Data from: 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
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.