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.
Appendix 1: Cr, 761 taxa
A 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.nex
Appendix 2: Cytb, 173 taxa
A 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.txt
Appendix 3: Cr, without DOM
A 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.nex
Appendix 4: Concatenated, 30 taxa
A 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.nex
Appendix 5: Cr, MUS
A 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.nex
Appendix 6: Cr, DOM
A 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.nex
Appendix 7: cytb, CAS
A 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.nex
Appendix 8: Cytb, DOM
A 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.nex
Appendix 9: Cytb, Mus
A 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.nex
Appendix 10: Concatenated, CAS
A 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.nex
Appendix 11: Concatenated, MUS
A 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.nex
Appendix 12: Supplementary Table S1
List of mouse individuals used in this study for determination of mitochondrial sequences.
Appendix_12_Supplementary_Table_S1.xlsx
Appendix 13: Supplementary Figure S1
Figure 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
