Genetic Diversity, Genetic Structure, and Demographic History of Black Snub‐Nosed Monkey (<i>Rhinopithecus strykeri</i>) in the Gaoligong Mountains, Southwestern China

The Gaoligong Mountains, located in the southeastern Tibetan Plateau, is one of the world's biodiversity hotspots and provides a refugium for many endangered endemic animals. In this study, we reported a population genetic study on black snub-nosed monkey (Rhinopithecus strykeri), a critically endangered primate endemic to the Gaoligong Mountains, yet their large-scale population genetic study remains underexplored. Here, we performed population genetic analyses from two geographical populations (Pianma and Luoma) based on targeted genomic single-nucleotide polymorphism (SNP) data (37.7 K) and mitochondrial DNA (mtDNA) control region (842 bp). Both nuclear SNP data and mtDNA revealed relatively low levels of genetic variation in both populations compared to other reported primates, which is most likely to be explained by loss of historical genetic diversity due to inbreeding and long-term small effective population size, thus potentially aggravating the effects of inbreeding and genetic depression. Phylogenetic and population structure analyses for mtDNA revealed two deep lineages (approximately 0.69 million years ago), but limited genetic differentiation in nuclear data, which might have been caused by the Late Cenozoic uplift of the Tibetan Plateau and glacial refuge, and subsequent secondary contact as a result of historically high and bidirectional gene flow between populations. Ecological niche modeling and landscape connectivity analyses also showed historical and recent connectivity between two geographical populations. The demographic history inferred from both mtDNA and nuclear data revealed at least two continuous declines in the effective population size occurring around 43 Kya and 8-10 Kya, respectively, probably due to Pleistocene glaciations and subsequent human activities. Our results provide the first detailed and comprehensive genetic insights into the genetic diversity, population structure, and demographic history of a critically endangered species, and provide essential baseline information to guide conservation efforts.