I am a biological anthropologist with research interests in human ecology, demography and life history theory, and the ecology and evolutionary biology of infectious disease. A sampling of current projects includes: (1) human dimensions of primate retroviral transmission, (2) the impact of mobility and social contacts on the spillover and transmission of avian influenza, (3) the demography of residential mobility among Hadza hunter-gatherers, (4) fertility change, economic shocks, and reproductive decisions.

Academic Appointments

Professional Education

  • Post-Doc, University of Washington, Center for AIDS and STD, Center for Statistics and the Social Sciences, Center for Studies in Demography and Ecology (2003)
  • Ph.D., Harvard University, Anthropology (2000)

Current Research and Scholarly Interests

I am a biological anthropologist with primary research interests in evolutionary demography and life history theory. In addition these fundamental interests in the evolution of human life histories, I work at the intersection of disease ecology, the analysis of dynamical systems, and social network analysis. My work combines the formalisms of population biology, statistics, and social network analysis to address fundamental problems in biodemography, epidemiology, and human decision-making in variable environments.


  • Coupled Contagion, Behavior-Change, and the Dynamics of Pro- and Anti-Social Behavior During the COVID-19 Pandemic

    The current COVID-19 pandemic involves both tremendous risk and tremendous uncertainty about that risk, at unprecedented scales and across demographic and cultural contexts. The situation offers a unique and time-sensitive opportunity to study the transmission and spread of behavioral responses, even as the transmission and spread of the SARS-CoV2 virus occurs in tandem. We are studying the coupled contagion dynamics of COVID-19 and related behavioral responses such as hand-washing, mask-wearing, and social distancing. We are gathering longitudinal data from a probability sample of Americans in three waves. Our surveys assess risk-reduction behaviors, compliance with public-health mandates, and hypothesized predictors of response including trust in various institutions, social capital, and sources of news and information. We are developing mathematical and simulation-based models that jointly track the dynamics of virus transmission and change in behavior, which we will parameterize with data collected in our survey. These models may provide insights for improving public-health interventions, motivating compliance, and stemming the spread of misinformation regarding the epidemic.



  • Evolutionary Anthropology and Climate-Change Adaptation, Stanford

    The idea of adaptation, in which an organism or population become better suited to their environment, is used in a variety of disciplines. Drawing originally from evolutionary biology, the study of adaptation has been a central theme in biological anthropology and human ecology. More recently, the study of adaptation specific to the context of human responses to the negative impacts of climate change has become an important topic and most current research in the social sciences on the adaptation falls into this category. While there are clearly commonalities to the different uses of the concept of adaptation, there are also substantial differences. We describe these differences and suggest that the study of climate-change adaptation could benefit from a re-integration with more broad-based biological and evolutionary conceptions of human adaptation. This integration would allow us to bring to bear the substantial theoretical tools of evolutionary biology to understanding system features that promote or impede adaptation. The evolutionary perspective on adaptation focuses overwhelmingly on diversity, since it is diversity that drives adaptive evolution. This suggests a focus for climate-change adaptation on the sources of innovation and the population structures that nurture innovations and allow them to spread. Just as adaptation thrives on diversity, the spread of innovations is facilitated by diversity in social structure. Truly innovative ideas are likely to arise on the periphery of cohesive social groups and spread inward. The evolutionary perspective also suggests that we pay careful attention to correlated traits which can distort adaptive trajectories. Finally, we suggest that climate-change evolution could benefit from a broader study on ongoing adaptations of local groups to their dynamic environments, a process we refer to as "autochthonous adaptation."

    This is a multi-stranded and ongoing project with a wide swath of collaborators at numerous institutions.


    Bolivia, Namibia

  • The Most Rational People in the World

    This is a book project exploring rationality, uncertainty, and the evolution of human behavior. It takes as its launching point a paradox which has only recently become apparent. By almost any measure, Homo sapiens is a spectacularly successful species. From humble origins approximately two million years ago, humans have grown to a population that exceeds seven billion and have colonized – and come to dominate – nearly every terrestrial biome. This phenomenal growth suggests that, on average, our ancestors made very good decisions. Yet a surging tide of work from psychology and economics makes the argument that the decision-making software that our brains run is profoundly flawed — that we are, in a word, irrational. How is it possible that a species apparently so defective in its ability to generate sound decisions can be so spectacularly successful?



  • Predictive Intelligence and Pandemic Preparedness



  • Subsistence Risk-Management Networks, Stanford



  • Ebola Modeling: Behavior, Asymptomatic Infection, and Contacts

    The impact of unrecognized Ebola virus (EBOV) infection (asymptomatic and symptomatic) on transmission dynamics during the 2013–2016 West Africa Ebola outbreak is poorly understood. Individuals who had asymptomatic EBOV infection or unrecognized symptomatic Ebola virus disease (EVD) represent two groups who may have had different levels of exposure and rates of EBOV transmission. Increasingly protective behaviors to avoid contact with EVD cases may have resulted in lower levels of exposure, and these exposures may be associated with asymptomatic EBOV infection. On the other hand, individuals who had symptomatic EVD but were never diagnosed may be disproportionately important to transmission dynamics because some of these individuals were part of transmission chains leading to Ebola outbreaks in previously unaffected communities.

    In collaboration with researchers at UCSF, UCLA, Harvard, and Georgia State University, our research question focuses on understanding the drivers of EBOV transmission leading to epidemic decline. Competing hypotheses are centered around issues of preventive behaviors, health-seeking behaviors, saturation of transmission among contacts, and asymptomatic EBOV infection. Newly available, detailed serologic, social network, behavioral, ethnographic, and vaccination data from research collaborations in Liberia, Sierra Leone, and Democratic Republic of Congo will allow us to test competing hypotheses in the following aims: (1) Dynamical effects of unrecognized EBOV infection in social network structure, (2) Unrecognized symptomatic EVD cases, barriers to care, and preventive behaviors, and (3) Causes of asymptomatic EBOV infection. These findings have the potential to quantify what ended the Ebola pandemic and improve mathematical models. Mathematical modeling applications will improve forecasting during new outbreaks and inform ways to deliver vaccines to contacts, by ring vaccination or novel social network algorithms.


    Sierra Leone

  • Comparative Ethnographic Networks

    Using relational data gathered from a variety of field contexts (Uganda, Bangladesh, Namibia), we are investigating the properties of sampled social networks, with an eye toward infectious disease transmission dynamics. Topics include: scale-up to landscape-level networks from egocentric samples, missing data models, and integrating spatial and relational dependencies.




    • Mary-Ashley Hazel, School of Earth, Energy & Environmental Sciences
    • Elspeth Lianne Ready, School of Humanities and Sciences

2022-23 Courses

Stanford Advisees

All Publications

  • Effective climate change adaptation means supporting community autonomy NATURE CLIMATE CHANGE Pisor, A. C., Basurto, X., Douglass, K. G., Mach, K. J., Ready, E., Tylianakis, J. M., Hazel, A., Kline, M. A., Kramer, K. L., Lansing, J., Moritz, M., Smaldino, P. E., Thornton, T. F., Jones, J. 2022
  • End-to-end Bayesian analysis for summarizing sets of radiocarbon dates JOURNAL OF ARCHAEOLOGICAL SCIENCE Price, M., Capriles, J. M., Hoggarth, J. A., Bocinsky, R., Ebert, C. E., Jones, J. 2021; 135
  • Reparations for Black American descendants of persons enslaved in the U.S. and their potential impact on SARS-CoV-2 transmission. Social science & medicine (1982) Richardson, E. T., Malik, M. M., Darity, W. A., Mullen, A. K., Morse, M. E., Malik, M., Maybank, A., Bassett, M. T., Farmer, P. E., Worden, L., Jones, J. H. 2021: 113741


    BACKGROUND: In the United States, Black Americans are suffering from a significantly disproportionate incidence of COVID-19. Going beyond mere epidemiological tallying, the potential for racial-justice interventions, including reparations payments, to ameliorate these disparities has not been adequately explored.METHODS: We compared the COVID-19 time-varying Rt curves of relatively disparate polities in terms of social equity (South Korea vs. Louisiana). Next, we considered a range of reproductive ratios to back-calculate the transmission rates betaij for 4 cells of the simplified next-generation matrix (from which R0 is calculated for structured models) for the outbreak in Louisiana. Lastly, we considered the potential structural effects monetary payments as reparations for Black American descendants of persons enslaved in the U.S. would have had on pre-intervention betaij and consequently R0.RESULTS: Once their respective epidemics begin to propagate, Louisiana displays Rt values with an absolute difference of 1.3-2.5 compared to South Korea. It also takes Louisiana more than twice as long to bring Rt below 1. Reasoning through the consequences of increased equity via matrix transmission models, we demonstrate how the benefits of a successful reparations program (reflected in the ratio betabb/betaww) could reduce R0 by 31-68%.DISCUSSION: While there are compelling moral and historical arguments for racial-injustice interventions such as reparations, our study considers potential health benefits in the form of reduced SARS-CoV-2 transmission risk. A restitutive program targeted towards Black individuals would not only decrease COVID-19 risk for recipients of the wealth redistribution; the mitigating effects would also be distributed across racial groups, benefiting the population at large.

    View details for DOI 10.1016/j.socscimed.2021.113741

    View details for PubMedID 33640157

  • Gendered movement ecology and landscape use in Hadza hunter-gatherers. Nature human behaviour Wood, B. M., Harris, J. A., Raichlen, D. A., Pontzer, H., Sayre, K., Sancilio, A., Berbesque, C., Crittenden, A. N., Mabulla, A., McElreath, R., Cashdan, E., Jones, J. H. 2021


    Understanding how gendered economic roles structure space use is critical to evolutionary models of foraging behaviour, social organization and cognition. Here, we examine hunter-gatherer spatial behaviour on a very large scale, using GPS devices worn by Hadza foragers to record 2,078 person-days of movement. Theory in movement ecology suggests that the density and mobility of targeted foods should predict spatial behaviour and that strong gender differences should arise in a hunter-gatherer context. As predicted, we find that men walked further per day, explored more land, followed more sinuous paths and were more likely to be alone. These data are consistent with the ecology of male- and female-targeted foods and suggest that male landscape use is more navigationally challenging in this hunter-gatherer context. Comparisons of Hadza space use with space use data available for non-human primates suggest that the sexual division of labour likely co-evolved with increased sex differences in spatial behaviour and landscape use.

