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.

本研究对采自北美太平洋沿岸、格陵兰及北欧的16个三刺棘鱼种群的81份全基因组序列开展了分析。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，种群聚类结果与其地理分布高度匹配，且太平洋种群间的遗传分化程度显著高于欧洲与格陵兰种群。线粒体基因组(mitogenome)序列分析结果表明，北欧种群构成单一的系统地理支系，而格陵兰种群尤其是太平洋种群则存在不同支系间的遗传混合现象。本研究采用带重组的全基因组溯祖分析方法对种群历史动态进行了估算：太平洋种群自超过10万年前便开始持续种群扩张，这可能与其在当前分布区附近的隐秘避难所中持续存续有关，但本研究并未排除古老遗传混合可能带来的影响。约1.4至1.5万年前出现的种群急剧缩减，被认为反映了由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，与末次冰盛期的结束时间高度吻合。在这两个区域中，海洋与淡水种群约在8至9千年前开始呈现出截然不同的种群动态轨迹，表明这一时间点即为淡水生境的重新定殖时期。北欧的这一定殖时间估计值出乎意料地晚，但1.2万年前的亚化石记录显示，当时存在多种淡水鱼类，却未发现三刺棘鱼的踪迹，这为该估计值提供了实证支持。本研究结果揭示了不同地理区域间种群历史动态存在显著差异，这可能对适应性进化过程产生潜在影响；同时，本研究也为此前的相关假设提供了实证支持——即淡水种群均由大规模、同质化的海洋种群独立奠基形成，而这一核心观点正是用于解释淡水三刺棘鱼种群中广泛存在平行进化现象的运输者假说(Transporter Hypothesis)的关键内容。