Resolving the Taxonomic Status of Chukotkan Snow Sheep (Ovis nivicola) Using Genome-Wide Single-Nucleotide Polymorphism (SNP) and Mitochondrial Data

The intraspecific taxonomy of snow sheep (Ovis nivicola) is one of the most controversial issues in Caprinae systematics. Although eight subspecies have been described using morphological traits, the validity of several taxa, particularly those in the eastern part of their geographical range, remains disputed. We investigated the phylogenetic relationships and genetic diversity of snow sheep in the Chukotka Autonomous Okrug using genome-wide single-nucleotide polymorphism (SNP) data (935 loci after filtering) and complete mitochondrial genomes from 57 individuals collected across the Russian Far East (Chukotka Autonomous Okrug, Kamchatka Krai, Magadan Oblast, and Republic of Sakha (Yakutia)). Post SNP-genotyping nuclear genomic studies using principal component analysis (PCA), ADMIXTURE, pairwise FST and Neighbor-Net revealed two clearly differentiated groups within Chukotka. One included individuals from the Koryak Mountains that are genetically indistinguishable from the Koryak subspecies (O. n. koriakorum) of northern Kamchatka. The other one encompassed individuals from the Anadyr Plateau and the Chukotka Mountains cluster with the Okhotsk subspecies (O. n. alleni) of the Kolyma Mountains. Bayesian phylogeny of complete mitochondrial genomes fully corroborated the nuclear results: Koryak Mountains samples formed a monophyletic clade, while Anadyr–Chukotka samples grouped with Kolyma Mountains individuals. Genetic diversity indices (UHE, AR, FIS) in both Chukotka groups were comparable to other studied populations and showed no signs of inbreeding depression. Our results provide important insights and can be used to develop science-based strategies for preserving the population-genetic diversity of snow sheep.