Insights into genetic differentiation and migration routes of rhesus macaques (Macaca mulatta) based on samples from almost all distribution areas

Abstract

Background Rhesus macaque (Macaca mulatta) is commonly used in biomedical research because of its high similarity with human beings, and understand the genetic diversity of wild macaques is necessary. Although there have been many genetic diversity reports on this species, there is still a deficiency of comprehensive understanding of genetic background due to limited sample range, especially, involving Qinghai-Tibet Plateau samples. Here, extensive sampling is conducted in macaque populations across almost all distribution areas, including China, India, Vietnam, Bangladesh, Nepal and Myanmar. It also focuses on genetic differentiation, migration diffusion and population dynamics in western China. Results 57 unique haplotypes were obtained from 452 samples in 34 geographical areas and 60 mtDNA haplotypes were downloaded, resulting in a total of 117 haplotypes covering almost all macaque distribution areas. The phylogenetic analysis exhibited three major haplogroups (Clade Ⅰ~Ⅲ) with obvious geographical distribution patterns. Clade Ⅰ is mainly composed of macaques from western China, Clade Ⅱ is from central and eastern China, Vietnam, India and Nepal, and Clade Ⅲ is from Bangladesh and Myanmar. The divergence age among three Clade is 1.67 ~ 2.81 Ma. Further, Clade Ⅰ from western China is divided into five obviously divergent subclades (Sub A-E). We found macaques in western Sichuan contain two morphology subspecies: M. m. lasiotus and M. m. vestita, different from the previous one subspecies (M. m. lasiotus) report. Notably, comprehensive analysis suggested that the populations in southeastern Sichuan, eastern Yunnan and Guizhou (Sub B) may be an independent new subspecies. We also found Bangladesh may be a re-radiation central of the whole rhesus macaques, and three possible radiation routes of rhesus macaques entering China were speculated: from Yunnan to western China, from Guangxi to central and eastern China, and along the coastline to Hainan. In addition, demographic history analysis revealed the macaque population is stable and has not experienced significant population expansion. Conclusions In conclusion, this study investigated the distribution patterns of different subspecies of macaques, and proposed possible radiation routes. To our knowledge, it’s the first comprehending analysis based on almost all distribution areas of rhesus macaques.

Effects of climate change and anthropogenic activity on ranges of vertebrate species endemic to the Qinghai–Tibet Plateau over 40 years

“…We obtained 2973 occurrence records on 19 endemic vertebrate species that met our selection criteria: 6 species of birds ( Ianthocincla maxima , Gyps himalayensis , Tetraophasis szechenyii , G. nigricollis , Pyrgilauda ruficollis , and Tetraogallus tibetanus ); 8 species of mammals ( Ochotona curzoniae , Marmota himalayana , Bos mutus , Pseudois nayaur , Vulpes ferrilata , Pa. hodgsonii , Macaca mulatta vestita , and E. kiang ); 3 species of amphibians ( Nanorana parkeri , Bufo tibetanus , and Scutiger boulengeri ); and 2 species of reptiles ( Laudakia sacra and Phrynocephalus theobaldi ) (Appendix S1). Macaca mulatta vestita is a subspecies of M. mulatta , on the basis of external morphological differences and skull characteristics and molecular data, and occurs in the Chinese provinces of Qinghai, Sichuan, Tibet, and Yunnan (Jiang et al., 1991; Zhang & Shi, 1993; Zhang et al., 2022).…”