    View details for DOI 10.1038/s41562-020-01002-7

    View details for PubMedID 33398143

  • Fitness-Maximizers Employ Pessimistic Probability Weighting in Decisions Under Risk Evolutionary Human Sciences Price, M. H., Jones, J. H. 2020; 2

    View details for DOI 10.1017/ehs.2020.28

  • Want climate-change adaptation? Evolutionary theory can help. American journal of human biology : the official journal of the Human Biology Council Jones, J. H., Ready, E. n., Pisor, A. C. 2020: e23539


    The idea of adaptation, in which an organism or population becomes better suited to its environment, is used in a variety of disciplines. Originating in evolutionary biology, adaptation has been a central theme in biological anthropology and human ecology. More recently, the study of adaptation in the context of climate change has become an important topic of research in the social sciences. While there are clearly commonalities in the different uses of the concept of adaptation in these fields, there are also substantial differences. We describe these differences and suggest that the study of climate-change adaptation could benefit from a re-integration with biological and evolutionary conceptions of human adaptation. This integration would allow us to employ the substantial theoretical tools of evolutionary biology and anthropology to understand what promotes or impedes adaptation. The evolutionary perspective on adaptation focuses on diversity because diversity drives adaptive evolution. Population structures are also critical in facilitating or preventing adaptation to local environmental conditions. This suggests that climate-change adaptation should focus on the sources of innovation and social structures that nurture innovations and allow them to spread. Truly innovative ideas are likely to arise on the periphery of cohesive social groups and spread inward. The evolutionary perspective also suggests that we pay careful attention to correlated traits, which can distort adaptive trajectories, as well as to the importance of risk management in adaptations to variable or uncertain environments. Finally, we suggest that climate-change adaptation could benefit from a broader study of how local groups adapt to their dynamic environments, a process we call "autochthonous adaptation."

    View details for DOI 10.1002/ajhb.23539

    View details for PubMedID 33247621

  • Contact structure, mobility, environmental impact and behaviour: the importance of social forces to infectious disease dynamics and disease ecology PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Arthur, R. F., Gurley, E. S., Salje, H., Bloomfield, L. S., Jones, J. H. 2017; 372 (1719)


    Human factors, including contact structure, movement, impact on the environment and patterns of behaviour, can have significant influence on the emergence of novel infectious diseases and the transmission and amplification of established ones. As anthropogenic climate change alters natural systems and global economic forces drive land-use and land-cover change, it becomes increasingly important to understand both the ecological and social factors that impact infectious disease outcomes for human populations. While the field of disease ecology explicitly studies the ecological aspects of infectious disease transmission, the effects of the social context on zoonotic pathogen spillover and subsequent human-to-human transmission are comparatively neglected in the literature. The social sciences encompass a variety of disciplines and frameworks for understanding infectious diseases; however, here we focus on four primary areas of social systems that quantitatively and qualitatively contribute to infectious diseases as social-ecological systems. These areas are social mixing and structure, space and mobility, geography and environmental impact, and behaviour and behaviour change. Incorporation of these social factors requires empirical studies for parametrization, phenomena characterization and integrated theoretical modelling of social-ecological interactions. The social-ecological system that dictates infectious disease dynamics is a complex system rich in interacting variables with dynamically significant heterogeneous properties. Future discussions about infectious disease spillover and transmission in human populations need to address the social context that affects particular disease systems by identifying and measuring qualitatively important drivers.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.

    View details for DOI 10.1098/rstb.2016.0454

    View details for Web of Science ID 000397800300016

    View details for PubMedID 28289265

  • Measuring selective constraint on fertility in human life histories PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Jones, J. H., Tuljapurkar, S. 2015; 112 (29): 8982-8986


    Human life histories combine late age at first reproduction, long reproductive span, relatively high fertility, and substantial postreproductive survival. However, even among the most fecund populations, human fertility falls far below its theoretical maximum. The extent of parental care required for successful offspring recruitment and widespread fertility decline under proper economic conditions suggest that selection on fertility is constrained by trade-offs with recruitment. Here we measure the trade-offs between life history traits under selection by approximating the slope of the selective constraint curve on two traits at the observed values. Using a selection of populations that span human demographic space, we find that the substitution elasticity of fertility for infant survival shows age-related patterns, with minimum substitution elasticities ranging from 14 to 22 for the four populations. The age of this minimum occurs earlier in the high-mortality populations relative to generation time than it does in the low-mortality populations. The human curves are qualitatively similar to one of two comparable nonhuman primate age-specific substitution elasticity curves. The curve for rhesus macaques has a similar shape but is shifted down, meaning that the threshold for switching from investing in survival to fertility is lower at all ages. The magnitude of the substitution elasticities is similar between chimpanzees and humans but the shape is quite different, rising more slowly for a longer fraction of the chimpanzee life cycle. The steeply rising substitution elasticities with age in humans has clear implications for the evolution of reproductive senescence.

    View details for DOI 10.1073/pnas.1422037112

    View details for Web of Science ID 000358225100062

    View details for PubMedID 26150499

    View details for PubMedCentralID PMC4517261

  • The evolutionary dynamics of timing of maternal immunity: evaluating the role of age-specific mortality. Journal of evolutionary biology Metcalf, C. J., Jones, J. H. 2015


    If a female survives an infection, she can transfer antibodies against that particular pathogen to any future offspring she produces. The resulting protection of offspring for a period after their birth is termed maternal immunity. Because infection in newborns is associated with high mortality, the duration of this protection is expected to be under strong selection. Evolutionary modeling structured around a trade-off between fertility and duration of maternal immunity has indicated selection for longer duration of maternal immunity for hosts with longer life-spans. Here we use a new modeling framework to extend this analysis to consider characteristics of pathogens (and hosts) in further detail. Importantly, given the challenges in characterising trade-offs linked to immune function empirically, our model makes no assumptions about costs of longer-lasting maternal immunity. Rather, a key component of this analysis is variation in mortality over age. We found that the optimal duration of maternal immunity is shaped by the shifting balance of the burden of infection between young and old individuals. As age of infection depends on characteristics of both the host and the pathogen, both affect the evolution of duration of maternal immunity. Our analysis provides additional support for selection for longer duration of maternal immunity in long-lived hosts, even in the absence of explicit costs linked to duration of maternal immunity. Further, the scope of our results provides explanations for exceptions to the general correlation between duration of maternal immunity and life-span, as we found that both pathogen characteristics and trans-generational effects can lead to important shifts in fitness linked to maternal immunity. Finally, our analysis points to new directions for quantifying the trade-offs that drive the development of the immune system. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1111/jeb.12583

    View details for PubMedID 25611057

  • Resource Transfers and Human Life-History Evolution ANNUAL REVIEW OF ANTHROPOLOGY, VOL 44 Jones, J. H. 2015; 44: 513-531
  • The marginal valuation of fertility. Evolution and human behavior : official journal of the Human Behavior and Evolution Society Jones, J. H., Bird, R. B. 2014; 35 (1): 65-71


    Substantial theoretical and empirical evidence demonstrates that fertility entails economic, physiological, and demographic trade-offs. The existence of trade-offs suggests that fitness should be maximized by an intermediate level of fertility, but this hypothesis has not had much support in the human life-history literature. We suggest that the difficulty of finding intermediate optima may be a function of the way fitness is calculated. Evolutionary analyses of human behavior typically use lifetime reproductive success as their fitness criterion. This fitness measure implicitly assumes that women are indifferent to the timing of reproduction and that they are risk-neutral in their reproductive decision-making. In this paper, we offer an alternative, easily-calculated fitness measure that accounts for differences in reproductive timing and yields clear preferences in the face of risky reproductive decision-making. Using historical demographic data from a genealogically-detailed dataset from 19th century Utah, we show that this measure is highly concave with respect to reproductive effort. This result has three major implications: (1) if births are properly timed, a lower-fertility reproductive strategy can have the same fitness as a high-fertility strategy, (2) intermediate optima are far more likely using fitness measures that are strongly concave with respect to effort, (3) we expect mothers to have strong investment preferences with respect to the risk inherent in reproduction.

    View details for DOI 10.1016/j.evolhumbehav.2013.10.002

    View details for PubMedID 24778546

    View details for PubMedCentralID PMC4000044

  • 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


    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

  • Plague outbreaks in prairie dog populations explained by percolation thresholds of alternate host abundance PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Salkeld, D. J., Salathe, M., Stapp, P., Jones, J. H. 2010; 107 (32): 14247-14250


    Highly lethal pathogens (e.g., hantaviruses, hendra virus, anthrax, or plague) pose unique public-health problems, because they seem to periodically flare into outbreaks before disappearing into long quiescent phases. A key element to their possible control and eradication is being able to understand where they persist in the latent phase and how to identify the conditions that result in sporadic epidemics or epizootics. In American grasslands, plague, caused by Yersinia pestis, exemplifies this quiescent-outbreak pattern, because it sporadically erupts in epizootics that decimate prairie dog (Cynomys ludovicianus) colonies, yet the causes of outbreaks and mechanisms for interepizootic persistence of this disease are poorly understood. Using field data on prairie community ecology, flea behavior, and plague-transmission biology, we find that plague can persist in prairie-dog colonies for prolonged periods, because host movement is highly spatially constrained. The abundance of an alternate host for disease vectors, the grasshopper mouse (Onychomys leucogaster), drives plague outbreaks by increasing the connectivity of the prairie dog hosts and therefore, permitting percolation of the disease throughout the primary host population. These results offer an alternative perspective on plague's ecology (i.e., disease transmission exacerbated by alternative hosts) and may have ramifications for plague dynamics in Asia and Africa, where a single main host has traditionally been considered to drive Yersinia ecology. Furthermore, abundance thresholds of alternate hosts may be a key phenomenon determining outbreaks of disease in many multihost-disease systems.

    View details for DOI 10.1073/pnas.1002826107

    View details for Web of Science ID 000280767700050

    View details for PubMedID 20660742

    View details for PubMedCentralID PMC2922574

  • Dynamics and Control of Diseases in Networks with Community Structure PLOS COMPUTATIONAL BIOLOGY Salathe, M., Jones, J. H. 2010; 6 (4)


    The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.

    View details for DOI 10.1371/journal.pcbi.1000736

    View details for Web of Science ID 000278125300012

    View details for PubMedID 20386735

    View details for PubMedCentralID PMC2851561

  • Narrative as cultural attractor. The Behavioral and brain sciences Jones, J. H., Hilde-Jones, C. 2023; 46: e98


    By structuring information in a systematic relational framework, narratives are cultural attractors that are particularly well-suited for transmission. The relational structure of narrative is partly what communicates causality, but this structure also complicates both transmission and selection on cultural elements by introducing correlations among narrative elements and between different narratives. These correlations have implications for adaptation, complexity, and robustness.

