Genetic characterization of rhesus macaque populations along the southeastern Qinghai-Tibetan plateau based on a mitochondrial ATP6 gene closely related to energy metabolism

Abstract Background Rhesus macaque ( Macaca mulatta ) is widely distributed in China, across different altitudes. The mitochondrial ATP6 gene,an ATPase subunit coding gene with fast evolution rate in the mitochondrial genome, plays an important role in the energy metabolism of animals, which may be a good molecular marker for studying the adaptive evolution of animals. Herein, we detected ATP6 genes of 334 rhesus macaques of 19 populations from multiple regions in China with an elevation span of 5-4000m, and mainly carried out the population genetic and evolutionary analysis in these macaques. Our aim is to explore the molecular mechanism of rhesus macaques in adapting to different environments, especially in high altitude extreme environments. Results A total of 50 haplotypes were identified, and significant differences were found in haplotype sequences of rhesus macaque ATP6 gene at different elevations, especially in the high altitude haplotypes with multiple specific variation sites, leading to some region-specific haplotypes. Population genetic analysis showed that rhesus macaque had high genetic diversity ( Pi =0.02332 ± 0.00226, Hd =0.802 ± 0.022 and K =14.982), and there was obvious genetic differentiation among different geographical populations. Conclusions The results showed that the ATP6 gene had undergone adaptive evolution in the process of rhesus macaque adapting to different elevations, especially the high altitude environments. We also found that geographical isolation was an important factor in the genetic differentiation of rhesus macaque. Phylogenetic analysis showed that there were two subspecies of rhesus macaque in western Sichuan, namely, M. m. lasiotus and M. m. vestita , the former distributed in the western Sichuan region of the Yalong River Basin and the Qinghai-Tibet Plateau, while the latter distributed in the Dadu River Basin and northwest Sichuan. We speculated that the Daxueshan Mountains in western Sichuan was a critical geographical barrier for the differentiation of the two subspecies populations.