Unraveling the genomic diversity and admixture history of captive tigers in the United States.
Title | Unraveling the genomic diversity and admixture history of captive tigers in the United States. |
Publication Type | Journal Article |
Year of Publication | 2024 |
Authors | Armstrong EE, Mooney JA, Solari KA, Kim BY, Barsh GS, Grant VB, Greenbaum G, Kaelin CB, Panchenko K, Pickrell JK, Rosenberg N, Ryder OA, Yokoyama T, Ramakrishnan U, Petrov DA, Hadly EA |
Journal | Proc Natl Acad Sci U S A |
Volume | 121 |
Issue | 39 |
Pagination | e2402924121 |
Date Published | 2024 Sep 24 |
ISSN | 1091-6490 |
Keywords | Animals, Animals, Zoo, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genome, Genomics, Phylogeny, Tigers, United States |
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 (), 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. |
DOI | 10.1073/pnas.2402924121 |
Alternate Journal | Proc Natl Acad Sci U S A |
PubMed ID | 39298482 |
PubMed Central ID | PMC11441546 |
Grant List | GRFP / / NSF | NSF Graduate Research Fellowship Program (GRFP) / HHMI Professors Program / / HHMI (HHMI) / |