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

Genomic studies of rare and endangered species have focused broadly on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, many studies do not consider genetic reserves that are potentially housed in captive populations. For tigers (Panthera tigris) in particular, captive individuals vastly outnumber those in the wild, and their diversity remains largely unexplored. Here, we present the first large-scale genetic study of the private (non-zoo) captive tiger population in the United States (U.S.), also known as ‘Generic’ tigers. We find that the U.S. Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies (P. t. altaica, Amur; P. t. tigris, Bengal; P. t. corbetti, Indochinese; P. t. jacksoni, Malayan; P. t. amoyensis, South China; P. t. sumatrae, Sumatran). We show that the Generic tiger population has a comparable amount of genetic diversity to most wild..., This dataset was collected through whole-genome sequence and subsequent variant calling of tigers (Panthera tigris). Variant calling was performed using GATK by Gencove Inc. Further details can be found in the available preprint: https://www.biorxiv.org/content/10.1101/2023.06.19.545608, , # Data from \"Unraveling the Genomic Diversity and Admixture History of Captive Tigers in the United States\"

[https://doi.org/10.5061/dryad.k0p2ngff1](https://doi.org/10.5061/dryad.k0p2ngff1)

A total of 155 tiger samples were collected opportunistically during routine vet care from sanctuary facilities (Supplementary Table 1) by vet and sanctuary staff. All samples were extracted using a Qiagen DNeasy kit (Cat. No. 69504) and samples were prepared using a modified Nextera library prep protocol. 78 of these samples were sequenced between approximately 2× and 5× depth. An additional 99, publicly available (as of December 2019) tiger genome samples were downloaded from NCBI. Reads were mapped to the GenTig1.0 genome using BWA-MEM v0.7.1728 and variant calling was subsequently performed by Gencove using the Genome Analysis Toolkit (GATK) v4.1.4.129 according to best practices. Initial variant calling was performed on all samples available at the time, excluding those sequenced at 0.25×, fo...