Unraveling the Genomic Diversity and Admixture History of Captive Tigers in the United States

Abstract

Genetic and 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 subspecies, relatively few private variants, and fewer deleterious mutations. We also observe inbreeding coefficients that are similar to wild populations, suggesting that inbreeding in captive populations is not prevalent as previously thought, although there are some individuals within the Generic population that are quite inbred. Our results reflect the complex demographic history of the Generic tiger population in the U.S. Additionally, we develop a reference panel for tigers and show that it can be used with imputation to accurately distinguish individuals and assign ancestry even with ultra-low coverage (0.25×) data. We anticipate this comprehensive study and panel will propel future research and preservation of tigers in the U.S. and globally.

Extreme in Every Way: Exceedingly Low Genetic Diversity in Snow Leopards Due to Persistently Small Population Size

“…Notably, snow leopard heterozygosity was lower than that of cheetahs, which have long been considered the archetype of low heterozygosity in big cats 11,38 . The relative values of observed heterozygosity among all the other species for which we calculated heterozygosity were consistent with previous work 12,[39][40][41] . Within snow leopards, we found observed heterozygosity to be consistently low across all sampled locations (Fig.…”

Counting the genetic ancestors from source populations in members of an admixed population

“…Our empirical focus has been on an example from human populations, but the model can be applied more generally to diploid species in which mechanistic admixture models and recombination models can be specified. To take one example, Armstrong et al (2023) have studied genetic variation in captive tigers, a population formed through admixture of wild source populations from several different parts of Asia. Armstrong et al (2023) have estimated genomic proportions that trace to the various source populations.…”

“…To take one example, Armstrong et al (2023) have studied genetic variation in captive tigers, a population formed through admixture of wild source populations from several different parts of Asia. Armstrong et al (2023) have estimated genomic proportions that trace to the various source populations. With a generalization to permit more than 2 sources, our model can assist in understanding the properties of the genetic ancestors that have given rise to typical individual captive tigers.…”

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

“…Samples were prepared and sequenced as described above. Kylo-Ren's 10x Genomics Chromium sequencing data were previously reported in (Armstrong et al 2022;Armstrong et al 2024) (NCBI accession SRR16296779, ). Additionally, standard paired-end libraries for all individuals were prepared using the Illumina Nextera DNA library preparation protocol with adjustments as described in (Baym et al 2015).…”