    View details for DOI 10.1017/S0140525X22002667

    View details for PubMedID 37154117

  • Urban wild meat markets in Cameroon: Actors and motives (vol 160, 106060, 2022) WORLD DEVELOPMENT Randolph, S. G., Ingram, D. J., Curran, L. M., Jones, J., Durham, W. H. 2023; 162
  • Urban wild meat markets in Cameroon: Actors and motives WORLD DEVELOPMENT Randolph, S. G., Ingram, D. J., Curran, L. M., Jones, J., Durham, W. H. 2022; 160
  • Social Network Analysis of Ebola Virus Disease During the 2014 Outbreak in Sukudu, Sierra Leone. Open forum infectious diseases Hazel, A., Davidson, M. C., Rogers, A., Barrie, M. B., Freeman, A., Mbayoh, M., Kamara, M., Blumberg, S., Lietman, T. M., Rutherford, G. W., Jones, J. H., Porco, T. C., Richardson, E. T., Kelly, J. D. 2022; 9 (11): ofac593


    Transmission by unreported cases has been proposed as a reason for the 2013-2016 Ebola virus (EBOV) epidemic decline in West Africa, but studies that test this hypothesis are lacking. We examined a transmission chain within social networks in Sukudu village to assess spread and transmission burnout.Network data were collected in 2 phases: (1) serological and contact information from Ebola cases (n = 48, including unreported); and (2) interviews (n = 148), including Ebola survivors (n = 13), to identify key social interactions. Social links to the transmission chain were used to calculate cumulative incidence proportion as the number of EBOV-infected people in the network divided by total network size.The sample included 148 participants and 1522 contacts, comprising 10 social networks: 3 had strong links (>50% of cases) to the transmission chain: household sharing (largely kinship), leisure time, and talking about important things (both largely non-kin). Overall cumulative incidence for these networks was 37 of 311 (12%). Unreported cases did not have higher network centrality than reported cases.Although this study did not find evidence that explained epidemic decline in Sukudu, it excluded potential reasons (eg, unreported cases, herd immunity) and identified 3 social interactions in EBOV transmission.

    View details for DOI 10.1093/ofid/ofac593

    View details for PubMedID 36467298

    View details for PubMedCentralID PMC9709704

  • Simulating the effects of a highly pathogenic virus across rural, peri-urban, and urban Bangladesh poultry worker's social networks Harryman, I., Hazel, A., Jones, J. H. WILEY. 2022: 79-80
  • The Emergent Structure of Subsistence Risk-Management Networks Jones, J., Ready, E. WILEY. 2022: 92
  • How environmental uncertainty and correlated payoffs drive the evolution of social learning Turner, M. A., Moya, C., Smaldino, P. E., Jones, J. WILEY. 2022: 186-187
  • Long-term consequences of food insecurity among Ebola virus disease-affected households after the 2013–2016 epidemic in rural communities of Kono District, Sierra Leone: A qualitative study PLOS Global Public Health Djomaleu*, M. l., Rogers*, A. B., Barrie*, M. B., Rutherford, G. W., Weiser, S. D., Kelly, J. D. 2022

    View details for DOI 10.1093/ofid/ofac593

  • Opportunities and constraints in women's resource security amid climate change: A case study of arid-living Namibian agro-pastoralists. American journal of human biology : the official journal of the Human Biology Council Hazel, A., Meeks, G., Bharti, N., Jakurama, J., Matundu, J., Jones, J. H. 2021: e23633


    OBJECTIVE: We describe the composition and variation of women's resource strategies in an arid-living Southern African agro-pastoralist society to gain insights into adaptation to climate-change-induced increased aridity.METHODS: Using cross-sectional data from 210 women collected in 2009 across 28 agro-pastoralist villages in Kaokoveld Namibia, we conducted principal-component (PC) analysis of resource variables and constructed profiles of resource strategies from the major PCs. Next, we explored associations between key resource strategies and demographic measures and fitness proxies.RESULTS: The first two PCs accounted for 43% of women's overall resource variation. PC1 reflects women's ability to access market resources via livestock trading, while PC2 captured women's direct food access. We found that market strategies were more common among married women and less common among women who have experienced child mortality. Women with higher subsistence security were more likely to be from the OvaHimba tribe and had a higher risk of gonorrhea exposure. We also qualitatively explored drought-induced pressure on women's livestock. Finally, we show that sexual networks were attenuated during drought, indicating strain on social support.CONCLUSIONS: Our results highlight how agro-pastoralist women manage critical resources in unpredictable environments, and how resource strategies distribute among the women in our study. Goats as a commodity to obtain critical resources suggests that some women have flexibility during drought when gardens fail and cattle die. However, increased aridity and drought may eventually overwhelm husbandry practices in this region.

    View details for DOI 10.1002/ajhb.23633

    View details for PubMedID 34181282

  • Commentary on the life history special issue: The behavioral sciences need to engage more deeply in life history theory EVOLUTION AND HUMAN BEHAVIOR Jones, J., Promislow, D. L. 2021; 42 (3): 284-286
  • How can evolutionary and biological anthropologists engage broader audiences? American journal of human biology : the official journal of the Human Biology Council Jones, J. H., Pisor, A. C., Douglass, K. G., Bird, R. B., Ready, E., Hazel, A., Hackman, J., Kramer, K. L., Kohler, T. A., Pontzer, H., Towner, M. C. 2021: e23592


    OBJECTIVES: With our diverse training, theoretical and empirical toolkits, and rich data, evolutionary and biological anthropologists (EBAs) have much to contribute to research and policy decisions about climate change and other pressing social issues. However, we remain largely absent from these critical, ongoing efforts. Here, we draw on the literature and our own experiences to make recommendations for how EBAs can engage broader audiences, including the communities with whom we collaborate, a more diverse population of students, researchers in other disciplines and the development sector, policymakers, and the general public. These recommendations include: (1) playing to our strength in longitudinal, place-based research, (2) collaborating more broadly, (3) engaging in greater public communication of science, (4) aligning our work with open-science practices to the extent possible, and (5) increasing diversity of our field and teams through intentional action, outreach, training, and mentorship.CONCLUSIONS: We EBAs need to put ourselves out there: research and engagement are complementary, not opposed to each other. With the resources and workable examples we provide here, we hope to spur more EBAs to action.

    View details for DOI 10.1002/ajhb.23592

    View details for PubMedID 33751710

  • Time Preferences, Risk Preferences, and Climate Change Adaptation Jones, J. WILEY. 2021: 52
  • Do people use long-distance relationships to respond to climate variability? Pisor, A. C., Jones, J. WILEY. 2021: 85
  • 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


    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

  • Human adaptation to climate change: An introduction to the special issue. American journal of human biology : the official journal of the Human Biology Council Pisor, A. C., Jones, J. H. 2020: e23530


    OBJECTIVES: Despite our focus on adaptation and human responses to climate, evolutionary and biological anthropologists (EBAs) are largely absent from conversations about contemporary "climate-change adaptation," a term popular in other disciplines, the development world, and related policy decisions. EBAs are missing a big opportunity to contribute to impactful, time-sensitive applied work: we have extensive theoretical and empirical knowledge pertinent to conversations about climate-change adaptation and to helping support communities as they cope. This special issue takes a tour of EBA contributions to our understanding of climate-change adaptation, from data on past and contemporary human communities to theoretically informed predictions about how individuals and communities will respond to climate change now and in the future. First, however, we must establish what we mean by "climate change" and "adaptation," along with other terms commonly used by EBAs; review what EBAs know about adaptation and about human responses to climate change; and identify just a few topics EBAs study that are pertinent to ongoing conversations about climate-change adaptation. In this article, we do just that.CONCLUSION: From our work on energy use to our work on demography, subsistence, social networks, and the salience of climate change to local communities, EBAs have an abundance of data and theoretical insights to help inform responses to contemporary climate change. We need to better reach the climate community and general public with our contributions.

    View details for DOI 10.1002/ajhb.23530

    View details for PubMedID 33230887

  • Do people manage climate risk through long-distance relationships? American journal of human biology : the official journal of the Human Biology Council Pisor, A. C., Jones, J. H. 2020: e23525


    OBJECTIVES: Long-distance social relationships have been a feature of human evolutionary history; evidence from the paleoanthropological, archeological, and ethnographic records suggest that one function of these relationships is to manage the risk of resource shortfalls due to climate variability. We should expect long-distance relationships to be especially important when shortfalls are chronic or temporally positively autocorrelated, as these are more likely to exhaust local adaptations for managing risk. Further, individuals who experience shortfalls not as rare shocks, but as patterned events, should be more likely to pay the costs of maintaining long-distance relationships. We test these hypotheses in the context of two communities of Bolivian horticulturalists, where climate variability-especially precipitation variability-is relevant to production and access to long-distance connections is improving.METHODS: Data on individuals' migration histories, social relationships, and other relevant variables were collected in 2017 (n = 119). Precipitation data were obtained from the US National Center for Atmospheric Research, allowing us to estimate participants' exposure to drought and excess precipitation.RESULTS: Exposure duration, proximity in time, and frequency did not predict having a greater number of long-distance relationships. Males, extraverted individuals, and those who had traveled more did have more long-distance relationships, however.CONCLUSION: Another function of long-distance relationships is to access resources that can never be obtained locally; ethnographic data suggest this is their primary function in rural Bolivia. We conclude by refining our predictions about the conditions under which long-distance relationships are likely to help individuals manage the risks posed by climate variability.

    View details for DOI 10.1002/ajhb.23525

    View details for PubMedID 33103823

  • Transmission-dynamics models for the SARS Coronavirus-2. American journal of human biology : the official journal of the Human Biology Council Jones, J. H., Hazel, A., Almquist, Z. 2020; 32 (5): e23512

    View details for DOI 10.1002/ajhb.23512

    View details for PubMedID 32978876

  • The impact of different types of violence on Ebola virus disease transmission during the 2018-2020 outbreak in the Democratic Republic of the Congo. The Journal of infectious diseases Kelly, J. D., Wannier, S. R., Sinai, C., Moe, C. A., Hoff, N. A., Blumberg, S., Selo, B., Mossoko, M., Chowell-Puente, G., Jones, J. H., Okitolonda-Wemakoy, E., Rutherford, G. W., Lietman, T. M., Muyembe-Tamfum, J. J., Rimoin, A. W., Porco, T. C., Richardson, E. T. 2020


    BACKGROUND: Our understanding of the different effects of targeted versus non-targeted violence on subsequent EVD transmission in the current outbreak in the eastern Democratic Republic of the Congo (DRC) is limited.METHODS: We used time-series data of case counts to compare individuals who lived in Ebola-affected health zones in DRC from April 2018 to August 2019. Exposure was number of violent events per health zone, categorized into "Ebola-targeted" or "Ebola-untargeted," and into "civilian-involvement," "militia/political," or "protests." The outcome was estimated daily reproduction number (Rt) by health zone. We fit a linear time-series regression to model the relationship.RESULTS: The average Rt was 1.06 (95% confidence interval [CI]: 1.02-1.11). A mean of 2.92 violent events resulted in a cumulative absolute increase in Rt of 0.10 (95%CI: 0.05-0.15). More violent events increased EVD transmission (p=0.03). Considering violent events in the 95th percentile over a 21-day interval and its relative impact on Rt, Ebola-targeted events corresponded to Rt of 1.52 (95%CI: 1.30-1.74) while these civilian-involved events corresponded to Rt of 1.43 (95%CI: 1.21-1.35). Untargeted events corresponded to Rt of 1.18 (95%CI: 1.02-1.35); among these, militia/political or ville morte events increased transmission.CONCLUSION: Ebola-targeted violence, primarily driven by civilian-involved events, had the largest impact on EVD transmission.

