Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.

解析种群内部与种群间的遗传变异在基因组中的分布规律，是生态遗传学与进化遗传学领域的核心基础命题。为解答这一科学问题，本研究以三棘刺鱼（threespine stickleback）为研究对象——当海洋刺鱼入侵淡水生境时，该物种会反复出现趋同的表型与遗传分化现象。尽管过往已有大量基于末次冰消期（距今约2万年）以来冰消地理区域内刺鱼样本的进化遗传学研究，但针对早于末次盛冰期的淡水刺鱼种群的相关研究仍较为匮乏。本研究针对末次盛冰期未受冰川覆盖的俄勒冈州全境的刺鱼样本，开展了基于限制性酶切位点相关DNA测序（restriction-site associated DNA-sequencing, RAD-seq）的群体基因组学分析。我们采集了俄勒冈州沿海、威拉米特盆地以及俄勒冈中部区域的刺鱼样本，通过RAD-seq技术分析其遗传多样性，开展群体结构分析，重建其系统地理历史，并验证了“刺鱼近期入侵俄勒冈中部”这一假说——该区域的刺鱼记录仅在近年才被报道。研究结果显示，沿海种群与内陆种群之间存在显著的系统地理分化断点，且海洋种群之间的遗传分化程度最低。威拉米特盆地与俄勒冈中部的种群构成了一个亲缘关系紧密的演化支，这一发现与刺鱼近期入侵俄勒冈中部的假说相符。最后，全基因组水平的遗传多样性π（nucleotide diversity）与亚种群内个体间等位基因相关性FIS（inbreeding coefficient）分析结果表明，沿海种群存在渐渗杂交现象，而俄勒冈中部种群则经历了近期的种群扩张。本研究结果证实了RAD-seq这类新一代测序基因组学方法在解析历史种群结构与近期定殖历史方面的应用潜力。