Data from: Phylogeographic history of Japanese macaques

Aim: Understanding patterns and processes of geographic genetic variation
within and among closely related species is the essence of phylogeography.
Japanese macaques, also called snow monkeys, have been extensively
studied, particularly in the fields of sociobiology, ecology, and
experimental biology; however, our knowledge of their evolutionary history
is relatively limited. In this study we aimed to elucidate the geographic
patterns of genetic variation in Japanese macaques and the processes that
underlie them. Location: Japan Taxon: Japanese macaque, Macaca fuscata;
rhesus macaque, M. mulatta; Taiwanese macaque, M. cyclopis Methods:
Double-digest restriction-site associated DNA (RAD) sequencing was used to
identify genome-wide single nucleotide variants. We used fineRADstructure,
ADMIXTURE, and principal component analyses to estimate the genetic
population structure. Phylogenetic relationships were then inferred based
on neighbour-net, neighbour-joining, maximum likelihood, and SVDquartets
algorithms. We assessed gene flow using demographic inference and
ABBA-BABA tests, and estimated past distributions during the Last Glacial
Maximum (LGM) using ecological niche modelling. Results: Japanese macaques
show a sister group relationship with a clade comprising Chinese rhesus,
Indian rhesus, and Taiwanese macaques. Japanese macaques comprise major
northeastern and southwestern clades, with a boundary located near central
Japan, and gene flow between the northeastern and southwestern lineages
was detected. Refugia during the LGM were estimated to be distributed in
limited areas along the south coasts of the Japanese archipelago. Main
Conclusions: Phylogeographic variation of Japanese macaques is likely due
mainly to northeast–southwest divergence, which resulted from withdrawal
into refugia during the glacial period, and subsequent gene flow.