This study focuses on the Siberian roe deer population in the Greater Khingan Mountains, Northeast China. The cold temperate forest ecosystem in this area is distinctive. The Siberian roe deer is a crucial ecological indicator species, and its living conditions hold significant importance for ecological balance. From the winter of 2019 to 2022, 269 fecal samples of Siberian roe deer were collected from four protected areas in the northern part of the Greater Khingan Mountains, Heilongjiang Province. These samples were comprehensively analyzed using mitochondrial DNA and microsatellite markers, combined with conservation genetics evaluation methods. The results revealed that 244 individuals were identified in the fecal samples. The results of a Cyt b genetic analysis of the samples indicated that the haplotype and nucleotide diversity were 88.1% and 20.3%, respectively. The evaluation of 14 pairs of microsatellite loci showed that the average number of alleles was 11.2, and the average expected and observed heterozygosity were 0.672 and 0.506, respectively. Therefore, the overall genetic diversity level is high, but some populations of Siberian roe deer are at risk. AMOVA analysis and STRUCTURE Bayesian clustering confirmed the existence of obvious genetic differentiation among the populations. Historical studies have shown that the HZ and SH populations underwent the earliest diffusion events, and the BJC and SL populations also exhibited related signs (HZ: Huzhong Nature Reserve in the Greater Khingan Mountains; SH: Shuanghe National Nature Reserve in Heilongjiang Province; BJC: Heilongjiang Beijicun National Nature Reserve; SL: Songling District in Heilongjiang Province). Mismatch distribution and neutral tests indicated no expansion events or bottleneck effects in the population, and the inbreeding coefficient was positive, suggesting the possibility of inbreeding. The development potential of the population in the future varies among the various local populations. This study supports the biodiversity of Siberian roe deer at the genetic level to save the population and provides important scientific basis and reference for the protection and management of Siberian roe deer.
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