Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

 

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Title Appendix 1: Cr, 761 taxa
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Description 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.
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Title Appendix 2: Cytb, 173 taxa
Downloaded 18 times
Description 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.
Download Appendix_2_Cytb_173taxa.txt (202.6 Kb)
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Title Appendix 3: Cr, without DOM
Downloaded 8 times
Description 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.
Download Appendix_3_Cr_withoutDOM.nex (199.5 Kb)
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Title Appendix 4: Concatenated, 30 taxa
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Description 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.
Download Appendix_4_Concatenated_30taxa.nex (61.09 Kb)
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Title Appendix 5: Cr, MUS
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Description 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.
Download Appendix_5_Cr_MUS.nex (122.6 Kb)
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Title Appendix 6: Cr, DOM
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Description 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.
Download Appendix_6_Cr_DOM.nex (494.3 Kb)
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Title Appendix 7: cytb, CAS
Downloaded 12 times
Description 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.
Download Appendix_7_Cytb_CAS.nex (44.71 Kb)
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Title Appendix 8: Cytb, DOM
Downloaded 8 times
Description 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.
Download Appendix_8_Cytb_DOM.nex (61.96 Kb)
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Title Appendix 9: Cytb, Mus
Downloaded 10 times
Description 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.
Download Appendix_9_Cytb_Mus.nex (103.2 Kb)
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Title Appendix 10: Concatenated, CAS
Downloaded 8 times
Description 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.
Download Appendix_10_Concatentated_CAS.nex (101.4 Kb)
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Title Appendix 11: Concatenated, MUS
Downloaded 12 times
Description 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.
Download Appendix_11_Concatenated_MUS.nex (79.26 Kb)
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Title Appendix 12: Supplementary Table S1
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Description List of mouse individuals used in this study for determination of mitochondrial sequences.
Download Appendix_12_Supplementary_Table_S1.xlsx (65.57 Kb)
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Title Appendix 13: Supplementary Figure S1
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Description 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.
Download Appendix_13_SupFig1_mismatch.pdf (106.8 Kb)
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When using this data, please cite the original publication:

Suzuki H, Nunome M, Kinotshita G, Aplin KP, Vogel P, Kryukov AP, Jin M, Han S, Maryanto I, Tsuchiya K, Ikeda H, Shiroishi T, Yonekawa H, Moriwaki K (2013) Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA. Heredity 111(5): 375–390. http://dx.doi.org/10.1038/hdy.2013.60

Additionally, please cite the Dryad data package:

Suzuki H, Nunome M, Kinotshita G, Aplin KP, Vogel P, Kryukov AP, Jin M, Han S, Maryanto I, Tsuchiya K, Ikeda H, Shiroishi T, Yonekawa H, Moriwaki K (2013) Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rf161
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