W., Chen, K. H., DORNBUSCH, S. M. 1982; 218 (4567): 19-27

    Abstract

    Cultural phenomena may show considerable stability over time and space. Transmission mechanisms responsible for their maintenance are worthy of theoretical and empirical inquiry; they are complex and each possible pathway has different effects on evolutionary stability of traits, as can be shown theoretically. A survey designed to evaluate the importance of some components of cultural transmission on a variety of traits showed that religion and politics are mostly determined in the family, a mode of transmission which guarantees high evolutionary stability and maintenance of high variation between and within groups.

    View details for Web of Science ID A1982PH19500008

    View details for PubMedID 7123211

  • ON EVOLUTIONARY GENETIC STABILITY OF THE SEX-RATIO THEORETICAL POPULATION BIOLOGY Eshel, I., Feldman, M. W. 1982; 21 (3): 430-439
  • A STUDY OF CULTURAL TRANSMISSION IN TAIWAN HUMAN ECOLOGY Chen, K. H., CAVALLISFORZA, L. L., Feldman, M. W. 1982; 10 (3): 365-382
  • Linkage relationships among five enzyme-coding gene loci in the copepod Tigriopus californicus: a genetic confirmation of achiasmiatic meiosis. Biochemical genetics Burton, R. S., Feldman, M. W., Swisher, S. G. 1981; 19 (11-12): 1237-1245

    Abstract

    Linkage relationships among five polymorphic enzyme-coding gene loci in the marine copepod Tigriopus californicus have been determined using electrophoretic analysis of progeny from laboratory matings. Phosphoglucose isomerase (PGI; EC 5.3.1.9) was found to be tightly linked to glutamate-pyruvate transaminase (GPT; EC 2.6..1.2), with only one recombinant observed in 364 progeny; glutamate-oxaloacetate transaminase (GOT; EC 2.6.1.1) is linked to the PGI-GPT pair, with a recombination fraction of approximately 0.20 in male double heterozygotes. Phosphoglucomutase (PGM; EC 2.7.5.1) and an esterase (EST; EC 3.1.1.1) are not linked to the PGI, GPT, GOT grouping, which has been designated linkage group I. Reciprocal crosses have revealed that no recombination occurs in female T. californicus; this observation confirms a previous report that meiosis in female Tigriopus is achiasmatic.

    View details for PubMedID 6461328

  • POPULATION GENETICS OF TIGRIOPUS CALIFORNICUS. II. DIFFERENTIATION AMONG NEIGHBORING POPULATIONS. Evolution; international journal of organic evolution Burton, R. S., Feldman, M. W. 1981; 35 (6): 1192-1205

    View details for DOI 10.1111/j.1558-5646.1981.tb04989.x

    View details for PubMedID 28563405

  • A THEORETICAL AND NUMERICAL ASSESSMENT OF GENETIC-VARIABILITY GENETICS Karlin, S., Feldman, M. W. 1981; 97 (2): 475-493

    Abstract

    The equilibrium behavior of one-locus viability selection models is studied numerically. The selection schemes include randomly chosen viabilities, viabilities chosen to measure a hypothetical distance between the alleles making up the genotype and viabilities that obey various allelic dominance relations. From 3 to 8 alleles are considered. Among the key conclusions are (1) equilibria that are most polymorphic do not usually have the highest mean fitness, (2) the more structure there is in the choice of the viability model, the greater is the level of polymorphism at equilibrium, and (3) for the numbers of alleles chosen here, the equilibrium reached by iteration from the centroid of the allele frequency simplex is the best predictor of the equilibrium attainable from randomly chosen starting vectors. Preliminary evidence shows that this is not the case for 16 alleles.

