Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.

摘要: Objectives Long‐tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding complex biogeographical history resulting from drastic changes in sea levels Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) long‐tailed macaque museum specimens have traced their colonization patterns archipelago, but mitogenomes trace only maternal history. Here, our objectives were to phylogeographic using low‐coverage nuclear DNA (nDNA) data specimens. Methods We performed population genetic analyses phylogenetic reconstruction single nucleotide polymorphisms (SNPs) shotgun sequencing 75 localities Asia. Results We show that yields sufficient genome coverage (average ~1.7%) reconstructing relationships SNP data. Contrary expectations divergent results between female philopatric species, phylogeographical SNPs proved be closely similar those found mitogenomes. In particular, nDNA identify two major clades within M. fascicularis: Clade A includes all individuals along with northern Sumatra, while B consists remaining island‐living individuals, including southern Sumatra. Conclusions Overall, we demonstrate provides enough examining broad patterns, although greater depth would needed distinguish very related populations, such as Philippines.