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

Tsuyoshi Ito, Sreetharan Kanthaswamy, Srichan Bunlungsup, Robert F. Oldt, Paul Houghton, Yuzuru Hamada, Suchinda Malaivijitnond

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1164-1179
Number of pages16
JournalJournal of Evolutionary Biology
Issue number9
StatePublished - Sep 1 2020


  • Indochina
  • RAD-seq
  • hybridization
  • reproductive isolation
  • speciation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics


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