Professional Education

  • Doctor of Philosophy, University of Wisconsin Madison (2022)
  • BS, Pennsylvania State University (2009)
  • MS, University of Florida (2014)
  • PhD, University of Wisconsin–Madison (2022)

Stanford Advisors

All Publications

  • Shared features underlying compact genomes and extreme habitat use in chironomid midges. Genome biology and evolution Nell, L. A., Weng, Y. M., Phillips, J. S., Botsch, J. C., Book, K. R., Einarsson, Á., Ives, A. R., Schoville, S. D. 2024


    Non-biting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the common ancestor of Chironomidae and Ceratopogonidae, and that this occurred mainly through reductions in non-coding regions (introns, intergenic sequences, and repeat elements). Significantly expanded gene families in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, carbohydrate transport, melanization defense response, and trehalose transport. We identified several positively selected genes in Chironomidae, notably sulfonylurea receptor, CREB-binding protein, and protein kinase D. Our results improve our understanding of the evolution of small genomes and extreme habitat use in this widely distributed group.

    View details for DOI 10.1093/gbe/evae086

    View details for PubMedID 38662498

  • Dispersal stabilizes coupled ecological and evolutionary dynamics in a host-parasitoid system. Science (New York, N.Y.) Nell, L. A., Kishinevsky, M., Bosch, M. J., Sinclair, C., Bhat, K., Ernst, N., Boulaleh, H., Oliver, K. M., Ives, A. R. 2024; 383 (6688): 1240-1244


    When ecological and evolutionary dynamics occur on comparable timescales, persistence of the ensuing eco-evolutionary dynamics requires both ecological and evolutionary stability. This unites key questions in ecology and evolution: How do species coexist, and what maintains genetic variation in a population? In this work, we investigated a host-parasitoid system in which pea aphid hosts rapidly evolve resistance to Aphidius ervi parasitoids. Field data and mathematical simulations showed that heterogeneity in parasitoid dispersal can generate variation in parasitism-mediated selection on hosts through time and space. Experiments showed how evolutionary trade-offs plus moderate host dispersal across this selection mosaic cause host-parasitoid coexistence and maintenance of genetic variation in host resistance. Our results show how dispersal can stabilize both the ecological and evolutionary components of eco-evolutionary dynamics.

    View details for DOI 10.1126/science.adg4602

    View details for PubMedID 38484053

  • Disentangling the drivers of decadal body size decline in an insect population GLOBAL CHANGE BIOLOGY Botsch, J. C., Zaveri, A. N., Nell, L. A., Mccormick, A. R., Book, K., Phillips, J. S., Einarsson, A., Ives, A. R. 2023: e17014


    While climate warming is widely predicted to reduce body size of ectotherms, evidence for this trend is mixed. Body size depends not only on temperature but also on other factors, such as food quality and intraspecific competition. Because temperature trends or other long-term environmental factors may affect population size and food sources, attributing trends in average body size to temperature requires the separation of potentially confounding effects. We evaluated trends in the body size of the midge Tanytarsus gracilentus and potential drivers (water temperature, population size, and food quality) between 1977 and 2015 at Lake Mývatn, Iceland. Although temperatures increased at Mývatn over this period, there was only a slight (non-significant) decrease in midge adult body size, contrary to theoretical expectations. Using a state-space model including multiple predictors, body size was negatively associated with both water temperature and midge population abundance, and it was positively associated with 13 C enrichment of midges (an indicator of favorable food conditions). The magnitude of these effects were similar, such that simultaneous changes in temperature, abundance, and carbon stable isotopic signature could counteract each other in the long-term body size trend. Our results illustrate how multiple factors, all of which could be influenced by global change, interact to affect average ectotherm body size.

    View details for DOI 10.1111/gcb.17014

    View details for Web of Science ID 001102604300001

    View details for PubMedID 37943090

  • Coevolution, diversification and alternative states in two-trophic communities. Ecology letters Northfield, T. D., Ripa, J., Nell, L. A., Ives, A. R. 2021; 24 (2): 269-278


    Single-trait eco-evolutionary models of arms races between consumers and their resource species often show inhibition rather than promotion of community diversification. In contrast, modelling arms races involving multiple traits, we found that arms races can promote diversification when trade-off costs among traits make simultaneous investment in multiple traits either more beneficial or more costly. Coevolution between resource and consumer species generates an adaptive landscape for each, with the configuration giving predictable suites of consumer and resource species. Nonetheless, the adaptive landscape contains multiple alternative stable states, and which stable community is reached depends on small stochastic differences occurring along evolutionary pathways. Our results may solve a puzzling conflict between eco-evolutionary theory that predicts community diversification via consumer-resource interactions will be rare, and empirical research that has uncovered real cases. Furthermore, our results suggest that these real cases might be just a subset of alternative stable communities.

