Genomic affinity following restoration of a locally extirpated species: a case study of desert bighorn sheep in Texas

Prior to its extirpation in the 1960s, Ovis canadensis texianus (a subspecies of desert bighorn sheep, DBS) occupied 16 mountain ranges in the Trans-Pecos Region of Texas. Restocking efforts relied on translocating individuals of DBS from Arizona, Nevada, Utah, and Mexico. One recipient site, Elephant Mountain Wildlife Management Area (WMA), now the primary source-stock for translocations in Texas, was examined to measure its genomic ancestry compared to other DBS from the Great Basin, Mojave, and Sonoran deserts. Genomic data (5,434–62,749 single nucleotide polymorphisms) were used to estimate kinship, inbreeding, and effective population size across three time periods (2000, 2017, and 2019). Individuals genetically were most similar to DBS from the Gabbs Valley Range and Muddy Mountains, Nevada (Mojave DBS lineage). Strong signatures of inbreeding were not detected among individuals. In addition, genetic pedigree reconstruction revealed familial relationships, including a four-generation pedigree, and indicated 39.51% and 41.89% of individuals translocated in 2017 and 2019, respectively, were parent–offspring or full-sibling pairs, suggesting capture methods tend to sample highly related individuals. In 2017, population estimates for Elephant Mountain WMA indicated 182 individuals with an effective population size (N_e) of 65, whereas in 2019, N_e was 92 with an estimated population size of 186. Although reintroduction efforts to Elephant Mountain WMA were successful, recurrent epizootic events since 2019 have reduced the population sizes of DBS across the Trans-Pecos Region. Our data illustrate how population genomics and overall assessments of genetic diversity can and should be used to guide management and conservation of DBS.