DOI: 10.5061/dryad.kt0s8
title: Data from: Ancient onset of geographic divergence, interpopulation genetic exchange, and natural selection on the Mc1r coat-color gene in the house mouse (Mus musculus) inferred from tandemly arranged nuclear gene markers

description: We examined genetic variation in house mice from India and Pakistan, a
 predominant part of the predicted homeland of this species and also the
 territory of the subspecies Mus musculus castaneus (CAS), using a nuclear
 marker for seven tandemly arranged genes
 (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those
 previously determined for mice from other parts of Eurasia. Construction
 of a network with the concatenate sequences yielded three distinct
 clusters representing the three major subspecies groups: CAS, Mus musculus
 domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis
 provided evidence for further subdivision of CAS into two main haplogroups
 within the Indian subcontinent. Single-gene networks revealed not only
 gene-specific architecture for subgrouping in CAS, but also allelic
 exchange among subspecies. These results suggest the earlier onset of
 allopatric divergence in the predicted homeland (the Middle East and
 Indian subcontinent) and subsequent intermittent admixing via gene flow
 across the CAS haplogroups and among the three subspecies groups. A
 comparison of the levels of nucleotide diversity among the gene regions
 revealed a less divergent state in the chromosome region containing Mc1r
 and its adjacent genes, indicative of a selective sweep, suggesting the
 involvement of natural selection in the Mc1r allelic variation
description: 1_Fig3_concatenated_Kodama.nexConcatenated sequences of the seven nuclear genes used for the building the Neighbor Net network shown in Fig. 3A (Kodama et al., 2015).2_FancaThe Fanca sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).3_Spire2The Spire2 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).4_Tcf25The Tcf25 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).5_Mc1r_409bpThe Mc1r sequence (409 bp) data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).6_Def8The Def8 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).7_Afg3l1_allThe Afg3lI sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).8_Dbndd1The Dbndd1 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).9_Mc1r948bp_ArlequinThe Mc1r sequence (948 bp) data used for population genetic analyses using Arlequin ver 3.5 (Kodama et al., 2015).11_BEAST_input_KodamaConcatenated sequences of the seven nuclear genes used for the BEAST analysis shown in Fig. 4 (Kodama et al., 2015).12_STRUCTURE_KodamaConcatenated sequence data used for assessment of population genetic structure using the dataset of the seven nuclear genes from 98 Mus musculus and the software STRUCTURE, version 2.3 (Fig. 3B, Kodama et al., 2015).10_Mc1r_upstream_NoncodingThe non-coding region immediately upstream of the Mc1r exon 1 region. The data were used for construction of the median joining network shown in Fig 5A (Kodama et al., 2015).