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 watershed...三棘刺鱼（Threespine stickleback）种群是研究适应性进化及其潜在遗传机制的经典模式系统。在加拿大西部近海的海达瓜依（Haida Gwaii）群岛的湖泊中，三棘刺鱼经历了显著的局域辐射进化，其表型多样性水平可与该物种全球分布区的表型多样性相媲美。为阐明该辐射进化的历史背景，本研究对100余个种群的三棘刺鱼开展了遗传变异分析，共检测了超过1000个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点。这些SNP位点既包含均匀分布于全基因组的遗传标记，也包含用于标识适应性基因组区域的候选SNP。基于均匀分布的SNP数据，本研究揭示的系统地理格局与此前在两个高度分化的线粒体DNA（mitochondrial DNA, mtDNA）支系间观测到的间断分布格局存在显著差异：SNP系统发育树呈现出强烈的流域内种群聚类特征，且不同流域在系统发育树的较深分支处以短分支相互分隔。上述数据与多数流域经历独立殖民事件的假说相一致……