The Hybrid Origin of the Indochinese Gray Langur Trachypithecus crepusculus

Abstract

Hybridization among formerly separated lineages is a common phenomenon in almost all groups of organisms, including primates. Indicators of hybridization include discordant phylogenies derived from different genetic markers or from genetic and phenotypic characters. Such conflicting phylogenies have been reported for the Indochinese gray langur, Trachypithecus crepusculus. To further investigate the evolutionary history of this species, we analyzed complete mitochondrial (mtDNA) genomes and 12 nuclear loci from several representatives of all four Trachypithecus species groups. Our nuclear DNA (nucDNA) phylogeny agreed with the external appearance of the groups: T. crepusculus clustered with the T. obscurus group, as sister to T. barbei. In contrast, mtDNA data suggested T. crepusculus is sister to the T. francoisi group. Coalescent-based methods favored hybridization as the main reason for the observed gene tree discordance and dated the divergence of T. crepusculus from the T. francoisi group (mtDNA) at ca. 2.45 million years ago (Ma) and from T. barbei (nucDNA) at ca. 0.36 Ma. We hypothesize that the most likely explanation for the observed pattern is male-mediated gene flow from T. barbei into an ancestral form of T. crepusculus, followed by nuclear swamping. This predicts that the nuclear genome of T. crepusculus might be highly similar to that of T. barbei, while the original mtDNA genome was retained as a relict of an otherwise extinct species. Our study provides further data about the putative hybrid status of a colobine taxon and highlights the need for multilocus analyses in phylogenetics.