    View details for DOI 10.1111/ele.13639

    View details for PubMedID 33201560

  • Transient top-down and bottom-up effects of resources pulsed to multiple trophic levels. Ecology McCary, M. A., Phillips, J. S., Ramiadantsoa, T., Nell, L. A., McCormick, A. R., Botsch, J. C. 2021; 102 (1): e03197


    Pulsed fluxes of organisms across ecosystem boundaries can exert top-down and bottom-up effects in recipient food webs, through both direct effects on the subsidized trophic levels and indirect effects on other components of the system. While previous theoretical and empirical studies demonstrate the influence of allochthonous subsidies on bottom-up and top-down processes, understanding how these forces act in conjunction is still limited, particularly when an allochthonous resource can simultaneously subsidize multiple trophic levels. Using the Lake Mývatn region in Iceland as an example system of allochthony and its potential effects on multiple trophic levels, we analyzed a mathematical model to evaluate how pulsed subsidies of aquatic insects affect the dynamics of a soil-plant-arthropod food web. We found that the relative balance of top-down and bottom-up effects on a given food web compartment was determined by trophic position, subsidy magnitude, and top predators' ability to exploit the subsidy. For intermediate trophic levels (e.g., detritivores and herbivores), we found that the subsidy could either alleviate or intensify top-down pressure from the predator. For some parameter combinations, alleviation and intensification occurred sequentially during and after the resource pulse. The total effect of the subsidy on detritivores and herbivores, including top-down and bottom-up processes, was determined by the rate at which predator consumption saturated with increasing size of the allochthonous subsidy, with greater saturation leading to increased bottom-up effects. Our findings illustrate how resource pulses to multiple trophic levels can influence food web dynamics by changing the relative strength of bottom-up and top-down effects, with bottom-up predominating top-down effects in most scenarios in this subarctic system.

    View details for DOI 10.1002/ecy.3197

    View details for PubMedID 32966617

  • phyr: Anrpackage for phylogenetic species-distribution modelling in ecological communities METHODS IN ECOLOGY AND EVOLUTION Li, D., Dinnage, R., Nell, L. A., Helmus, M. R., Ives, A. R. 2020; 11 (11): 1455-1463
  • jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator. Molecular ecology resources Nell, L. A. 2020; 20 (4): 1132-1140


    High-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage and bioinformatic tools. Simulating HTS data better informs these decisions, as users can validate software by comparing output to the known simulation parameters. However, current standalone HTS simulators cannot generate variant haplotypes under even somewhat complex evolutionary scenarios, such as recombination or demographic change. This greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) sets of variant haplotypes from a reference genome and (ii) reads from both Illumina and Pacific Biosciences platforms. Haplotypes can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing and optical/PCR duplicates. It can read reference genomes from fasta files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows and Linux systems.

    View details for DOI 10.1111/1755-0998.13173

    View details for PubMedID 32320523

  • Morphological bases for intestinal paracellular absorption in bats and rodents. Journal of morphology Brun, A., Fernández Marinone, G., Price, E. R., Nell, L. A., Simões, B. M., Castellar, A., Gontero-Fourcade, M., Cruz-Neto, A. P., Karasov, W. H., Caviedes-Vidal, E. 2019; 280 (9): 1359-1369


    Flying mammals present unique intestinal adaptations, such as lower intestinal surface area than nonflying mammals, and they compensate for this with higher paracellular absorption of glucose. There is no consensus about the mechanistic bases for this physiological phenomenon. The surface area of the small intestine is a key determinant of the absorptive capacity by both the transcellular and the paracellular pathways; thus, information about intestinal surface area and micro-anatomical structure can help explain differences among species in absorptive capacity. In order to elucidate a possible mechanism for the high paracellular nutrient absorption in bats, we performed a comparative analysis of intestinal villi architecture and enterocyte size and number in microchiropterans and rodents. We collected data from intestines of six bat species and five rodent species using hematoxylin and eosin staining and histological measurements. For the analysis we added measurements from published studies employing similar methodology, making in total a comparison of nine species each of rodents and bats. Bats presented shorter intestines than rodents. After correction for body size differences, bats had ~41% less nominal surface area (NSA) than rodents. Villous enhancement of surface area (SEF) was ~64% greater in bats than in rodents, mainly because of longer villi and a greater density of villi in bat intestines. Both taxa exhibited similar enterocyte diameter. Bats exceeded rodents by ~103% in enterocyte density per cm2 NSA, but they do not significantly differ in total number of enterocytes per whole animal. In addition, there is a correlation between SEF and clearance per cm2 NSA of L-arabinose, a nonactively transported paracellular probe. We infer that an increased enterocyte density per cm2 NSA corresponds to increased density of tight junctions per cm2 NSA, which provides a partial mechanistic explanation for understanding the high paracellular absorption observed in bats compared to nonflying mammals.