    View details for Web of Science ID A1981MA93500015

    View details for PubMedID 17249079

  • A SINGLE LOCUS MODEL OF SELECTION IN PERMANENT TRANSLOCATION HETEROZYGOTES THEORETICAL POPULATION BIOLOGY Holsinger, K. E., Feldman, M. W. 1981; 20 (2): 218-240
  • POPULATION GENETIC THEORY OF KIN SELECTION - MULTIPLE ALLELES AT ONE LOCUS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES Uyenoyama, M. K., Feldman, M. W., Mueller, L. D. 1981; 78 (8): 5036-5040

    Abstract

    Exact population genetic models of one-locus sib-to-sib kin selection with an arbitrary number of alleles are studied. First, a natural additive scaling is established for the genotypic value associated with probabilities of performance of altruism. Two classes of polymorphic equilibria are possible, one corresponding to the usual one-locus viability equilibria and the other reflecting the kin-selection assumptions of the model. At both, the covariance between additive genotypic value and genotypic fitness vanish. Further, the sign of this covariance determines the fate of rare alleles introduced near the first class of equilibria. In addition, the covariance explains the differences between Hamilton's rule, which results from Hardy-Weinberg assumptions, and exact initial increase conditions.

    View details for Web of Science ID A1981MG53400078

    View details for PubMedID 16593074

  • ON RELATEDNESS AND ADAPTIVE TOPOGRAPHY IN KIN SELECTION THEORETICAL POPULATION BIOLOGY Uyenoyama, M. K., Feldman, M. W. 1981; 19 (1): 87-123
  • LINKAGE RELATIONSHIPS AMONG 5 ENZYME-CODING GENE LOCI IN THE COPEPOD TIGRIOPUS-CALIFORNICUS - A GENETIC CONFIRMATION OF ACHIASMATIC MEIOSIS BIOCHEMICAL GENETICS Burton, R. S., Feldman, M. W., Swisher, S. G. 1981; 19 (11-1): 1237-1245
  • MODELS OF SPOUSE INFLUENCE AND THEIR APPLICATION TO SMOKING-BEHAVIOR SOCIAL BIOLOGY Price, R. A., Chen, K. H., CAVALLISFORZA, L. L., Feldman, M. W. 1981; 28 (1-2): 14-29

    View details for Web of Science ID A1981PH76000002

    View details for PubMedID 7348442

  • POPULATION-GENETICS OF TIGRIOPUS-CALIFORNICUS .2. DIFFERENTIATION AMONG NEIGHBORING POPULATIONS EVOLUTION Burton, R. S., Feldman, M. W. 1981; 35 (6): 1192-1205
  • DISEQUILIBRIUM BETWEEN LINKED INVERSIONS - AN ALTERNATIVE HYPOTHESIS HEREDITY Clark, A. G., Feldman, M. W. 1981; 46 (JUN): 379-390
  • THE ESTIMATION OF EPISTASIS IN COMPONENTS OF FITNESS IN EXPERIMENTAL POPULATIONS OF DROSOPHILA-MELANOGASTER .2. ASSESSMENT OF MEIOTIC DRIVE, VIABILITY, FECUNDITY AND SEXUAL SELECTION HEREDITY Clark, A. G., Feldman, M. W. 1981; 46 (JUN): 347-377
  • THE ESTIMATION OF EPISTASIS IN COMPONENTS OF FITNESS IN EXPERIMENTAL POPULATIONS OF DROSOPHILA-MELANOGASTER .1. A 2 STAGE MAXIMUM-LIKELIHOOD MODEL HEREDITY Clark, A. G., Feldman, M. W., Christiansen, F. B. 1981; 46 (JUN): 321-346
  • ASSORTATIVE MATING, SELECTION AND MUTATION MODELS FOR CONTINUOUS VARIATION - REPLY THEORETICAL POPULATION BIOLOGY Feldman, M. W., CAVALLISFORZA, L. L. 1981; 19 (3): 370-377
  • Cultural transmission and evolution: a quantitative approach. Monographs in population biology Cavalli-Sforza, L. L., Feldman, M. W. 1981; 16: 1-388

    View details for PubMedID 7300842

  • DENSITY-DEPENDENT FERTILITY SELECTION IN EXPERIMENTAL POPULATIONS OF DROSOPHILA-MELANOGASTER GENETICS Clark, A. G., Feldman, M. W. 1981; 98 (4): 849-869

    Abstract

    The effects of larval density on components of fertility fitness were investigated with two mutant lines of Drosophila melanogaster. The differences in adult body weight, wing length, larval survivorship and development time verified that flies reared at high density were resource limited. Experimental results indicate that: (1) relative fecundities of both sexes show density-dependent effects, (2) there is a strong density effect on male and female mating success, and (3) in general, there is a reduction in fecundity differences between genotypes at high density. These results imply that it may be important to consider fertility in models of density-dependent natural selection.

