Data from: Genomics of end-Pleistocene population replacement in a small mammal

Current species’ distributions at high latitudes are the product of expansion from glacial refugia into previously uninhabitable areas at the end of the last glaciation. The traditional view of postglacial colonization is that southern populations expanded their ranges into unoccupied northern territories. Recent findings on mitochondrial DNA (mtDNA) of British small mammals have challenged this simple colonization scenario by demonstrating a more complex genetic turnover in Britain during the Pleistocene-Holocene transition where one mtDNA clade of each species was replaced by another mtDNA clade of the same species. Here, we provide evidence for one of those small mammals, the bank vole (Clethrionomys glareolus), that the replacement was genome-wide. Using more than 10,000 autosomal SNPs we found that similar to mtDNA, bank vole genomes in Britain form two (north and south) clusters which admix. Therefore, the genome of the original post-glacial colonists (the northern cluster) was likely replaced by another wave of migration from a different continental European population (the southern cluster), and we gained support for this by modelling with approximate Bayesian computation. This finding emphasises the importance of analysis of genome-wide diversity within species under changing climate in creating opportunities for sophisticated testing of population history scenarios.当前高纬度地区的物种分布格局，是末次冰期结束时物种从冰期避难所扩散至此前不适宜居住区域的结果。传统的冰后期拓殖理论认为，南部种群会将分布范围扩张至未被占据的北部领地。针对英国小型哺乳动物的线粒体DNA（mitochondrial DNA, mtDNA）的最新研究显示，在更新世-全新世过渡阶段的英国境内存在更为复杂的遗传更替过程：每一物种的一个线粒体DNA进化支被其同一物种的另一线粒体DNA进化支所替代，这一发现对这一简单的拓殖假说提出了质疑。本研究针对其中一类小型哺乳动物——普通田鼠（bank vole, *Clethrionomys glareolus*）——提供了证据，证明这种更替是全基因组层面的。通过对超过10000个常染色体单核苷酸多态性（single nucleotide polymorphism, SNP）位点的分析，我们发现，与线粒体DNA的结果类似，英国境内的普通田鼠基因组可分为南北两个聚类群，且二者存在基因混合现象。因此，最初的冰后期拓殖者的基因组（即北部聚类群）极有可能被另一波来自欧洲大陆不同种群的移民所替换（即南部聚类群），我们通过近似贝叶斯计算（approximate Bayesian computation, ABC）建模为这一假说提供了支持。这一研究结果强调，在气候变化背景下开展物种全基因组多样性分析，可为精准检验种群历史假说提供重要契机。