    View details for DOI 10.1093/infdis/jiaa163

    View details for PubMedID 32255180

  • Time Preferences, Risk Preferences, and Climate Change Adaptation Jones, J. WILEY. 2020: 133
  • Inequality in the Household and Rural–Urban Migration in Ethiopian Farmers Evolutionary Human Sciences Clech, L., Jones, J. H., Gibson, M. 2020; 2

    View details for DOI 10.1017/ehs.2020.10

  • Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018-2019. Epidemics Wannier, S. R., Worden, L., Hoff, N. A., Amezcua, E., Selo, B., Sinai, C., Mossoko, M., Njoloko, B., Okitolonda-Wemakoy, E., Mbala-Kingebeni, P., Ahuka-Mundeke, S., Muyembe-Tamfum, J. J., Richardson, E. T., Rutherford, G. W., Jones, J. H., Lietman, T. M., Rimoin, A. W., Porco, T. C., Kelly, J. D. 2019: 100353


    INTRODUCTION: As of April 2019, the current Ebola virus disease (EVD) outbreak in the Democratic Republic of the Congo (DRC) is occurring in a longstanding conflict zone and has become the second largest EVD outbreak in history. It is suspected that after violent events occur, EVD transmission will increase; however, empirical studies to understand the impact of violence on transmission are lacking. Here, we use spatial and temporal trends of EVD case counts to compare transmission rates between health zones that have versus have not experienced recent violent events during the outbreak.METHODS: We collected daily EVD case counts from DRC Ministry of Health. A time-varying indicator of recent violence in each health zone was derived from events documented in the WHO situation reports. We used the Wallinga-Teunis technique to estimate the reproduction number R for each case by day per zone in the 2018-2019 outbreak. We fit an exponentially decaying curve to estimates of R overall and by health zone, for comparison to past outbreaks.RESULTS: As of 16 April 2019, the mean overall R for the entire outbreak was 1.11. We found evidence of an increase in the estimated transmission rates in health zones with recently reported violent events versus those without (p = 0.008). The average R was estimated as between 0.61 and 0.86 in regions not affected by recent violent events, and between 1.01 and 1.07 in zones affected by violent events within the last 21 days, leading to an increase in R between 0.17 and 0.53. Within zones with recent violent events, the mean estimated quenching rate was lower than for all past outbreaks except the 2013-2016 West African outbreak.CONCLUSION: The difference in the estimated transmission rates between zones affected by recent violent events suggests that violent events are contributing to increased transmission and the ongoing nature of this outbreak.

    View details for DOI 10.1016/j.epidem.2019.100353

    View details for PubMedID 31378584

  • New Estimates of Hunter-Gatherer Mortality Patterns From Improved Fits of the Siler Model Jones, J., Gurven, M. D., Price, M. H. WILEY. 2019: 116
  • Hadza Hunter-Gatherers Exhibit Gender Differences in Space Use and Spatial Cognition Consistent with the Ecology of Male and Female Targeted Foods Wood, B. M., Harris, J. A., Vashro, L., Sayre, M., Raichlen, D. A., Pontzer, H., Sancilio, A., Berbesque, J., Crittenden, A. N., Mabulla, A. P., Jones, J. H., Cashdan, E. WILEY. 2019: 273–74
  • Temporal clustering of sexual contacts can maintain endemic sexually transmitted virus in mobile subsistence populations Hazel, A., Jones, J. WILEY. 2019: 99–100
  • Genome-wide patterns of gene expression in a wild primate indicate species-specific mechanisms associated with tolerance to natural simian immunodeficiency virus infection. Genome biology and evolution Simons, N. D., Eick, G. N., Ruiz-Lopez, M. J., Hyeroba, D. n., Omeja, P. A., Weny, G. n., Chapman, C. A., Goldberg, T. L., Zheng, H. n., Shankar, A. n., Switzer, W. M., Frost, S. D., Jones, J. H., Sterner, K. N., Ting, N. n. 2019


    Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to HIV in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts, and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.

    View details for DOI 10.1093/gbe/evz099

    View details for PubMedID 31106820

  • Flexible Labors: The Work Mobility of Female Sex Workers (FSWs) in Post-Socialist China HUMAN ORGANIZATION Yu, Y., McCarty, C., Jones, J. 2018; 77 (2): 146–56
  • Anatomy of a Hotspot: Chain and Seroepidemiology of Ebola Virus Transmission, Sukudu, Sierra Leone, 2015-16 JOURNAL OF INFECTIOUS DISEASES Kelly, J., Barrie, M., Mesman, A. W., Karku, S., Quiwa, K., Drasher, M., Schlough, G., Dierberg, K., Koedoyoma, S., Lindan, C. P., Jones, J., Chamie, G., Worden, L., Greenhouse, B., Weiser, S. D., Porco, T. C., Rutherford, G. W., Richardson, E. T. 2018; 217 (8): 1214–21


    Studies have yet to include minimally symptomatic Ebola virus (EBOV) infections and unrecognized Ebola virus disease (EVD) in Ebola-related transmission chains and epidemiologic risk estimates. We conducted a cross-sectional, sero-epidemiological survey from October 2015 to January 2016 among 221 individuals living in quarantined households from November 2014 to February 2015 during the Ebola outbreak in the village of Sukudu, Sierra Leone. Of 48 EBOV-infected persons, 25% (95% confidence interval [CI], 14%-40%) had minimally symptomatic EBOV infections and 4% (95% CI, 1%-14%) were unrecognized EVD cases. The pattern of minimally symptomatic EBOV infections in the transmission chain was nonrandom (P < .001, permutation test). Not having lived in the same house as an EVD case was significantly associated with minimally symptomatic infection. This is the first study to investigate a chain of EBOV transmission inclusive of minimally symptomatic EBOV infections and unrecognized EVD. Our findings provide new insights into Ebola transmission dynamics and quarantine practices.

    View details for PubMedID 29325149

  • Opportunities and constraints in women's resource security among agro-pastoralists in Kaokoveld, Namibia Hazel, A., Meeks, G., Jones, J. WILEY. 2018: 115
  • Response to Economic Crisis Reveals Risk-Averse Fertility Preferences Jones, J. WILEY. 2018: 134
  • Addressing the Challenges of Missing Data in Anthropological Networks Ready, E., Hazel, A., Jones, J. WILEY. 2018: 221
  • A novel, age-structured model of the evolution of economic preferences Price, M. H., Jones, J. H. WILEY. 2018: 214
  • Remoteness influences access to sexual partners and drives patterns of viral sexually transmitted infection prevalence among nomadic pastoralists PLOS ONE Hazel, A., Jones, J. 2018; 13 (1): e0191168


    Sexually transmitted infections (STIs) comprise a significant portion of the infectious-disease burden among rural people in the Global South. Particular characteristics of ruralness-low-density settlements and poor infrastructure-make healthcare provision difficult, and remoteness, typically a characteristic of ruralness, often compounds the difficultly. Remoteness may also accelerate STI transmission, particularly that of viral STIs, through formation of small, highly connected sexual networks through which pathogens can spread rapidly, especially when partner concurrency is broadly accepted. Herein, we explored the effect of remoteness on herpes simplex virus type-2 (HSV-2) epidemiology among semi-nomadic pastoralists in northwestern (Kaokoveld) Namibia, where, in 2009 we collected HSV-2-specific antibody status, demographic, sexual network, and travel data from 446 subjects (women = 213, men = 233) in a cross-sectional study design. HSV-2 prevalence was high overall in Kaokoveld (>35%), but was heterogeneously distributed across locally defined residential regions: some regions had significantly higher HSV-2 prevalence (39-48%) than others (21-33%). Using log-linear models, we asked the following questions: 1) Are sexual contacts among people in high HSV-2-prevalence regions more likely to be homophilous (i.e., from the same region) than those among people from low-prevalence regions? 2) Are high-prevalence regions more "functionally" remote, in that people from those regions are more likely to travel within their own region than outside, compared to people from other regions? We found that high-prevalence regions were more sexually homophilous than low-prevalence regions and that those regions also had higher rates of within-region travel than the other regions. These findings indicate that remoteness can create contact structures for accelerated STI transmission among people who are already disproportionately vulnerable to consequences of untreated STIs.

    View details for DOI 10.1371/journal.pone.0191168

    View details for Web of Science ID 000423668400036

    View details for PubMedID 29385170

    View details for PubMedCentralID PMC5791958

  • Redefine statistical significance NATURE HUMAN BEHAVIOUR Benjamin, D. J., Berger, J. O., Johannesson, M., Nosek, B. A., Wagenmakers, E., Berk, R., Bollen, K. A., Brembs, B., Brown, L., Camerer, C., Cesarini, D., Chambers, C. D., Clyde, M., Cook, T. D., De Boeck, P., Dienes, Z., Dreber, A., Easwaran, K., Efferson, C., Fehr, E., Fidler, F., Field, A. P., Forster, M., George, E. I., Gonzalez, R., Goodman, S., Green, E., Green, D. P., Greenwald, A., Hadfield, J. D., Hedges, L. V., Held, L., Ho, T., Hoijtink, H., Hruschka, D. J., Imai, K., Imbens, G., Ioannidis, J. A., Jeon, M., Jones, J., Kirchler, M., Laibson, D., List, J., Little, R., Lupia, A., Machery, E., Maxwell, S. E., McCarthy, M., Moore, D., Morgan, S. L., Munafo, M., Nakagawa, S., Nyhan, B., Parker, T. H., Pericchi, L., Perugini, M., Rouder, J., Rousseau, J., Savalei, V., Schoenbrodt, F. D., Sellke, T., Sinclair, B., Tingley, D., Van Zandt, T., Vazire, S., Watts, D. J., Winship, C., Wolpert, R. L., Xie, Y., Young, C., Zinman, J., Johnson, V. E. 2018; 2 (1): 6–10
  • Redefine statistical significance. Nature human behaviour Benjamin, D. J., Berger, J. O., Johannesson, M., Nosek, B. A., Wagenmakers, E. J., Berk, R., Bollen, K. A., Brembs, B., Brown, L., Camerer, C., Cesarini, D., Chambers, C. D., Clyde, M., Cook, T. D., De Boeck, P., Dienes, Z., Dreber, A., Easwaran, K., Efferson, C., Fehr, E., Fidler, F., Field, A. P., Forster, M., George, E. I., Gonzalez, R., Goodman, S., Green, E., Green, D. P., Greenwald, A. G., Hadfield, J. D., Hedges, L. V., Held, L., Hua Ho, T., Hoijtink, H., Hruschka, D. J., Imai, K., Imbens, G., Ioannidis, J. P., Jeon, M., Jones, J. H., Kirchler, M., Laibson, D., List, J., Little, R., Lupia, A., Machery, E., Maxwell, S. E., McCarthy, M., Moore, D. A., Morgan, S. L., Munafó, M., Nakagawa, S., Nyhan, B., Parker, T. H., Pericchi, L., Perugini, M., Rouder, J., Rousseau, J., Savalei, V., Schönbrodt, F. D., Sellke, T., Sinclair, B., Tingley, D., Van Zandt, T., Vazire, S., Watts, D. J., Winship, C., Wolpert, R. L., Xie, Y., Young, C., Zinman, J., Johnson, V. E. 2018; 2 (1): 6-10