    View details for Web of Science ID A1981MX82400012

    View details for PubMedID 17249109

  • FURTHER REMARKS ON DARWINIAN SELECTION AND ALTRUISM THEORETICAL POPULATION BIOLOGY Feldman, M. W., CAVALLISFORZA, L. L. 1981; 19 (2): 251-260
  • EVOLUTION OF RECOMBINATION IN A CONSTANT ENVIRONMENT PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES Feldman, M. W., Christiansen, F. B., Brooks, L. D. 1980; 77 (8): 4838-4841

    Abstract

    The theory of evolution at a selectively neutral locus that controls the recombination between two major loci that are under selection is studied. If the major loci are at a stable equilibrium in linkage disequilibrium under selection and recombination, then a mutation at the modifier locus will increase in frequency when rare if and only if it decreases the recombination fraction. If the major loci are in disequilibrium at a balance between selection against deleterious alleles and mutation towards them, then two new phenomena are observed. First, a recombination increasing mutation will succeed if the disequilibrium is negative and the modifier is sufficiently tightly linked to the major loci. Second, depending on the strength of selection, even if the disequilibrium is negative, recombination reduction may occur for looser linkage between the major and modifier loci.

    View details for Web of Science ID A1980KG46700092

    View details for PubMedID 16592864

  • ON THE EVOLUTIONARY SIGNIFICANCE OF MENDELS RATIOS THEORETICAL POPULATION BIOLOGY Liberman, U., Feldman, M. W. 1980; 17 (1): 1-15

    View details for Web of Science ID A1980JM20600001

    View details for PubMedID 7404430

  • THEORIES OF KIN AND GROUP SELECTION - A POPULATION-GENETICS PERSPECTIVE THEORETICAL POPULATION BIOLOGY UYENOYAMA, M., Feldman, M. W. 1980; 17 (3): 380-414

    View details for Web of Science ID A1980KG14000007

    View details for PubMedID 7434256

  • EXPERIMENTAL AND THEORETICAL-ANALYSIS OF THE SEX-RATIO POLYMORPHISM IN DROSOPHILA-PSEUDOOBSCURA GENETICS Curtsinger, J. W., Feldman, M. W. 1980; 94 (2): 445-466

    Abstract

    The Sex-ratio chromosome (SR) is a widespread, multiply inverted rearrangement of the X chromosome present in several species of Drosophila. Male carriers transmit mostly X-bearing sperm. In the absence of strong counteracting selection, SR is expected to increase rapidly to fixation, causing extinction. The present study incorporates a selection-components analysis of SR in laboratory populations, using the closely linked Esterase-5 locus as a marker. Estimated fitnesses show directional viability selection against SR in both males and females, heterosis for fertility and no significant effects on virility, the male adult component of fitness. Estimated fitnesses satisfy conditions for protected polymorphism and accurately predict gene-frequency trajectories in experimental populations. A model of SR gene-frequency evolution is developed, which incorporates sex-linkage, meiotic drive, viability, fertility and virility selecton. We show that conditions for protected polymorphisms are not unduly restrictive and that differential fitness among males is not sufficient for protected polymorphism, irrespective of the degree of meiotic drive.

    View details for Web of Science ID A1980JX23500012

    View details for PubMedID 17249004

  • ASPECTS OF VARIANCE AND COVARIANCE ANALYSIS WITH CULTURAL INHERITANCE THEORETICAL POPULATION BIOLOGY Feldman, M. W., CAVALLISFORZA, L. L. 1979; 15 (3): 276-307

    View details for Web of Science ID A1979HN07600001

    View details for PubMedID 515973

  • EVOLUTIONARY EFFECTS OF CONTAGIOUS AND FAMILIAL TRANSMISSION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA UYENOYAMA, M., Feldman, M. W., CAVALLISFORZA, L. L. 1979; 76 (1): 420-424

