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

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

本研究以印度与巴基斯坦的小家鼠为研究对象——该区域是该物种预测起源地的核心组成部分，同时也是小家鼠卡氏亚种（Mus musculus castaneus，CAS）的分布范围——利用覆盖7个串联排列核基因（Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1）的核标记开展遗传变异分析，并将分析结果与此前欧亚大陆其他地区小家鼠的相关数据进行了比对。基于串联序列构建的单倍型网络得到了3个独立的聚类簇，分别对应3个主要亚种类群：CAS、小家鼠家屋亚种（Mus musculus domesticus，DOM）以及小家鼠指名亚种（Mus musculus musculus，MUS）。STRUCTURE群体结构分析结果显示，在印度次大陆范围内，CAS可进一步划分为两个主要单倍群。单基因网络分析不仅揭示了CAS内亚群划分的基因特异性结构，还发现了亚种间的等位基因交流事件。上述结果表明，该物种的预测起源地（中东与印度次大陆）更早出现了异域分化过程，随后卡氏单倍群内部以及三个亚种类群之间通过基因流发生了间歇性的基因混合。对各基因区域的核苷酸多样性水平进行比较后发现，包含Mc1r及其邻近基因的染色体区域呈现出更低的分化程度，这提示存在选择性清除现象，表明自然选择参与了Mc1r基因的等位变异演化。