    View details for DOI 10.1038/s41562-017-0189-z

    View details for PubMedID 30980045

  • Remoteness Influences Access to Sexual Partners and Drives Patterns of Viral Sexually Transmitted Disease Prevalence among Nomadic Pastoralists Hazel, A., Jones, J. WILEY. 2017: 212–13
  • The Shape of Selection on Human Life Histories Jones, J. WILEY. 2017: 234–35
  • The Importance of Ethnographic Data and Social Network Structures in Determining Infection Risk for Individuals in Rural Communities of Bangladesh and Uganda Bloomfield, L. P., Hazel, A., Jones, J. H. WILEY. 2017: 124
  • Uncertainty about future payoffs makes impatience rational BEHAVIORAL AND BRAIN SCIENCES Jones, J. 2017; 40: e330


    Uncertainty (i.e., variable payoffs with unknown probabilities) brings together a number of features of the authors' argument. It leads to present bias, even for completely rational agents with time-consistent preferences. As an evolutionary product of Pleistocene climate instability, humans possess broad adaptations to environmental uncertainty, giving rise to key features of the behavioral constellation of deprivation (BCD).

    View details for PubMedID 29342752

  • Minimally Symptomatic Infection in an Ebola 'Hotspot': A Cross-Sectional Serosurvey PLOS NEGLECTED TROPICAL DISEASES Richardson, E. T., Kelly, J. D., Barrie, M. B., Mesman, A. W., Karku, S., Quiwa, K., Marsh, R. H., Koedoyoma, S., Daboh, F., Barron, K. P., Grady, M., Tucker, E., Dierberg, K. L., Rutherford, G. W., Barry, M., Jones, J. H., Murray, M. B., Farmer, P. E. 2016; 10 (11)


    Evidence for minimally symptomatic Ebola virus (EBOV) infection is limited. During the 2013-16 outbreak in West Africa, it was not considered epidemiologically relevant to published models or projections of intervention effects. In order to improve our understanding of the transmission dynamics of EBOV in humans, we investigated the occurrence of minimally symptomatic EBOV infection in quarantined contacts of reported Ebola virus disease cases in a recognized 'hotspot.'We conducted a cross-sectional serosurvey in Sukudu, Kono District, Sierra Leone, from October 2015 to January 2016. A blood sample was collected from 187 study participants, 132 negative controls (individuals with a low likelihood of previous exposure to Ebola virus), and 30 positive controls (Ebola virus disease survivors). IgG responses to Ebola glycoprotein and nucleoprotein were measured using Alpha Diagnostic International ELISA kits with plasma diluted at 1:200. Optical density was read at 450 nm (subtracting OD at 630nm to normalize well background) on a ChroMate 4300 microplate reader. A cutoff of 4.7 U/mL for the anti-GP ELISA yielded 96.7% sensitivity and 97.7% specificity in distinguishing positive and negative controls. We identified 14 seropositive individuals not known to have had Ebola virus disease. Two of the 14 seropositive individuals reported only fever during quarantine while the remaining 12 denied any signs or symptoms during quarantine.By using ELISA to measure Zaire Ebola virus antibody concentrations, we identified a significant number of individuals with previously undetected EBOV infection in a 'hotspot' village in Sierra Leone, approximately one year after the village outbreak. The findings provide further evidence that Ebola, like many other viral infections, presents with a spectrum of clinical manifestations, including minimally symptomatic infection. These data also suggest that a significant portion of Ebola transmission events may have gone undetected during the outbreak. Further studies are needed to understand the potential risk of transmission and clinical sequelae in individuals with previously undetected EBOV infection.

    View details for DOI 10.1371/journal.pntd.0005087

    View details for Web of Science ID 000392154400022

    View details for PubMedID 27846221

  • Assessing Commitment and Reporting Fidelity to a Text Message-Based Participatory Surveillance in Rural Western Uganda PLOS ONE Lester, J., Paige, S., Chapman, C. A., Gibson, M., Jones, J. H., Switzer, W. M., Ting, N., Goldberg, T. L., Frost, S. D. 2016; 11 (6)
  • Assessing Commitment and Reporting Fidelity to a Text Message-Based Participatory Surveillance in Rural Western Uganda. PloS one Lester, J., Paige, S., Chapman, C. A., Gibson, M., Holland Jones, J., Switzer, W. M., Ting, N., Goldberg, T. L., Frost, S. D. 2016; 11 (6)


    Syndromic surveillance, the collection of symptom data from individuals prior to or in the absence of diagnosis, is used throughout the developed world to provide rapid indications of outbreaks and unusual patterns of disease. However, the low cost of syndromic surveillance also makes it highly attractive for the developing world. We present a case study of electronic participatory syndromic surveillance, using participant-mobile phones in a rural region of Western Uganda, which has a high infectious disease burden, and frequent local and regional outbreaks. Our platform uses text messages to encode a suite of symptoms, their associated durations, and household disease burden, and we explore the ability of participants to correctly encode their symptoms, with an average of 75.2% of symptom reports correctly formatted between the second and 11th reporting timeslots. Concomitantly we identify divisions between participants able to rapidly adjust to this unusually participatory style of data collection, and those few for whom the study proved more challenging. We then perform analyses of the resulting syndromic time series, examining the clustering of symptoms by time and household to identify patterns such as a tendency towards the within-household sharing of respiratory illness.

    View details for DOI 10.1371/journal.pone.0155971

    View details for PubMedID 27281020

  • In-Transitivity: Network Patterns of Female Sex Workers (FSWs) in China HUMAN ORGANIZATION Yu, Y. J., McCarty, C., Jones, J. H., Li, X. 2016; 75 (4): 358-370
  • Human Social Behavior and Demography Drive Patterns of Fine-Scale Dengue Transmission in Endemic Areas of Colombia PLOS ONE Padmanabha, H., Correa, F., Rubio, C., Baeza, A., Osorio, S., Mendez, J., Jones, J. H., Diuk-Wasser, M. A. 2015; 10 (12)

    View details for DOI 10.1371/journal.pone.0144451

    View details for PubMedID 26656072

  • Beyond Bushmeat: Animal Contact, Injury, and Zoonotic Disease Risk in Western Uganda ECOHEALTH Paige, S. B., Frost, S. D., Gibson, M. A., Jones, J. H., Shankar, A., Switzer, W. M., Ting, N., Goldberg, T. L. 2015; 11 (4): 534-543
  • Pursuit: A Foraging Simulation Tool for Research and Teaching EVOLUTIONARY PSYCHOLOGY Wood, B. M., Jones, J. H. 2015; 13 (4)
  • Public health perspective on patterns of biodiversity and zoonotic disease PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Salkeld, D. J., Padgett, K. A., Jones, J. H., Antolin, M. F. 2015; 112 (46): E6261-E6261

    View details for DOI 10.1073/pnas.1517640112

    View details for Web of Science ID 000365170400001

    View details for PubMedID 26508633

  • Genomic Resources Notes Accepted 1 December 2014-31 January 2015 MOLECULAR ECOLOGY RESOURCES Blanchet, S., Bouchez, O., Chapman, C. A., Etter, P. D., Goldberg, T. L., Johnson, E. A., Jones, J. H., Loot, G., Omeja, P. A., Rey, O., Ruiz-Lopez, M. J., Switzer, W. M., Ting, N. 2015; 15 (3): 684-684


    This article documents the public availability of (i) transcriptome sequence data and assembly for the rostrum dace (Leuciscus burdigalensis) naturally infected by a copepod ectoparasite (Tracheliastes polycolpus) and (ii) SNPs identified and validated from RAD sequencing for the Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing.

    View details for DOI 10.1111/1755-0998.12388

    View details for Web of Science ID 000352653700020

    View details for PubMedID 25857929

    View details for PubMedCentralID PMC4491430

  • Gender inequality and HIV transmission: a global analysis JOURNAL OF THE INTERNATIONAL AIDS SOCIETY Richardson, E. T., Collins, S. E., Kung, T., Jones, J. H., Tram, K. H., Boggiano, V. L., Bekker, L., Zolopa, A. R. 2014; 17
  • Beyond Bushmeat: Animal Contact, Injury, and Zoonotic Disease Risk in Western Uganda. EcoHealth Paige, S. B., Frost, S. D., Gibson, M. A., Jones, J. H., Shankar, A., Switzer, W. M., Ting, N., Goldberg, T. L. 2014


    Zoonotic pathogens cause an estimated 70% of emerging and re-emerging infectious diseases in humans. In sub-Saharan Africa, bushmeat hunting and butchering is considered the primary risk factor for human-wildlife contact and zoonotic disease transmission, particularly for the transmission of simian retroviruses. However, hunting is only one of many activities in sub-Saharan Africa that bring people and wildlife into contact. Here, we examine human-animal interaction in western Uganda, identifying patterns of injuries from animals and contact with nonhuman primates. Additionally, we identify individual-level risk factors associated with contact. Nearly 20% (246/1,240) of participants reported either being injured by an animal or having contact with a primate over their lifetimes. The majority (51.7%) of injuries were dog bites that healed with no long-term medical consequences. The majority (76.8%) of 125 total primate contacts involved touching a carcass; however, butchering (20%), hunting (10%), and touching a live primate (10%) were also reported. Red colobus (Piliocolobus rufomitratus tephrosceles) accounted for most primate contact events. Multivariate logistic regression indicated that men who live adjacent to forest fragments are at elevated risk of animal contact and specifically primate contact. Our results provide a useful comparison to West and Central Africa where "bushmeat hunting" is the predominant paradigm for human-wildlife contact and zoonotic disease transmission.

