DOI: 10.5061/dryad.rf161
title: Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

description: We examined sequence variation of mitochondrial DNA control region and
 cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from
 ca. 200 localities, with 290 new samples drawn primarily from previously
 unsampled portions of their Eurasian distribution and with the objective
 of further clarifying evolutionary episodes of this species before and
 after the onset of human-mediated long-distance dispersals. Phylogenetic
 analysis of the expanded data detected five equally distinct clades, with
 geographic ranges of northern Eurasia (musculus, MUS), India and Southeast
 Asia (castaneus, CAS), Nepal (unspecified), western Europe (domesticus,
 DOM), and Yemen (gentilulus). Our results confirm previous suggestions of
 Southwestern Asia as the likely place of origin of M. musculus and the
 region of Iran, Afghanistan, Pakistan, and northern India, specifically as
 the ancestral homeland of CAS. The divergence of the subspecies lineages
 and of internal sublineage differentiation within CAS were estimated to be
 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a
 split of M. musculus and Mus spretus at 1.7 mya. Of four CAS sublineages
 detected, only one extends to eastern parts of India, Southeast Asia,
 Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin
 and Japan, implying a dramatic range expansion of CAS out of its homeland
 during an evolutionary short time, perhaps associated with the spread of
 agricultural practices. Multiple and non-coincident eastward dispersal
 events of MUS sublineages to distant geographic areas, such as northern
 China, Russia, and Korea, are inferred, with the possibility of several
 different routes.
description: Appendix 1: Cr, 761
 taxaA
 nexus file having mitochondrial control region sequences from 760 house
 mice (Mus musculus) and one from outgroup taxon Mus macedonicus being
 modified for alignment. This nexus file was used to construct maximum
 likelihood trees and Neighbor-Net networks.Appendix_1_Cr_761taxa.nexAppendix 2: Cytb, 173 taxaA nexus file having mitochondrial cytochrome b gene sequences (1140 bp) from 169 house mice (Mus musculus) and four from outgroup taxa. This nexus file was used for the maximum likelihood, Neighbor Net and BEAST analyses.Appendix_2_Cytb_173taxa.txtAppendix 3: Cr, without DOMA nexus file having mitochondrial control region sequences from 213 house mice (Mus musculus) and one from outgroup taxon Mus macedonicus being modified for alignment. This nexus file was created by removing sequences genotyped for Mus musculus domesticus from the input file of Appendix 1 and used to construct Neighbor-Net networks.Appendix_3_Cr_withoutDOM.nexAppendix 4: Concatenated, 30 taxaA nexus file having concatenated mitochondrial DNA haplotypes (control region and cytochrome b gene) representing the four major haplogroups of Mus musculus and a outgroup taxon M. macedonicus. This nexus file was used to construct phylogenetic trees using the maximum likelihood, maximum parsimonious and neighbor joining methods.Appendix_4_Concatenated_30taxa.nexAppendix 5: Cr, MUSA nexus file having mitochondrial control region sequences from 132 house mice (Mus musculus) belong to the subspecies group Mus musculus musculus (MUS). This nexus file was used to construct Neighbor-Net networks.Appendix_5_Cr_MUS.nexAppendix 6: Cr, DOMA nexus file having mitochondrial control region sequences from 561 house mice (Mus musculus) belong to the subspecies group Mus musculus domesticus (DOM). This nexus file was used to construct Neighbor-Net networks.Appendix_6_Cr_DOM.nexAppendix 7: cytb, CASA nexus file having mitochondrial cytochrome b gene sequences from 38 house mice (Mus musculus) belong to the subspecies group Mus musculus castaneus (CAS). This nexus file was used for construction of Neighbor-Net networks and further analyses using DnaSP v5 and Arlequin version 3.5.Appendix_7_Cytb_CAS.nexAppendix 8: Cytb, DOMA nexus file having mitochondrial cytochrome b gene sequences from 88 house mice (Mus musculus) belong to the subspecies group Mus musculus musculus (MUS). This nexus file was used for construction of Neighbor-Net networks and further analyses using DnaSP v5 and Arlequin version 3.5.Appendix_8_Cytb_DOM.nexAppendix 9: Cytb, MusA nexus file having mitochondrial cytochrome b gene sequences from 53 house mice (Mus musculus) belong to the subspecies group Mus musculus domesticus (DOM). This nexus file was used for construction of Neighbor-Net networks and further analyses using DnaSP v5 and Arlequin version 3.5.Appendix_9_Cytb_Mus.nexAppendix 10: Concatenated, CASA nexus file having 49 concatenated mitochondrial DNA haplotypes (control region and cytochrome b gene) belong to the subgroup CAS-1 of the subspecies group Mus musculus castaneus (CAS) and a outgroup taxon belong to the subgroup CAS-2 (BRC3024). This nexus file was used to construct Neighbor-Net networks.Appendix_10_Concatentated_CAS.nexAppendix 11: Concatenated, MUSA nexus file having 39 concatenated mitochondrial DNA haplotypes (control region and cytochrome b gene) representing the subspecies group Mus musculus musculus (MUS) and a outgroup taxon Mus musculus castaneus (HI481). This nexus file was used to construct Neighbor-Net networks.Appendix_11_Concatenated_MUS.nexAppendix 12: Supplementary Table S1List of mouse individuals used in this study for determination of mitochondrial sequences.Appendix_12_Supplementary_Table_S1.xlsxAppendix 13: Supplementary Figure S1Figure S1. Mismatch distributions for Mus musculus subspecies groups and sub-groups therein in a variety of datasets, CAS-1 (a), CAS-1a (b), CAS-1b (c), MUS (d), MUS-1 (e), MUS-1a (f), MUS-1b (g), MUS-1c (h), MUS-2 (i), and DOM (j) using DNASP v5. X axis: number of pairwise differences. Y axis: the continuous and interrupted (connecting circles) lines indicate the expected and observed distributions.Appendix_13_SupFig1_mismatch.pdf