    Abstract

    Two models involving non-Mendelian transmission of a discrete valued trait through within- and across-generation contagion are proposed in an investigation of the joint evolution of phenotype and genotype. A single locus with two alleles determines susceptibility to contagion. The incorporation of within-generation contagious transmission extends the parameter ranges allowing phenotypic polymorphism and introduces a new phenotypic equilibrium configuration. The latter is characterized by a threshold in the initial value of the trait which determines whether the trait can increase. Phenotypic evolution is accelerated by within-generation contagion, but the rate of genetic evolution is retarded relative to that under uniparental transmission across generations. The second model studied allows the trait to be acquired, at genotype-dependent rates, even if the transmitting parent does not have the trait. Both the pattern of phenotypic transmission and the selection on the trait influence the course of evolution. Some important aspects of the structure of the one locus-two allele model are shown to be preserved with more alleles. At equilibrium, the leading eigenvalue of the transmission-selection matrix assumes the role of genotypic fitness.

    View details for Web of Science ID A1979GF88500090

    View details for PubMedID 284358

  • POPULATION-GENETICS OF TIGRIOPUS-CALIFORNICUS (COPEPODA, HARPACTICOIDA) .1. POPULATION-STRUCTURE ALONG THE CENTRAL CALIFORNIA COAST MARINE ECOLOGY PROGRESS SERIES Burton, R. S., Feldman, M. W., Curtsinger, J. W. 1979; 1 (1): 29-39
  • On hereditary transmission in diseases of complex etiology. Progress in clinical and biological research Feldman, M. W., Cavalli-Sforza, L. L. 1979; 32: 203-227

    View details for PubMedID 523470

  • EVOLUTION OF CONTINUOUS VARIATION .3. JOINT TRANSMISSION OF GENOTYPE, PHENOTYPE AND ENVIRONMENT GENETICS CAVALLISFORZA, L. L., Feldman, M. W. 1978; 90 (2): 391-425

    Abstract

    Evolutionary models of continuous traits are developed. The models are based on the ideas that: (1) the phenotype is the result of the interaction between genotype and environment; (2) the phenotype is the object of natural selection; (3) not only the genotype but also environmental variables and even phenotypes can be directly transmitted. The phenotype of an offspring at birth is a linear combination of its genotypic value, the phenotypic values of its parents, and their environmental values, all measured on the phenotypic scale. The genetic effects are additive polygenic, and a mutation contribution to the within family variance is admitted.-The values of the offspring phenotype and environment before selection are each linear combinations of these values at birth, the coefficients defining what we call "development." Selection is mostly stabilizing of the Gaussian type, but directional selection is introduced using a Gaussian fitness function with a large variance and a mean far from the current population.-Assortative mating for both phenotype and environment are considered. The analysis in all cases is made by iteration of the means, variances and covariances of the trivariate random variable (genotype, phenotype, environment) whose changes over time completely specify the evolution. In most cases numerical methods are used. The problems of estimating the relative roles of each of the variates in the parents in determining the variates in the offspring are discussed. The major results concern the relative magnitudes of the variances and correlations of the three variates, genotype, phenotype and environment, in a variety of selective, developmental and assorting situations with complex transmission in which G-(genetic), F-(phenotypic), E-(environment) inheritance mechanisms operate jointly. The transmission rules and development patterns (i.e., interactions between phenotype and environment during development) are of major importance in determining qualitative features of the equilibrium distribution.

    View details for Web of Science ID A1978FV72000013

    View details for PubMedID 17248869

  • REPLICATED COLLECTION OF SITE SURFACES AMERICAN ANTIQUITY Ammerman, A. J., Feldman, M. W. 1978; 43 (4): 734-740
  • GENETICS OF SEX-RATIO DISTORTION BY CYTOPLASMIC INFECTION UNDER MATERNAL AND CONTAGIOUS TRANSMISSION - EPIDEMIOLOGICAL-STUDY THEORETICAL POPULATION BIOLOGY Uyenoyama, M. K., Feldman, M. W. 1978; 14 (3): 471-497

    View details for Web of Science ID A1978GL07800010

    View details for PubMedID 751271

  • SIMULTANEOUS STABILITY OF D EQUAL-TO 0 AND D NOT-EQUAL-TO 0 FOR MULTIPLICATIVE VIABILITIES AT 2 LOCI GENETICS Karlin, S., Feldman, M. W. 1978; 90 (4): 813-825

    Abstract

    The two-locus, two-allele multiplicative viability model is investigated. It is shown that the well-known region of recombination values for which D = 0 is locally stable does not preclude the local stability of an equilibrium with D not equal 0. This is shown numerically and is true for every case investigated in which both loci are overdominant and the viabilities not symmetric.