    View details for DOI 10.1007/s10393-014-0942-y

    View details for PubMedID 24845574

    View details for PubMedCentralID PMC4240769

  • The marginal valuation of fertility EVOLUTION AND HUMAN BEHAVIOR Jones, J. H., Bird, R. B. 2014; 35 (1): 65-71
  • Gender inequality and HIV transmission: a global analysis. Journal of the International AIDS Society Richardson, E. T., Collins, S. E., Kung, T., Jones, J. H., Hoan Tram, K., Boggiano, V. L., Bekker, L., Zolopa, A. R. 2014; 17: 19035-?


    The HIV pandemic disproportionately impacts young women. Worldwide, young women aged 15-24 are infected with HIV at rates twice that of young men, and young women alone account for nearly a quarter of all new HIV infections. The incommensurate HIV incidence in young - often poor - women underscores how social and economic inequalities shape the HIV epidemic. Confluent social forces, including political and gender violence, poverty, racism, and sexism impede equal access to therapies and effective care, but most of all constrain the agency of women.HIV prevalence data was compiled from the 2010 UNAIDS Global Report. Gender inequality was assessed using the 2011 United Nations Human Development Report Gender Inequality Index (GII). Logistic regression models were created with predominant mode of transmission (heterosexual vs. MSM/IDU) as the dependent variable and GII, Muslim vs. non-Muslim, Democracy Index, male circumcision rate, log gross national income (GNI) per capita at purchasing power parity (PPP), and region as independent variables.There is a significant correlation between having a predominantly heterosexual epidemic and high gender inequality across all models. There is not a significant association between whether a country is predominantly Muslim, has a high/low GNI at PPP, has a high/low circumcision rate, and its primary mode of transmission. In addition, there are only three countries that have had a generalized epidemic in the past but no longer have one: Cambodia, Honduras, and Eritrea. GII data are available only for Cambodia and Honduras, and these countries showed a 37 and 34% improvement, respectively, in their Gender Inequality Indices between 1995 and 2011. During the same period, both countries reduced their HIV prevalence below the 1% threshold of a generalized epidemic. This represents limited but compelling evidence that improvements in gender inequality can lead to the abatement of generalized epidemics.Gender inequality is an important factor in the maintenance - and possibly in the establishment of - generalized HIV epidemics. We should view improvements in gender inequality as part of a broader public health strategy.

    View details for DOI 10.7448/IAS.17.1.19035

    View details for PubMedID 24976436

    View details for PubMedCentralID PMC4074603

  • Metapopulation Dynamics Enable Persistence of Influenza A, Including A/H5N1, in Poultry PLOS ONE Hosseini, P. R., Fuller, T., Harrigan, R., Zhao, D., Arriola, C. S., Gonzalez, A., Miller, M. J., Xiao, X., Smith, T. B., Jones, J. H., Daszak, P. 2013; 8 (12)


    Highly pathogenic influenza A/H5N1 has persistently but sporadically caused human illness and death since 1997. Yet it is still unclear how this pathogen is able to persist globally. While wild birds seem to be a genetic reservoir for influenza A, they do not seem to be the main source of human illness. Here, we highlight the role that domestic poultry may play in maintaining A/H5N1 globally, using theoretical models of spatial population structure in poultry populations. We find that a metapopulation of moderately sized poultry flocks can sustain the pathogen in a finite poultry population for over two years. Our results suggest that it is possible that moderately intensive backyard farms could sustain the pathogen indefinitely in real systems. This fits a pattern that has been observed from many empirical systems. Rather than just employing standard culling procedures to control the disease, our model suggests ways that poultry production systems may be modified.

    View details for DOI 10.1371/journal.pone.0080091

    View details for Web of Science ID 000327944500010

    View details for PubMedID 24312455

    View details for PubMedCentralID PMC3846554

  • Interactions between Social Structure, Demography, and Transmission Determine Disease Persistence in Primates PLOS ONE Ryan, S. J., Jones, J. H., Dobson, A. P. 2013; 8 (10)


    Catastrophic declines in African great ape populations due to disease outbreaks have been reported in recent years, yet we rarely hear of similar disease impacts for the more solitary Asian great apes, or for smaller primates. We used an age-structured model of different primate social systems to illustrate that interactions between social structure and demography create 'dynamic constraints' on the pathogens that can establish and persist in primate host species with different social systems. We showed that this varies by disease transmission mode. Sexually transmitted infections (STIs) require high rates of transmissibility to persist within a primate population. In particular, for a unimale social system, STIs require extremely high rates of transmissibility for persistence, and remain at extremely low prevalence in small primates, but this is less constrained in longer-lived, larger-bodied primates. In contrast, aerosol transmitted infections (ATIs) spread and persist at high prevalence in medium and large primates with moderate transmissibility;, establishment and persistence in small-bodied primates require higher relative rates of transmissibility. Intragroup contact structure - the social network - creates different constraints for different transmission modes, and our model underscores the importance of intragroup contacts on infection prior to intergroup movement in a structured population. When alpha males dominate sexual encounters, the resulting disease transmission dynamics differ from when social interactions are dominated by mother-infant grooming events, for example. This has important repercussions for pathogen spread across populations. Our framework reveals essential social and demographic characteristics of primates that predispose them to different disease risks that will be important for disease management and conservation planning for protected primate populations.

    View details for DOI 10.1371/journal.pone.0076863

    View details for Web of Science ID 000326029300057

    View details for PubMedID 24204688

  • To kill a kangaroo: understanding the decision to pursue high-risk/high-gain resources. Proceedings. Biological sciences / The Royal Society Jones, J. H., Bird, R. B., Bird, D. W. 2013; 280 (1767): 20131210-?


    In this paper, we attempt to understand hunter-gatherer foraging decisions about prey that vary in both the mean and variance of energy return using an expected utility framework. We show that for skewed distributions of energetic returns, the standard linear variance discounting (LVD) model for risk-sensitive foraging can produce quite misleading results. In addition to creating difficulties for the LVD model, the skewed distributions characteristic of hunting returns create challenges for estimating probability distribution functions required for expected utility. We present a solution using a two-component finite mixture model for foraging returns. We then use detailed foraging returns data based on focal follows of individual hunters in Western Australia hunting for high-risk/high-gain (hill kangaroo) and relatively low-risk/low-gain (sand monitor) prey. Using probability densities for the two resources estimated from the mixture models, combined with theoretically sensible utility curves characterized by diminishing marginal utility for the highest returns, we find that the expected utility of the sand monitors greatly exceeds that of kangaroos despite the fact that the mean energy return for kangaroos is nearly twice as large as that for sand monitors. We conclude that the decision to hunt hill kangaroos does not arise simply as part of an energetic utility-maximization strategy and that additional social, political or symbolic benefits must accrue to hunters of this highly variable prey.

    View details for DOI 10.1098/rspb.2013.1210

    View details for PubMedID 23884091

    View details for PubMedCentralID PMC3735252

  • A meta-analysis suggesting that the relationship between biodiversity and risk of zoonotic pathogen transmission is idiosyncratic ECOLOGY LETTERS Salkeld, D. J., Padgett, K. A., Jones, J. H. 2013; 16 (5): 679-686


    Zoonotic pathogens are significant burdens on global public health. Because they are transmitted to humans from non-human animals, the transmission dynamics of zoonoses are necessarily influenced by the ecology of their animal hosts and vectors. The 'dilution effect' proposes that increased species diversity reduces disease risk, suggesting that conservation and public health initiatives can work synergistically to improve human health and wildlife biodiversity. However, the meta-analysis that we present here indicates a weak and highly heterogeneous relationship between host biodiversity and disease. Our results suggest that disease risk is more likely a local phenomenon that relies on the specific composition of reservoir hosts and vectors, and their ecology, rather than patterns of species biodiversity.

    View details for DOI 10.1111/ele.12101

    View details for Web of Science ID 000318077200014

    View details for PubMedID 23489376

  • To kill a kangaroo: understanding the decision to pursue high-risk/high-gain resources. Proceedings. Biological sciences / The Royal Society Jones, J. H., Bird, R. B., Bird, D. W. 2013; 280 (1767): 20131210-?


    In this paper, we attempt to understand hunter-gatherer foraging decisions about prey that vary in both the mean and variance of energy return using an expected utility framework. We show that for skewed distributions of energetic returns, the standard linear variance discounting (LVD) model for risk-sensitive foraging can produce quite misleading results. In addition to creating difficulties for the LVD model, the skewed distributions characteristic of hunting returns create challenges for estimating probability distribution functions required for expected utility. We present a solution using a two-component finite mixture model for foraging returns. We then use detailed foraging returns data based on focal follows of individual hunters in Western Australia hunting for high-risk/high-gain (hill kangaroo) and relatively low-risk/low-gain (sand monitor) prey. Using probability densities for the two resources estimated from the mixture models, combined with theoretically sensible utility curves characterized by diminishing marginal utility for the highest returns, we find that the expected utility of the sand monitors greatly exceeds that of kangaroos despite the fact that the mean energy return for kangaroos is nearly twice as large as that for sand monitors. We conclude that the decision to hunt hill kangaroos does not arise simply as part of an energetic utility-maximization strategy and that additional social, political or symbolic benefits must accrue to hunters of this highly variable prey.

    View details for DOI 10.1098/rspb.2013.1210

    View details for PubMedID 23884091

    View details for PubMedCentralID PMC3735252

  • Prevalences of sexually transmitted infections in young adults and female sex workers in Peru: a national population-based survey LANCET INFECTIOUS DISEASES Carcamo, C. P., Campos, P. E., Garcia, P. J., Hughes, J. P., Garnett, G. P., Holmes, K. K. 2012; 12 (10): 765-773


    We assessed prevalences of seven sexually transmitted infections (STIs) in Peru, stratified by risk behaviours, to help to define care and prevention priorities.In a 2002 household-based survey of the general population, we enrolled randomly selected 18-29-year-old residents of 24 cities with populations greater than 50 000 people. We then surveyed female sex workers (FSWs) in these cities. We gathered data for sexual behaviour; vaginal specimens or urine for nucleic acid amplification tests for Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis; and blood for serological tests for syphilis, HIV, and (in subsamples) herpes simplex virus 2 (HSV2) and human T-lymphotropic virus. This study is a registered component of the PREVEN trial, number ISRCTN43722548.15 261 individuals from the general population and 4485 FSWs agreed to participate in our survey. Overall prevalence of infection with HSV2, weighted for city size, was 13·5% in men, 13·6% in women, and 60·6% in FSWs (all values in FSWs standardised to age composition of women in the general population). The prevalence of C trachomatis infection was 4·2% in men, 6·5% in women, and 16·4% in FSWs; of T vaginalis infection was 0·3% in men, 4·9% in women, and 7·9% in FSWs; and of syphilis was 0·5% in men, 0·4% in women, and 0·8% in FSWs. N gonorrhoeae infection had a prevalence of 0·1% in men and women, and of 1·6% in FSWs. Prevalence of HIV infection was 0·5% in men and FSWs, and 0·1% in women. Four (0·3%) of 1535 specimens were positive for human T-lymphotropic virus 1. In men, 65·0% of infections with HIV, 71·5% of N gonorrhoeae, and 41·4% of HSV2 and 60·9% of cases of syphilis were in the 13·3% who had sex with men or unprotected sex with FSWs in the past year. In women from the general population, 66·7% of infections with HIV and 16·7% of cases of syphilis were accounted for by the 4·4% who had been paid for sex by any of their past three partners.Defining of high-risk groups could guide targeting of interventions for communicable diseases-including STIs-in the general Peruvian population.Wellcome Trust-Burroughs Wellcome Fund Infectious Disease Initiative and US National Institutes of Health.

