Data from: Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences

We analyzed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genome-wide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting > 100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations.本研究分析了采自北美太平洋沿岸、格陵兰及北欧的81条三棘刺鱼（threespine sticklebacks）全基因组序列，涵盖16个种群。基于核单核苷酸多态性（nuclear single nucleotide polymorphisms, SNPs）的主成分分析（Principal Component Analysis）结果显示，种群按地理区域聚类，其中太平洋种群相较于欧洲与格陵兰种群彼此间分化程度更高。线粒体基因组序列（mitogenome sequences）分析表明，北欧种群构成单一的系统地理支系（phylogeographical lineage），而格陵兰种群尤其是太平洋种群则存在不同支系间的基因混合现象。本研究采用全基因组重组溯祖分析方法（genome-wide coalescence with recombination approach）对种群历史动态进行估算：太平洋种群自超过10万年前便开始持续的种群扩张，这可能反映其在当前分布区域附近的隐蔽避难所（cryptic refuges）中持续存续，尽管本研究未排除古老基因混合（ancient admixture）可能带来的影响。约1.4至1.5万年前出现的剧烈种群缩减，被认为反映了海洋祖先种群奠基形成淡水种群的过程。格陵兰与北欧的种群扩张则始于约2至2.5万年前，与末次盛冰期（Last Glacial Maximum）的结束时间相吻合。两个区域内的海洋与淡水种群均在约8至9千年前开始呈现分化的种群动态轨迹，表明此时为种群重新拓殖（recolonization）的关键时期。北欧的这一时间估算结果出人意料地偏晚，但亚化石证据（subfossil evidence）显示，1.2万年前当地存在多种淡水鱼类却未发现刺鱼，为该结论提供了支持。本研究结果揭示了不同地理区域间截然不同的种群历史动态，这对适应性演化过程（adaptive processes）可能产生潜在影响。同时，本研究为此前的相关假设提供了实证支持：淡水种群均由大型连续的海洋种群独立奠基形成，这也是用于解释淡水刺鱼种群广泛存在平行演化（parallel evolution）现象的转运假说（Transporter Hypothesis）的核心论点。