    View details for Web of Science ID A1978GB78600012

    View details for PubMedID 17248876

  • TOWARDS A THEORY OF CULTURAL EVOLUTION INTERDISCIPLINARY SCIENCE REVIEWS CAVALLISFORZA, L. L., Feldman, M. W. 1978; 3 (2): 99-107
  • DARWINIAN SELECTION AND ALTRUISM THEORETICAL POPULATION BIOLOGY CAVALLISFORZA, L. L., Feldman, M. W. 1978; 14 (2): 268-280

    View details for Web of Science ID A1978GA18900007

    View details for PubMedID 746492

  • A comparison of HLA data of the North American black with African black and North American caucasoid populations. Tissue antigens Payne, R., Feldman, M., Cann, H., Bodmer, J. G. 1977; 9 (3): 135-147

    Abstract

    For purposes of genetic comparison, the available HLA data on United States and African Black, together with United States Caucasoid populations, are summarized. Antigen frequencies and pairwise linkage disequilibria are presented for the HLA-A, -B and -C loci in Black populations typed for the 1975 Histocompatibility Testing Workshop. The Black population samples comprise 356 North American Blacks and 411 African Blacks of whom 222 were Bantu. These are compared with a sample of 503 American Caucasoids. All significant linkage disequilibria between the A and B loci found in North American Blacks were also present in the North American Caucasoids. Between the B and C loci, Bw35 and Cw4 were in strong linkage disequilibrium in all groups. Significantly stron association between the A and C loci (Aw28 with Cw3) were observed only in the African Blacks. There were unique disequilibria both in the American Caucasoids and African Blacks. Although the frequencies of many antigens in U.S. Blacks lie between those in Africans and U.S. Caucasoids, there are exceptions such as Aw33, Bw35, Cw4.

    View details for PubMedID 67653

  • EVOLUTION OF CONTINUOUS VARIATION .2. COMPLEX TRANSMISSION AND ASSORTATIVE MATING THEORETICAL POPULATION BIOLOGY Feldman, M. W., CAVALLISFORZA, L. L. 1977; 11 (2): 161-181
  • 2 LOCI WITH 2 ALLELES - LINKAGE EQUILIBRIUM AND LINKAGE DISEQUILIBRIUM CAN BE SIMULTANEOUSLY STABLE THEORETICAL POPULATION BIOLOGY Franklin, I. R., Feldman, M. W. 1977; 12 (1): 95-113

    View details for Web of Science ID A1977DV55900007

    View details for PubMedID 918875

  • COMPARISON OF HLA DATA OF NORTH-AMERICAN BLACK WITH AFRICAN BLACK AND NORTH-AMERICAN CAUCASOID POPULATIONS TISSUE ANTIGENS Payne, R., Feldman, M., Cann, H., Bodmer, J. G., Biegel, A., Duquesnoy, R., Perkins, H., Rodey, G., Shaw, J. F., Stastny, P., Ward, F. E. 1977; 9 (3): 135-147
  • CULTURAL AND BIOLOGICAL EVOLUTIONARY PROCESSES, SELECTION FOR A TRAIT UNDER COMPLEX TRANSMISSION THEORETICAL POPULATION BIOLOGY Feldman, M. W., CAVALLISFORZA, L. L. 1976; 9 (2): 238-259

    View details for Web of Science ID A1976BU02400008

    View details for PubMedID 1273802

  • POPULATION-GENETICS OF MODIFIERS OF MEIOTIC DRIVE .3. EQUILIBRIUM-ANALYSIS OF A GENERAL MODEL FOR GENETIC-CONTROL OF SEGREGATION DISTORTION THEORETICAL POPULATION BIOLOGY Thomson, G. J., Feldman, M. W. 1976; 10 (1): 10-25