    View details for DOI 10.1016/S1473-3099(12)70144-5

    View details for Web of Science ID 000309631200024

    View details for PubMedID 22878023

  • The role of social sciences in predicting and responding to emerging zoonotic diseases The Lancet Janes, C., Corbett, K., Jones, J. H., Trostle, J. 2012; 380 (9857): 1884-1886
  • Primates and the Evolution of Long, Slow Life Histories CURRENT BIOLOGY Jones, J. H. 2011; 21 (18): R708-R717


    Primates are characterized by relatively late ages at first reproduction, long lives and low fertility. Together, these traits define a life-history of reduced reproductive effort. Understanding the optimal allocation of reproductive effort, and specifically reduced reproductive effort, has been one of the key problems motivating the development of life-history theory. Because of their unusual constellation of life-history traits, primates play an important role in the continued development of life-history theory. In this review, I present the evidence for the reduced reproductive effort life histories of primates and discuss the ways that such life-history tactics are understood in contemporary theory. Such tactics are particularly consistent with the predictions of stochastic demographic models, suggesting a key role for environmental variability in the evolution of primate life histories. The tendency for primates to specialize in high-quality, high-variability food items may make them particularly susceptible to environmental variability and explains their low reproductive-effort tactics. I discuss recent applications of life-history theory to human evolution and emphasize the continuity between models used to explain peculiarities of human reproduction and senescence with the long, slow life histories of primates more generally.

    View details for DOI 10.1016/j.cub.2011.08.025

    View details for Web of Science ID 000295423400015

    View details for PubMedID 21959161

    View details for PubMedCentralID PMC3192902

  • Phenotypic quality influences fertility in Gombe chimpanzees JOURNAL OF ANIMAL ECOLOGY Jones, J. H., Wilson, M. L., Murray, C., Pusey, A. 2010; 79 (6): 1262-1269


    1. Fertility is an important fitness component, but is difficult to measure in slowly reproducing, long-lived animals such as chimpanzees (Pan troglodytes). 2. We measured fertility and the effect of measured covariates on fertility in a 43-year sample of birth intervals of chimpanzees from the Gombe National Park, Tanzania using Cox proportional hazards regression with individual-level random effects. 3. The birth hazard declined with mothers' age at a rate of 0·84 per year following age at first reproduction. This value is somewhat stronger than previous estimates. 4. Loss of the infant that opened the birth interval increased the birth hazard 134-fold. 5. Birth intervals following the first complete birth interval were shorter than this first interval, while sex of the previous infant had no significant effect. 6. Maternal dominance rank was significant at the P < 0·1 level when coded as high/middle/low but was highly significant when we simply considered high rank vs. others. 7. Individual heterogeneity had a substantial impact on birth interval duration. We interpret this individual effect as a measure of phenotypic quality, controlling for the measured covariates such as dominance rank. This interpretation is supported by the correlation of individual heterogeneity scores with similar independent measures of body mass.

    View details for DOI 10.1111/j.1365-2656.2010.01687.x

    View details for Web of Science ID 000283074000013

    View details for PubMedID 20412347

    View details for PubMedCentralID PMC3192870

  • Impact of Simian Immunodeficiency Virus Infection on Chimpanzee Population Dynamics PLOS PATHOGENS Rudicell, R. S., Jones, J. H., Wroblewski, E. E., Learn, G. H., Li, Y., Robertson, J. D., Greengrass, E., Grossmann, F., Kamenya, S., Pintea, L., Mjungu, D. C., Lonsdorf, E. V., Mosser, A., Lehman, C., Collins, D. A., Keele, B. F., Goodall, J., Hahn, B. H., Pusey, A. E., Wilson, M. L. 2010; 6 (9)


    Like human immunodeficiency virus type 1 (HIV-1), simian immunodeficiency virus of chimpanzees (SIVcpz) can cause CD4+ T cell loss and premature death. Here, we used molecular surveillance tools and mathematical modeling to estimate the impact of SIVcpz infection on chimpanzee population dynamics. Habituated (Mitumba and Kasekela) and non-habituated (Kalande) chimpanzees were studied in Gombe National Park, Tanzania. Ape population sizes were determined from demographic records (Mitumba and Kasekela) or individual sightings and genotyping (Kalande), while SIVcpz prevalence rates were monitored using non-invasive methods. Between 2002-2009, the Mitumba and Kasekela communities experienced mean annual growth rates of 1.9% and 2.4%, respectively, while Kalande chimpanzees suffered a significant decline, with a mean growth rate of -6.5% to -7.4%, depending on population estimates. A rapid decline in Kalande was first noted in the 1990s and originally attributed to poaching and reduced food sources. However, between 2002-2009, we found a mean SIVcpz prevalence in Kalande of 46.1%, which was almost four times higher than the prevalence in Mitumba (12.7%) and Kasekela (12.1%). To explore whether SIVcpz contributed to the Kalande decline, we used empirically determined SIVcpz transmission probabilities as well as chimpanzee mortality, mating and migration data to model the effect of viral pathogenicity on chimpanzee population growth. Deterministic calculations indicated that a prevalence of greater than 3.4% would result in negative growth and eventual population extinction, even using conservative mortality estimates. However, stochastic models revealed that in representative populations, SIVcpz, and not its host species, frequently went extinct. High SIVcpz transmission probability and excess mortality reduced population persistence, while intercommunity migration often rescued infected communities, even when immigrating females had a chance of being SIVcpz infected. Together, these results suggest that the decline of the Kalande community was caused, at least in part, by high levels of SIVcpz infection. However, population extinction is not an inevitable consequence of SIVcpz infection, but depends on additional variables, such as migration, that promote survival. These findings are consistent with the uneven distribution of SIVcpz throughout central Africa and explain how chimpanzees in Gombe and elsewhere can be at equipoise with this pathogen.

    View details for DOI 10.1371/journal.ppat.1001116

    View details for Web of Science ID 000282373000015

    View details for PubMedID 20886099

    View details for PubMedCentralID PMC2944804

  • The Effect of the Civil War on Southern Marriage Patterns JOURNAL OF SOUTHERN HISTORY Hacker, J. D., Hilde, L., Jones, J. H. 2010; 76 (1): 39-70
  • Early Assessment of Anxiety and Behavioral Response to Novel Swine-Origin Influenza A(H1N1) PLOS ONE Jones, J. H., Salathe, M. 2009; 4 (12)


    Since late April, 2009, a novel influenza virus A (H1N1), generally referred to as the "swine flu," has spread around the globe and infected hundreds of thousands of people. During the first few days after the initial outbreak in Mexico, extensive media coverage together with a high degree of uncertainty about the transmissibility and mortality rate associated with the virus caused widespread concern in the population. The spread of an infectious disease can be strongly influenced by behavioral changes (e.g., social distancing) during the early phase of an epidemic, but data on risk perception and behavioral response to a novel virus is usually collected with a substantial delay or after an epidemic has run its course.Here, we report the results from an online survey that gathered data (n = 6,249) about risk perception of the Influenza A(H1N1) outbreak during the first few days of widespread media coverage (April 28-May 5, 2009). We find that after an initially high level of concern, levels of anxiety waned along with the perception of the virus as an immediate threat. Overall, our data provide evidence that emotional status mediates behavioral response. Intriguingly, principal component analysis revealed strong clustering of anxiety about swine flu, bird flu and terrorism. All three of these threats receive a great deal of media attention and their fundamental uncertainty is likely to generate an inordinate amount of fear vis-a-vis their actual threat.Our results suggest that respondents' behavior varies in predictable ways. Of particular interest, we find that affective variables, such as self-reported anxiety over the epidemic, mediate the likelihood that respondents will engage in protective behavior. Understanding how protective behavior such as social distancing varies and the specific factors that mediate it may help with the design of epidemic control strategies.

    View details for DOI 10.1371/journal.pone.0008032

    View details for Web of Science ID 000272829000001

    View details for PubMedID 19997505

    View details for PubMedCentralID PMC2779851

  • The force of selection on the human life cycle EVOLUTION AND HUMAN BEHAVIOR Jones, J. H. 2009; 30 (5): 305-314
  • Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz NATURE Keele, B. F., Jones, J. H., Terio, K. A., Estes, J. D., Rudicell, R. S., Wilson, M. L., Li, Y., Learn, G. H., Beasley, T. M., Schumacher-Stankey, J., Wroblewski, E., Mosser, A., Raphael, J., Kamenya, S., Lonsdorf, E. V., Travis, D. A., Mlengeya, T., Kinsel, M. J., Else, J. G., Silvestri, G., Goodall, J., Sharp, P. M., Shaw, G. M., Pusey, A. E., Hahn, B. H. 2009; 460 (7254): 515-519


    African primates are naturally infected with over 40 different simian immunodeficiency viruses (SIVs), two of which have crossed the species barrier and generated human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2). Unlike the human viruses, however, SIVs do not generally cause acquired immunodeficiency syndrome (AIDS) in their natural hosts. Here we show that SIVcpz, the immediate precursor of HIV-1, is pathogenic in free-ranging chimpanzees. By following 94 members of two habituated chimpanzee communities in Gombe National Park, Tanzania, for over 9 years, we found a 10- to 16-fold higher age-corrected death hazard for SIVcpz-infected (n = 17) compared to uninfected (n = 77) chimpanzees. We also found that SIVcpz-infected females were less likely to give birth and had a higher infant mortality rate than uninfected females. Immunohistochemistry and in situ hybridization of post-mortem spleen and lymph node samples from three infected and two uninfected chimpanzees revealed significant CD4(+) T-cell depletion in all infected individuals, with evidence of high viral replication and extensive follicular dendritic cell virus trapping in one of them. One female, who died within 3 years of acquiring SIVcpz, had histopathological findings consistent with end-stage AIDS. These results indicate that SIVcpz, like HIV-1, is associated with progressive CD4(+) T-cell loss, lymphatic tissue destruction and premature death. These findings challenge the prevailing view that all natural SIV infections are non-pathogenic and suggest that SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild.

