Unraveling the genomic diversity and admixture history of captive tigers in the United States

作者：Ellie E. Armstrong, Jazlyn A. Mooney, Katherine A. Solari, Bernard Kim, Gregory S. Barsh, Victoria B. Grant, Gili Greenbaum, Christopher B. Kaelin, К.А. Панченко, Joseph K. Pickrell, Noah A. Rosenberg, Oliver A. Ryder, Tsuya Yokoyama, Uma Ramakrishnan, Dmitri A. Petrov, Elizabeth A. Hadly · 发表于：Proceedings of the National Academy of Sciences · 年份：2024 · DOI：10.1073/pnas.2402924121 · 被引用次数：16 · 研究领域：Genetic and phenotypic traits in livestock、Genetic diversity and population structure、Genetic Mapping and Diversity in Plants and Animals

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 dis...