    View details for Web of Science ID A1976CH12600002

    View details for PubMedID 973199

  • EVOLUTION OF CONTINUOUS VARIATION - DIRECT APPROACH THROUGH JOINT DISTRIBUTION OF GENOTYPES AND PHENOTYPES .1. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA CAVALLISFORZA, L. L., Feldman, M. W. 1976; 73 (5): 1689-1692

    Abstract

    The evolutionary dynamics of the joint distribution of genotypes and phenotypes is studied. The model, originally devised to study the joint effects of Mendelian and other types of transmissions, provides results of interest also to the theory of direct Mendelian transmission with natural selection. Assuming bivariate normal distributions, it is shown that in the latter case genotypic and phenotypic means and variances, and genotype-phenotype correlation can be expressed recursively as functions of the parameters for the selection, environmental, and mutation variance. Equilibria and rates of approach for these moments are calculated. It is also proved that in the presence of selection the heritability,defined as the ratio of expected genotypic to expected phenotypic variance after selection, is greater than that before selection by a predictable amount and that it can be greater than unity.

    View details for Web of Science ID A1976BS77400071

    View details for PubMedID 1064041

  • SPECIES PACKING AND PREDATION PRESSURE ECOLOGY Roughgarden, J., Feldman, M. 1975; 56 (2): 489-492
  • SELECTION IN COMPLEX GENETIC SYSTEMS .4. MULTIPLE ALLELES AND INTERACTIONS BETWEEN 2 LOCI JOURNAL OF MATHEMATICAL BIOLOGY Christiansen, F. B., Feldman, M. W. 1975; 2 (2): 179-204
  • POPULATION GENETICS OF MODIFIERS OF MEIOTIC DRIVE .4. EVOLUTION OF SEX-RATIO DISTORTION THEORETICAL POPULATION BIOLOGY Thomson, G. J., Feldman, M. W. 1975; 8 (2): 202-211

    View details for Web of Science ID A1975AX21600005

    View details for PubMedID 1198352

  • SUBDIVIDED POPULATIONS - REVIEW OF ONE-LOCUS AND 2-LOCUS DETERMINISTIC THEORY THEORETICAL POPULATION BIOLOGY Christiansen, F. B., Feldman, M. W. 1975; 7 (1): 13-38

    View details for Web of Science ID A1975V784500002

    View details for PubMedID 1129715

  • MODELS FOR CULTURAL INHERITANCE - GENERAL LINEAR-MODEL ANNALS OF HUMAN BIOLOGY Feldman, M. W., CAVALLISFORZA, L. L. 1975; 2 (3): 215-226

    Abstract

    A theory of cultural evolution is proposed based on a general linear mode of cultural transmission. The trait of an individual is assumed to depend on the values of the same trait in other individuals of the same, the previous or earlier generation. The transmission matrix W has as its elements the proportional contributions of each individual (i) of one generation to each individual (j) of another. In addition, there is random variation (copy error or innovation) for each individual. Means and variances of a group of N individuals change with time and will stabilize asymptotically if the matrix W is irreducible and aperiodic. The rate of convergence is geometric and is governed by the largest non-unit eigenvalue of W. Groups fragment and evolve independently if W is reducible. The means of independent groups vary at random at a predicted rate, a phenomenon termed "random cultural drift". Variances within a group tend to be small, assuming cultural homogeneity. Transmission matrices of the teacher/leader type, and of parental type have been specifically considered, as well as social hierarchies. Various limitations, extensions, and some chances of application are discussed.

