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尾三刺鱼（threespine sticklebacks）的全基因组序列，共计覆盖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, PCA）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，彼此间的遗传分化程度更高。对线粒体基因组序列（mitogenome sequences）的分析表明，北欧种群构成单一的系统地理谱系，而格陵兰种群尤其是太平洋种群则存在不同谱系间的遗传混合。本研究采用全基因组重组溯祖分析方法估算种群历史动态。太平洋种群的渐进式种群扩张始于距今10万年前以上，这可能反映其在当前分布区附近的隐蔽避难所中持续存续，不过本研究未排除古代遗传混合可能带来的影响。约1.4万至1.5万年前出现的种群骤减现象，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始于约2万至2.5万年前，与末次冰盛期（Last Glacial Maximum）的结束时间相吻合。在这两个区域，海洋与淡水种群约在8千至9千年前开始呈现出截然不同的种群动态轨迹，表明这一时期为种群重新定殖的关键节点。北欧的这一定殖时间估算结果出乎意料地晚，但得到了亚化石证据的支持——1.2万年前当地已存在多种淡水鱼类，但未发现三刺鱼的亚化石记录。本研究结果揭示了不同地理区域间种群历史动态的显著差异，这对适应性演化过程具有潜在影响。同时，研究结果为此前的相关假设提供了实证支持：淡水种群均由大规模、同质化的海洋种群独立奠基形成，这一核心论点正是用于解释淡水三刺鱼种群中平行演化广泛存在的转运假说（Transporter Hypothesis）的关键内容。