Liu Shenglin, Hansen Michael M, Jacobsen Magnus W
Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark.
Mol Ecol. 2016 Oct;25(20):5187-5202. doi: 10.1111/mec.13827. Epub 2016 Sep 14.
We analysed 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 genomewide 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.
我们分析了来自北美太平洋地区、格陵兰岛和北欧的81个三刺鱼全基因组序列，这些序列代表了16个种群。对核单核苷酸多态性（SNP）进行主成分分析，结果显示种群按地理位置聚类，相对于欧洲和格陵兰岛的种群，太平洋地区的种群彼此之间差异更大。对线粒体基因组序列的分析表明，北欧种群代表单一的系统地理谱系，而格陵兰岛种群，尤其是太平洋地区的种群，显示出谱系间的混合。我们使用一种结合重组的全基因组溯祖方法来估计种群历史。太平洋地区的种群显示出从超过10万年前开始的逐渐种群扩张，这可能反映了在当前分布范围附近的隐秘避难所中的种群延续，尽管我们不排除古代混合的可能影响。约1.4 - 1.5万年前的急剧种群下降被认为反映了海洋祖先对淡水种群的奠基。在格陵兰岛和北欧，种群扩张始于约2.0 - 2.5万年前，与末次盛冰期的结束时间一致。在这两个地区，海洋和淡水种群在约8 - 9千年前开始呈现不同的种群动态轨迹，这表明这是重新定殖的时间。在北欧，这个估计时间出人意料地晚，但在亚化石证据中得到了支持，该证据表明1.2万年前存在几种淡水鱼类，但没有三刺鱼。结果表明不同地理区域有着截然不同的种群历史，这对适应性过程可能产生影响。它们还为先前关于淡水种群独立于大型、连贯的海洋种群而形成的假设提供了实证支持，这是运输假说中的一个关键要素，该假说用于解释淡水三刺鱼种群中平行进化的广泛发生。
