Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping

Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine–freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.

三刺棘鱼（Threespine stickleback）种群是研究适应性演化及其潜在遗传机制的模式生物体系。在加拿大西部近海的海达瓜伊群岛（Haida Gwaii archipelago）的湖泊中，三刺棘鱼经历了显著的局域适应性辐射，其表型多样性可与该物种全球分布范围内的表型多样性相媲美。
为了为这一适应性辐射提供演化历史背景，我们对来自100余个种群的三刺棘鱼开展了遗传变异检测，共分析了超过1000个单核苷酸多态性（SNP, single nucleotide polymorphism）位点。这些SNP位点既包含均匀分布于全基因组的标记，也包含标记适应性基因组区域的候选SNP。
基于全基因组均匀分布的SNP数据，其揭示的系统地理格局与此前在两个高度分化的线粒体DNA（mtDNA, mitochondrial DNA）谱系间观察到的间断格局截然不同。SNP系统发育树反而显示出大量流域内种群聚类的特征，且不同流域在树的深层以较短的分支相互分隔。
尽管部分独立水系间存在潜在的遗传联系，但这些数据与多数流域的独立殖民历史相符。这一结果支持了此前的假说：流域间观察到的形态多样性是独立演化形成的，例如完全丢失侧骨板以及体型巨大的种群分别在多个不同的演化支（clade）中独立出现。
在整个群岛范围内，我们观察到多个全球尺度上海洋-淡水种群分化的基因组区域（如EDA、Na/K ATPase）所标记的淡水适应性变异位点均受到了反复选择。
在河口生境中，海洋和淡水的等位变异均被频繁检测到。我们还发现少数淡水湖泊（尤其是保留完全骨板形态的种群）中存在典型的海洋等位基因。
本研究结果为棘鱼在冰期后殖民淡水生境提供了通用的演化模型，同时也阐明了全基因组SNP数据集在解析近期适应性分化的格局与过程方面的巨大潜力。