Two ancient mitochondrial genomes belonging to the Siberian roe deer (Capreolus pygargus) from Northern China reveal regional genetic structure of populations.

Ancient mitochondrial DNA informs the evolutionary history and regional differentiation of prehistoric wildlife. Two ancient Siberian roe deer specimens, XTS03G from the Xiaotangshan site in eastern Inner Mongolia (ca. 3,500-3,300 BP) and SZC01S from the Shizhaocun site in southeastern Gansu (ca. 6,000 BP), were analyzed by high-throughput sequencing. The datasets exhibited characteristic ancient DNA damage patterns, supporting sample authenticity. A maximum-likelihood phylogenetic tree demonstrated that XTS03G belonged to a previously described subclade P2, whereas SZC01S belonged to another previously described subclade P1 and clustered with previously published ancient samples from northwestern China, forming a distinct prehistoric northwestern Chinese cluster. Our results indicate regional differentiation in the maternal genetic structure of ancient Siberian roe deer in northern China. Nucleotide diversity was slightly higher in ancient than modern populations. Bayesian skyline plot analysis suggested population expansion before approximately 12,000 BP, relative stability with a slight decline between approximately 12,000 and 5,000 BP, and a more pronounced decline after approximately 5,000 BP toward modern times. Our findings provide new molecular evidence for the genetic history of Siberian roe deer in northern China and highlight the value of integrating ancient and modern genetic data for understanding long-term wildlife evolution and conservation.