Contact

  • Academic
    vbg6@stanford.edu
    University - Student Department: Biology Position: Graduate

All Publications

  • Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator. bioRxiv : the preprint server for biology Grant, V. B., Hunnicutt, K., Schroeder, M., Küsters, M., Oppenheimer, J., Banerjee, S., Baczenas, J. J., Petrov, D., Bishop, J. M., Lamberski, N., Wilson, B., Sliwa, A., Shapiro, B., Solari, K. A., Aguillón, S. M., Armstrong, E. E., Schumer, M. 2026

    Abstract

    Black-footed cats (Felis nigripes) are one of Africa's least studied felines. The population dynamics and demographic history of this solitary species have not been well-described. Reports of ongoing decline of present-day populations resulted in the IUCN Red List categorizing the species as vulnerable to extinction. As populations decline and become isolated from each other, they become susceptible to strong genetic drift and inbreeding, which can lead to the accumulation of deleterious alleles and increased extinction risk. However, the IUCN cited data deficiencies across the species range as a limitation in this categorization for black-footed cats. In cases where ecological surveys are lacking, range-wide population genomic surveys can improve our understanding of population dynamics.In the first genomic study of free-roaming individuals, we sequenced whole genomes of black-footed cats (N=44) from across their distribution. To do so, we incorporated whole genome sequences generated from both modern biological samples and century-old museum specimens. We assembled a highly contiguous reference genome using a combination of PacBio HiFi data and publicly available Hi-C data and investigated the demographic history, population structure, and genetic diversity of wild black-footed cats. We found evidence of historical effective population sizes of ~11,500 individuals, which is lower than estimates reported in other felid species. Consistent with modest historical population sizes, we found that present-day genome-wide diversity was low (π ≈ 0.0004). However, despite low genetic diversity, we find that black-footed cat genomes do not harbor long runs of homozygosity. Simulation results indicate that low present-day genetic diversity may simply result from modest historical population size. However, other analyses point to evidence of a population contraction in the last 50 generations, which could contribute to future genomic erosion. We also compared genomic variation in populations across the range to evaluate patterns of population structure, finding evidence of higher genetic similarity between individuals in closer geographic proximity.Overall, these results provide range-wide information about the demographic history and present-day genetic diversity of an understudied species. Together with analyses of population structure, we speculate that there may be greater connectivity between populations of black-footed cats than previously assumed. Our study underscores the utility of genomic data in providing insights into population dynamics for better conservation management.

    View details for DOI 10.64898/2026.05.29.728895

    View details for PubMedID 42282534

    View details for PubMedCentralID PMC13251930

  • Unraveling the genomic diversity and admixture history of captive tigers in the United States. Proceedings of the National Academy of Sciences of the United States of America Armstrong, E. E., Mooney, J. A., Solari, K. A., Kim, B. Y., Barsh, G. S., Grant, V. B., Greenbaum, G., Kaelin, C. B., Panchenko, K., Pickrell, J. K., Rosenberg, N., Ryder, O. A., Yokoyama, T., Ramakrishnan, U., Petrov, D. A., Hadly, E. A. 2024; 121 (39): e2402924121

    Abstract

    Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (Panthera tigris), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25×) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex- and in situ populations.

    View details for DOI 10.1073/pnas.2402924121

    View details for PubMedID 39298482

  • Genomic insights into variation in thermotolerance between hybridizing swordtail fishes. Molecular ecology Payne, C., Bovio, S., Powell, D., Gunn, T., Banerjee, S., Grant, V., Rosenthal, G. G., Schumer, M. 2022

    Abstract

    Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.

    View details for DOI 10.1111/mec.16489

    View details for PubMedID 35510780