    View details for DOI 10.1038/nature08200

    View details for Web of Science ID 000268257000039

    View details for PubMedID 19626114

    View details for PubMedCentralID PMC2872475

  • Demographic and Social Predictors of Intimate Partner Violence in Colombia HUMAN NATURE-AN INTERDISCIPLINARY BIOSOCIAL PERSPECTIVE Jones, J. H., Ferguson, B. 2009; 20 (2): 184-203
  • Demographic and social predictors of intimate partner violence in Colombia : a dyadic power perspective. Human nature (Hawthorne, N.Y.) Jones, J. H., Ferguson, B. 2009; 20 (2): 184-203


    Intimate partner violence (IPV) is a major health and human rights problem globally. However, empirical findings on the predictors of IPV cross-culturally are highly inconsistent, and the theory of IPV is underdeveloped. We propose a new analytical framework based on cooperative game theory in which IPV is a function of the power relations of the dyadic relationship, not simply the actors involved. Using data from the 2005 Colombian Demographic and Health Survey, we test the hypothesis that IPV is predicted by large asymmetries in dyadic power using a hierarchical generalized linear model. Results suggest that education, urban residence, age at sexual debut, whether the woman has other sexual partners, and the age difference between spouses have strong effects on the log-odds of a woman experiencing IPV. Cooperative game theory and social network analysis offer a general approach to the problem of intimate partner interactions which can be applied broadly cross-culturally.

    View details for DOI 10.1007/s12110-009-9064-6

    View details for PubMedID 25526957

  • The "fire stick farming" hypothesis: Australian Aboriginal foraging strategies, biodiversity, and anthropogenic fire mosaics PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bird, R. B., Bird, D. W., Codding, B. F., PARKER, C. H., Jones, J. H. 2008; 105 (39): 14796-14801


    Aboriginal burning in Australia has long been assumed to be a "resource management" strategy, but no quantitative tests of this hypothesis have ever been conducted. We combine ethnographic observations of contemporary Aboriginal hunting and burning with satellite image analysis of anthropogenic and natural landscape structure to demonstrate the processes through which Aboriginal burning shapes arid-zone vegetational diversity. Anthropogenic landscapes contain a greater diversity of successional stages than landscapes under a lightning fire regime, and differences are of scale, not of kind. Landscape scale is directly linked to foraging for small, burrowed prey (monitor lizards), which is a specialty of Aboriginal women. The maintenance of small-scale habitat mosaics increases small-animal hunting productivity. These results have implications for understanding the unique biodiversity of the Australian continent, through time and space. In particular, anthropogenic influences on the habitat structure of paleolandscapes are likely to be spatially localized and linked to less mobile, "broad-spectrum" foraging economies.

    View details for DOI 10.1073/pnas.0804757105

    View details for Web of Science ID 000259840500012

    View details for PubMedID 18809925

  • Aging and fertility patterns in wild chimpanzees provide insights into the evolution of menopause CURRENT BIOLOGY Thompson, M. E., Jones, J. H., Pusey, A. E., Brewer-Marsden, S., Goodall, J., Marsden, D., Matsuzawa, T., Nishida, T., Reynolds, V., Sugiyama, Y., Wrangham, R. W. 2007; 17 (24): 2150-2156


    Human menopause is remarkable in that reproductive senescence is markedly accelerated relative to somatic aging, leaving an extended postreproductive period for a large proportion of women. Functional explanations for this are debated, in part because comparative data from closely related species are inadequate. Existing studies of chimpanzees are based on very small samples and have not provided clear conclusions about the reproductive function of aging females. These studies have not examined whether reproductive senescence in chimpanzees exceeds the pace of general aging, as in humans, or occurs in parallel with declines in overall health, as in many other animals. In order to remedy these problems, we examined fertility and mortality patterns in six free-living chimpanzee populations. Chimpanzee and human birth rates show similar patterns of decline beginning in the fourth decade, suggesting that the physiology of reproductive senescence was relatively conserved in human evolution. However, in contrast to humans, chimpanzee fertility declines are consistent with declines in survivorship, and healthy females maintain high birth rates late into life. Thus, in contrast to recent claims, we find no evidence that menopause is a typical characteristic of chimpanzee life histories.

    View details for DOI 10.1016/j.cub.2007.11.033

    View details for Web of Science ID 000251852200028

    View details for PubMedID 18083515

    View details for PubMedCentralID PMC2190291

  • demogR: A package for the construction and analysis of age-structured demographic models in R JOURNAL OF STATISTICAL SOFTWARE Jones, J. H. 2007; 22 (10): 1-28
  • Interval estimates for epidemic thresholds in two-sex network models THEORETICAL POPULATION BIOLOGY Handcock, M. S., Jones, J. H. 2006; 70 (2): 125-134


    Epidemic thresholds in network models of heterogeneous populations characterized by highly right-skewed contact distributions can be very small. When the population is above the threshold, an epidemic is inevitable and conventional control measures to reduce the transmissibility of a pathogen will fail to eradicate it. We consider a two-sex network model for a sexually transmitted disease which assumes random mixing conditional on the degree distribution. We derive expressions for the basic reproductive number (R(0)) for one and heterogeneous two-population in terms of characteristics of the degree distributions and transmissibility. We calculate interval estimates for the epidemic thresholds for stochastic process models in three human populations based on representative surveys of sexual behavior (Uganda, Sweden, USA). For Uganda and Sweden, the epidemic threshold is greater than zero with high confidence. For the USA, the interval includes zero. We discuss the implications of these findings along with the limitations of epidemic models which assume random mixing.

    View details for DOI 10.1016/j.tpb.2006.02.004

    View details for Web of Science ID 000239979000003

    View details for PubMedID 16714041

  • The Marriage Squeeze in Colombia, 1973-2005: The Role of Excess Male Death Social Biology Jones, J. H., Ferguson, B. D. 2006; 53 (3-4): 140-151
  • Fetal programming: Adaptive life-history tactics or making the best of a bad start? 29th Annual Meeting of the Human-Biology-Association Jones, J. H. WILEY-LISS. 2005: 22–33


    Fetal programming is an ontogenetic phenomenon of increasing interest to human biologists. Because the downstream consequences of fetal programming have clear impacts on specific life-history traits (e.g., age at first reproduction and the general age-pattern of reproductive investments), a number of authors have raised the question of the adaptive significance of fetal programming. In this paper, I review in some detail several classical models in life-history theory and discuss their relative merits and weaknesses for human biology. I suggest that an adequate model of human life-history evolution must account for the highly structured nature of the human life cycle, with its late age at first reproduction, large degree of iteroparity, highly overlapping generations, and extensive, post-weaning parental investment. I further suggest that an understanding of stochastic demography is essential for answering the question of the adaptive significance of fetal programming, and specifically the finding of low birth weight on smaller adult body size and earlier age at first reproduction. Using a stage-structured stochastic population model, I show that the downstream consequences of early deprivation may be "making the best of a bad start" rather than an adaptation per se. When a high-investment strategy entails survival costs, the alternate strategy of early reproduction with relatively low investment may have higher fitness than trying to play the high-investment strategy and failing.

    View details for DOI 10.1002/ajhb.20099

    View details for Web of Science ID 000226105500003

    View details for PubMedID 15611978

  • Likelihood-based inference for stochastic models of sexual network formation THEORETICAL POPULATION BIOLOGY Handcock, M. S., Jones, J. H. 2004; 65 (4): 413-422


    Sexually-transmitted diseases (STDs) constitute a major public health concern. Mathematical models for the transmission dynamics of STDs indicate that heterogeneity in sexual activity level allow them to persist even when the typical behavior of the population would not support endemicity. This insight focuses attention on the distribution of sexual activity level in a population. In this paper, we develop several stochastic process models for the formation of sexual partnership networks. Using likelihood-based model selection procedures, we assess the fit of the different models to three large distributions of sexual partner counts: (1) Rakai, Uganda, (2) Sweden, and (3) the USA. Five of the six single-sex networks were fit best by the negative binomial model. The American women's network was best fit by a power-law model, the Yule. For most networks, several competing models fit approximately equally well. These results suggest three conclusions: (1) no single unitary process clearly underlies the formation of these sexual networks, (2) behavioral heterogeneity plays an essential role in network structure, (3) substantial model uncertainty exists for sexual network degree distributions. Behavioral research focused on the mechanisms of partnership formation will play an essential role in specifying the best model for empirical degree distributions. We discuss the limitations of inferences from such data, and the utility of degree-based epidemiological models more generally.

    View details for DOI 10.1016/j.tpb.2003.09.006

    View details for Web of Science ID 000221621800009

    View details for PubMedID 15136015

  • An assessment of preferential attachment as a mechanism for human sexual network formation PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Jones, J. H., Handcock, M. S. 2003; 270 (1520): 1123-1128


    Recent research into the properties of human sexual-contact networks has suggested that the degree distribution of the contact graph exhibits power-law scaling. One notable property of this power-law scaling is that the epidemic threshold for the population disappears when the scaling exponent rho is in the range 2 < rho < or = 3. This property is of fundamental significance for the control of sexually transmitted diseases (STDs) such as HIV/AIDS since it implies that an STD can persist regardless of its transmissibility. A stochastic process, known as preferential attachment, that yields one form of power-law scaling has been suggested to underlie the scaling of sexual degree distributions. The limiting distribution of this preferential attachment process is the Yule distribution, which we fit using maximum likelihood to local network data from samples of three populations: (i) the Rakai district, Uganda; (ii) Sweden; and (iii) the USA. For all local networks but one, our interval estimates of the scaling parameters are in the range where epidemic thresholds exist. The estimate of the exponent for male networks in the USA is close to 3, but the preferential attachment model is a very poor fit to these data. We conclude that the epidemic thresholds implied by this model exist in both single-sex and two-sex epidemic model formulations. A strong conclusion that we derive from these results is that public health interventions aimed at reducing the transmissibility of STD pathogens, such as implementing condom use or high-activity anti-retroviral therapy, have the potential to bring a population below the epidemic transition, even in populations exhibiting large degrees of behavioural heterogeneity.

    View details for DOI 10.1098/rspb.2003.2369

    View details for Web of Science ID 000183400900003

    View details for PubMedID 12816649

    View details for PubMedCentralID PMC1691356

  • Sexual contacts and epidemic thresholds NATURE Jones, J. H., Handcock, M. S. 2003; 423 (6940): 605-606

    View details for DOI 10.1038/423605a

    View details for Web of Science ID 000183301200030

  • Social networks: Sexual contacts and epidemic thresholds. Nature Jones, J. H., Handcock, M. S. 2003; 423 (6940): 605-6; discussion 606

    View details for DOI 10.1038/423605a

    View details for PubMedID 12789329

  • The raw and the stolen - Cooking and the ecology of human origins CURRENT ANTHROPOLOGY Wrangham, R. W., Jones, J. H., Laden, G., Pilbeam, D., Conklin-Brittain, N. 1999; 40 (5): 567-594