Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus)

General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and extensive genome information is available. We have used high-density single nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genet...

自然种群中正向选择的发生频率、作用强度，以及基因渐渗（introgression）的调控机制等选择相关核心参数，目前仍未得到充分阐释。小家鼠（Mus musculus）是探究此类问题的绝佳模式系统，其亚种与种群分化历史明确，且已有丰富的基因组数据储备。本研究采用高密度单核苷酸多态性（SNP）分型阵列，对小家鼠家栖亚种（M. m. domesticus）与小家鼠蒙古亚种（M. m. musculus）各两个自然种群的基因组正向选择模式与等位基因渐渗特征展开解析。通过应用多种统计分析方法，我们鉴定出大量呈现明显选择性清除（selective sweep）特征的基因组区域，这表明稀有等位基因或新发突变正经历频繁的正向选择。上述区域内的基因涵盖已被深入研究的印记基因座（例如Plagl1/Zac1）、参与人类适应性演化的同源基因（例如α-淀粉酶基因）以及与