DOI: 10.5061/dryad.mcvdnck0b
title: Data from: Phylogeographic history of Japanese macaques

description: 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.
description: We used 113 blood- or tissue-derived DNA samples from 10
 populations of <i>Macaca fuscata </i>(<i>N </i>=
 102), the Chinese and Indian populations of <i>M. mulatta
 </i>(<i>N </i>= 6), <i>M. cyclopis
 </i>(<i>N </i>= 2), and <i>M. fascicularis
 </i>(<i>N </i>= 3). The ddRAD library preparation
 followed the quaddRAD procedure of Franchini et al. (2017) with minor
 modifications.
description: fasta_chr.zip: consensus sequences of each chromosome in fasta
 format for the calculation of nucleotide diversity (the outputs from
 Stacks populations function with --fasta-samples option)
 fastsimcoal2.zip: data and model settings for fastsimcoal2
 demographic analyses<br>     data: five replicates of
 multidimensional folded SFS<br>     models: template (.tpl) and
 estimation (.est) files of eight demographic models
 paup.zip: nexus files for phylogenetic inference using
 PAUP<br>     nj_a.nexus: autosomal SNVs for NJ phylogenetic
 inference<br>     nj_x.nexus: X-chromosome SNVs for NJ phylogenetic
 inference<br>     nj_y.nexus : Y-chromosome SNVs for NJ phylogenetic
 inference<br>     svdq_ind.nexus: autosomal SNVs for
 individual-level SVDquartets phylogenetic inference<br>   
  svdq_pop.nexus: autosomal SNVs for population-level SVDquartets
 phylogenetic inference populations.haps.radpainter:
 haplotype data for fineRADstructure analysis raxml.phy:
 autosomal SNVs in phylip format for ML phylogenetic inference using
 RAxML-NG sex_pop_cluster_list.txt: tab-delimited text
 file of id, sex (female or male), population, and cluster
 splitstree4.dist: uncorrected p-distance data for phylogenetic
 network analysis using SplitsTree4 (the outputs from PAUP)
 treemix.zip: allele frequency data for TreeMix analysis<br>
     treemix_full.frq.gz: full dataset<br>     treemix_sub.frq.gz:
 subset with no missing data vcf.zip: vcf files for
 population structure analyses (used after only Japanese macaque samples
 were extracted)<br>     a.vcf: autosomal SNVs for ADMIXTURE and
 PCA<br>     x.vcf: X-chromosome SNVs for ADMIXTURE