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

被引：1

作者：

Armstrong, Ellie E. ^{[1
]}

Mooney, Jazlyn A. ^{[1
,2
]}

Solari, Katherine A. ^{[1
]}

Kim, Bernard Y. ^{[1
]}

Barsh, Gregory S. ^{[3
,4
]}

Grant, Victoria B. ^{[1
]}

Greenbaum, Gili ^{[1
,5
]}

Kaelin, Christopher B.

Panchenko, Katya ^{[1
]}

Pickrell, Joseph K. ^{[6
]}

Rosenberg, Noah ^{[1
]}

Ryder, Oliver A. ^{[7
]}

Yokoyama, Tsuya ^{[1
]}

Ramakrishnan, Uma ^{[8
]}

Petrov, Dmitri A. ^{[1
,9
,10
]}

Hadly, Elizabeth A. ^{[1
,11
,12
,13
]}

机构：

[1] Stanford Univ, Dept Biol, Stanford, CA 94305 USA

[2] Univ Southern Calif, Dept Quantitat & Computat Biol, Los Angeles, CA 90089 USA

[3] HudsonAlpha Inst Biotechnol, Huntsville, AL 35806 USA

[4] Stanford Univ, Sch Medine, Dept Genet, Stanford, CA 94305 USA

[5] Hebrew Univ Jerusalem, Dept Ecol Evolut & Behav, Jerusalem, Israel

[6] New York City Dept Educ, New York, NY 11101 USA

[7] San Diego Zoo Wildlife Alliance, Escondido, CA 92027 USA

[8] Tata Inst Fundamental Res, Natl Ctr Biol Sci, Bangalore 560065, India

[9] Chan Zuckerberg Biohub, San Francisco, CA 94158 USA

[10] Stanford Univ, Sch Med, Stanford Canc Inst, Stanford, CA 94305 USA

[11] Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA

[12] Stanford Univ, Woods Inst Environm, Stanford, CA 94305 USA

[13] Stanford Univ, Ctr Innovat Global Hlth, Stanford, CA 94305 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2024年 / 121卷 / 39期

关键词：

Panthera tigris; inbreeding; captive tigers; admixture; BREEDING PROGRAMS; GENETICS; INFERENCE; DECLINE; DRIFT;

D O I：

10.1073/pnas.2402924121

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 "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 (0.25x) 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.

引用

页数：11

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