Comprehensive identification and description of mitochondrial DNA haplogroups and sub-haplogroups in snow sheep (Ovis nivicola) in support of their evolutionary history and conservation

Simple Summary: Snow sheep (Ovis nivicola) are wild animals inhabiting remote and isolated mountain ranges across Siberia and the Russian Far East. Because of strong geographic isolation, different populations have accumulated distinct genetic differences over time. Until now, a comprehensive understanding of their maternal genetic lineages was lacking. In this study, we analyzed complete mitochondrial DNA genomes from 257 snow sheep collected across the entire species range. We identified four major maternal lineages (we called these haplogroups A, B, C, and D) and numerous sublineages within them, each associated with specific geographic regions. For example, haplogroup A is almost exclusively found in Kamchatka, whereas haplogroup C is the most widespread. Some traditionally recognized subspecies were shown to contain multiple maternal lineages, indicating that they are genetically more complex than previously thought. Our results suggest that snow sheep survived the climatic fluctuations of the Ice Age in separate mountain refugia and subsequently expanded from these isolated areas. This new mitochondrial haplogroup classification system will support more effective conservation strategies, help define appropriate management units, and improve our understanding of how large mammals persisted across Siberia and the Russian Far East during periods of dramatic climate change.

Abstract: Mitochondrial DNA is a powerful marker for reconstructing maternal lineages and phylogeographic history in wild species. The snow sheep (Ovis nivicola), a mountain ungulate endemic to Siberia and the Russian Far East, is characterized by strong geographic fragmentation and a complex taxonomic structure. A formal mitochondrial haplogroup classification system for the species has, however, been lacking. In this study, we sequenced and analyzed 257 complete mitochondrial genomes representing all major populations across the species’ range. Using phylogenetic reconstruction and diagnostic mutations (present in 100% of individuals within clades), we identified four major haplogroups (A–D) and multiple nested sub-haplogroups with clear geographic structuring. Divergence times were estimated using Bayesian analysis in BEAST 2.7.7 with a relaxed lognormal clock model, calibrated by the divergence between O. dalli and O. canadensis. The results showed that haplogroup A is almost exclusive to Kamchatka, haplogroup B is predominant in northern populations, haplogroup C is the most widespread and diverse across the species range, and haplogroup D is largely restricted to the Verkhoyansk region. The mitochondrial data largely support traditional subspecies taxonomy but reveal mitochondrial polyphyly in some subspecies, particularly O. n. lydekkeri and O. n. koriakorum. This study provides the first comprehensive mitochondrial haplogroup system for snow sheep and shows that the observed mitochondrial phylogeographic patterns are consistent with an important influence of Pleistocene glacial cycles and prolonged geographic isolation on its current genetic structure. These findings offer important insights for conservation management and for understanding the evolutionary history of wild sheep in Northeast Asia.