    View details for DOI 10.1002/jmor.21037

    View details for PubMedID 31301093

  • Pilot study: use of contrast-enhanced ultrasonography in feline renal transplant recipients. Journal of feline medicine and surgery Greenbarg, E. H., Jiménez, D. A., Nell, L. A., Schmiedt, C. W. 2018; 20 (4): 393-398


    Objectives The study aims were to evaluate the feasibility of contrast-enhanced ultrasonography in feline renal transplant recipients in the post-transplantation period and to report findings in a case with presumptive delayed allograft ischemia. Methods Cats were imaged postoperatively using contrast harmonic ultrasonography after a bolus injection of a microbubble contrast medium. Time/mean pixel intensity curves were generated for cortical and medullary regions of interest in the renal allograft in each cat. Arrival time, time to peak, wash-in slope, wash-out slope, mean transit time and renal blood flow were calculated for each area. Results Within the renal cortices of cats without ureteral obstruction 1 day post-transplantation, arrival time was 2.0-6.3 s, time to peak was 3.6-30.1 s, wash-in rate was 2.45-41.14 mean pixel intensity (MPI)/s, wash-out rate was -2.01 to -0.47 MPI/s and blood flow was 6.1-106.5 MPI/s. Ratio mean transit time was 0.29-1.29. Typical cortical and medullary perfusion patterns were observed in these cats. In one cat with delayed graft ischemia followed by presumptive acute transplant rejection, dynamic and heterogeneous cortical and medullary perfusion was demonstrated. Decreases in cortical blood flow were paralleled by elevated serum creatinine. Conclusions and relevance Contrast-enhanced ultrasonography can be used in feline renal transplant recipients and provides both qualitative and quantitative data regarding renal allograft perfusion.

    View details for DOI 10.1177/1098612X17713855

    View details for PubMedID 28621156

  • Presence of Breeding Birds Improves Body Condition for a Crocodilian Nest Protector. PloS one Nell, L. A., Frederick, P. C., Mazzotti, F. J., Vliet, K. A., Brandt, L. A. 2016; 11 (3): e0149572


    Ecological associations where one species enhances habitat for another nearby species (facilitations) shape fundamental community dynamics and can promote niche expansion, thereby influencing how and where species persist and coexist. For the many breeding birds facing high nest-predation pressure, enemy-free space can be gained by nesting near more formidable animals for physical protection. While the benefits to protected species seem well documented, very few studies have explored whether and how protector species are affected by nest protection associations. Long-legged wading birds (Pelecaniformes and Ciconiiformes) actively choose nesting sites above resident American alligators (Alligator mississippiensis), apparently to take advantage of the protection from mammalian nest predators that alligator presence offers. Previous research has shown that wading bird nesting colonies could provide substantial food for alligators in the form of dropped chicks. We compared alligator body condition in similar habitat with and without wading bird nesting colonies present. Alligator morphometric body condition indices were significantly higher in colony than in non-colony locations, an effect that was statistically independent of a range of environmental variables. Since colonially nesting birds and crocodilians co-occur in many tropical and subtropical wetlands, our results highlight a potentially widespread keystone process between two ecologically important species-groups. These findings suggest the interaction is highly beneficial for both groups of actors, and illustrate how selective pressures may have acted to form and reinforce a strongly positive ecological interaction.

    View details for DOI 10.1371/journal.pone.0149572

    View details for PubMedID 26934602

    View details for PubMedCentralID PMC4775066

  • Fallen Nestlings and Regurgitant as Mechanisms of Nutrient Transfer from Nesting Wading Birds to Crocodilians WETLANDS Nell, L. A., Frederick, P. C. 2015; 35 (4): 723-732
  • The evolutionary consequences of blood-stage vaccination on the rodent malaria Plasmodium chabaudi. PLoS biology Barclay, V. C., Sim, D., Chan, B. H., Nell, L. A., Rabaa, M. A., Bell, A. S., Anders, R. F., Read, A. F. 2012; 10 (7): e1001368


    Malaria vaccine developers are concerned that antigenic escape will erode vaccine efficacy. Evolutionary theorists have raised the possibility that some types of vaccine could also create conditions favoring the evolution of more virulent pathogens. Such evolution would put unvaccinated people at greater risk of severe disease. Here we test the impact of vaccination with a single highly purified antigen on the malaria parasite Plasmodium chabaudi evolving in laboratory mice. The antigen we used, AMA-1, is a component of several candidate malaria vaccines currently in various stages of trials in humans. We first found that a more virulent clone was less readily controlled by AMA-1-induced immunity than its less virulent progenitor. Replicated parasites were then serially passaged through control or AMA-1 vaccinated mice and evaluated after 10 and 21 rounds of selection. We found no evidence of evolution at the ama-1 locus. Instead, virulence evolved; AMA-1-selected parasites induced greater anemia in naïve mice than both control and ancestral parasites. Our data suggest that recombinant blood stage malaria vaccines can drive the evolution of more virulent malaria parasites.

    View details for DOI 10.1371/journal.pbio.1001368

    View details for PubMedID 22870063

    View details for PubMedCentralID PMC3409122