    View details for Web of Science ID A1975AF95300001

    View details for PubMedID 16431675

  • POPULATIONS STATIONARY DISTRIBUTION AND CHANCE OF EXTINCTION IN A STOCHASTIC ENVIRONMENT WITH REMARKS ON THEORY OF SPECIES PACKING THEORETICAL POPULATION BIOLOGY Feldman, M. W., Roughgarden, J. 1975; 7 (2): 197-207

    View details for Web of Science ID A1975W295600005

    View details for PubMedID 1145503

  • HERITABILITY HANG-UP SCIENCE Feldman, M. W., Lewontin, R. C. 1975; 190 (4220): 1163-1168

    View details for Web of Science ID A1975AY85500008

    View details for PubMedID 1198102

  • SELECTION IN COMPLEX GENETIC SYSTEMS .3. EFFECT OF ALLELE MULTIPLICITY WITH 2 LOCI GENETICS Feldman, M. W., Lewontin, R. C., Franklin, I. R., Christiansen, F. B. 1975; 79 (2): 333-347

    Abstract

    A two-locus model with three alleles at one locus and two at the other is studied. The viability system is such that all double heterozygotes have fitness unity, all single heterozygotes have fitness w smaller than 1 and all double homozygotes have fitness w-2. The following are the major findings: 1. There are more stable equilibria for tight linkage than in the corresponding three-locus model, even though the number of chromosomes is lower. 2. The equilibria stable for tight linkage do not belong to a unique high complementarity class, as is the case for two alleles at each locus. Instead the strength of selection determines the structure of the equilibrium. 3. The increase in number of alleles seems to reduce the possible extent of association between the loci. 4. The measure of this association is not well defined, although we have suggested a statistically standard way of getting over this. 5. A mutation introduced while a population is in linkage disequilibrium may, per medium only of the change in number of alleles, destroy the linkage disequilibrium.

    View details for Web of Science ID A1975AB22300013

    View details for PubMedID 1132683

  • EFFECT OF POPULATION SUBDIVISION ON 2 LOCI WITHOUT SELECTION GENETICAL RESEARCH Feldman, M. W., Christiansen, F. B. 1974; 24 (2): 151-162

    View details for Web of Science ID A1974V776500004

    View details for PubMedID 4452480

  • POPULATION GENETICS OF MODIFIERS OF MEIOTIC DRIVE .2. LINKAGE MODIFICATION IN SEGREGATION DISTORTION SYSTEM THEORETICAL POPULATION BIOLOGY Thomson, G. J., Feldman, M. W. 1974; 5 (2): 155-162

    View details for Web of Science ID A1974S754200003

    View details for PubMedID 4207693

  • MAKING OF AN ASSEMBLAGE OF STONE TOOLS AMERICAN ANTIQUITY Ammerman, A. J., Feldman, M. W. 1974; 39 (4): 610-616
  • SELECTION IN COMPLEX GENETIC SYSTEMS .1. SYMMETRIC EQUILIBRIA OF 3-LOCUS SYMMETRIC VIABILITY MODEL GENETICS Feldman, M. W., Franklin, I., Thomson, G. J. 1974; 76 (1): 135-162

    Abstract

    The symmetric equilibria of the three-locus symmetric viability model are determined and their stability analyzed. For tight linkage there may be four stable equilibria, each characterized by having one pair of complementary chromosomes in high frequencies, with all others low. For looser linkage the only stable symmetric equilibrium is that with complete linkage equilibrium. For intermediate recombination values both types of equilibria may be stable. A new class of equilibria with all pairwise linkage disequilibria zero, but with third order linkage disequilibrium, has been discovered. It may be stable for tight linkage.

    View details for Web of Science ID A1974S325400012

    View details for PubMedID 4818262

  • Cultural versus biological inheritance: phenotypic transmission from parents to children. (A theory of the effect of parental phenotypes on children's phenotypes). American journal of human genetics Cavalli-Sforza, L. L., Feldman, M. W. 1973; 25 (6): 618-637

    View details for PubMedID 4797967

    View details for PubMedCentralID PMC1762580

  • SELECTION FOR LINKAGE MODIFICATION .2. RECOMBINATION BALANCE FOR NEUTRAL MODIFIERS GENETICS Feldman, M. W., Balkau, B. 1973; 74 (4): 713-726

    Abstract

    A stable polymorphic equilibrium may be established at a selectively-neutral gene locus which controls the extent of recombination between two other selected loci. The condition for the existence of the stable polymorphism is analogous to heterozygous advantage. The heterozygote at the modifying locus should produce a recombination fraction allowing the greatest linkage disequilibrium. In the models treated this has the effect of producing the highest mean fitness. The relationship of these findings to general problems of coadaptation is discussed.

