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.

Population Structure of Macaca fascicularis aurea, and their Genetic Relationships with M. f. fascicularis and M. mulatta Determined by 868 RADseq‐Derived Autosomal SNPs—A consideration for biomedical research

“…mulatta on the genetic composition of M . fascicularis populations in Indochina 23,30,34,36 . Based on the ML tree and the highest posterior probability of three genetic groups (Figure 2B), the separation between the Indochinese and Sundaic M .…”

“…fascicularis exhibit varying levels of M . mulatta genetic ancestry, which gradually decline from the north to the south of their distribution range 24,34 …”

“…fascicularis is lacking compared to what is known to occur between populations of M mulatta and M . fascicularis 2,22,23,24,27,28,29,33,34,35,36 . To gain more detailed information on the genetic structure and composition of M .…”

Importance of Thai macaque bioresources for biological research and human health

“…fascicularis and M . mulatta in Thailand 64 . The researchers hypothesized that secondary contact might have occurred between the two species, resulting in interspecific gene flow from M .…”

Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European range

“…In such cases, reconstructing the divergence history between the two species would depend on the geographic location of the set of populations sampled, because populations also evolve in space (see Bradburd & Ralph, 2019 for a recent review on spatial population genetics). While some studies have previously reconstructed the divergence history between several species using multiple population pairs (e.g., Zieliński et al, 2016;Filatov et al, 2016;Pabijan et al, 2017;Rougemont and Bernatchez, 2018;Ito et al, 2020;Garcia-Erill et al, 2021), to our knowledge variation inferred between the multiple comparisons has not been reported.…”