Secondary contact and genomic admixture between rhesus and long‐tailed macaques in the Indochina Peninsula

Abstract

Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome‐scale analysis and a geographically wide sampling of wild populations. Our study applied double‐digest restriction site‐associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long‐tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long‐tailed macaque distribution (south) as well as the presence of one northern population of long‐tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long‐tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque‐biased alleles have widely introgressed into long‐tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species‐specific morphological characteristics.