    View details for Web of Science ID A1973R136700016

    View details for PubMedID 17248638

  • MODELS FOR CULTURAL INHERITANCE .1. GROUP MEAN AND WITHIN GROUP VARIATION THEORETICAL POPULATION BIOLOGY CAVALLIS, L., Feldman, M. W. 1973; 4 (1): 42-55
  • SELECTION FOR MIGRATION MODIFICATION GENETICS Balkau, B. J., Feldman, M. W. 1973; 74 (1): 171-174

    Abstract

    Simple models for the genetic control of the tendency to migrate are considered. It is shown that migration from a more favorable regime to a less favorable regime is selected against. The ramifications for general modifier theory are discussed.

    View details for Web of Science ID A1973Q085100012

    View details for PubMedID 17248608

    View details for PubMedCentralID PMC1212934

  • MATING SYSTEMS AND POPULATION STRUCTURE IN 2 CLOSELY RELATED SPECIES OF WHEAT GROUP .1. VARIATION BETWEEN AND WITHIN POPULATIONS HEREDITY Hillel, J., Feldman, M. W., Simchen, G. 1973; 30 (APR): 141-167
  • MATING SYSTEMS AND POPULATION STRUCTURE IN 2 CLOSELY RELATED SPECIES OF WHEAT GROUP .3. CHIASMA FREQUENCY AND POPULATION STRUCTURE HEREDITY Hillel, J., Feldman, M. W., Simchen, G. 1973; 31 (AUG): 1-9
  • The evolution of dominance: a direct approach through the theory of linkage and selection. Theoretical population biology Feldman, M. W., Karlin, S. 1971; 2 (4): 482-492

    View details for PubMedID 5170720

  • Linkage and selection: two locus symmetric viability model. Theoretical population biology Karlin, S., Feldman, M. W. 1970; 1 (1): 39-71

    View details for PubMedID 5527625

  • On the evolutionary effect of recombination. Theoretical population biology Eshel, I., Feldman, M. W. 1970; 1 (1): 88-100

    View details for PubMedID 5527627

  • CONVERGENCE TO EQUILIBRIUM OF 2 LOCUS ADDITIVE VIABILITY MODEL JOURNAL OF APPLIED PROBABILITY Karlin, S., Feldman, M. W. 1970; 7 (2): 262-?
  • LINKAGE AND SELECTION - NEW EQUILIBRIUM PROPERTIES OF 2-LOCUS SYMMETRIC VIABILITY MODEL PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Karlin, S., Feldman, M. W. 1969; 62 (1): 70-?

    Abstract

    In the two-locus symmetric viability model with recombination, conditions for the existence and stability of a new class of polymorphic equilibria are given. These "unsymmetric" equilibria, which exist for relatively loose linkage, can be explicitly obtained, in contrast to the previously known symmetric equilibria which are generally given by the solutions of a cubic equation. For sufficiently tight linkage, there is always at least one stable symmetric equilibrium. Seven is the precise maximum for the number of interior equilibria. The qualitative consequences of these results are briefly examined. In particular it is pointed out that since for some linkage values no stable polymorphic equilibria exist, there is no "overdominance theorem" comparable to the single-locus case.

    View details for Web of Science ID A1969C892200011

    View details for PubMedID 5253665

    View details for PubMedCentralID PMC285956

  • ANALYSIS OF MODELS WITH HOMOZYGOTEXHETEROZYGOTE MATINGS GENETICS Karlin, S., Feldman, M. W. 1968; 59 (1): 105-?

    View details for Web of Science ID A1968B291200011

    View details for PubMedID 5683636

    View details for PubMedCentralID PMC1211926

  • FURTHER ANALYSIS OF NEGATIVE ASSORTATIVE MATING GENETICS Karlin, S., Feldman, M. W. 1968; 59 (1): 117-?

    View details for Web of Science ID A1968B291200012

    View details for PubMedID 5683637

    View details for PubMedCentralID PMC1211928