Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management.本研究针对分布于阿拉斯加库克湾（Cook Inlet）、沿北美西海岸至哥伦比亚河流域的12个太平洋细齿鲑（eulachon，*Thaleichthys pacificus*，胡瓜鱼科Osmeridae）种群开展分析，采用限制性位点相关DNA测序（restriction-site-associated DNA sequencing）解析该高基因流物种的中性与适应性遗传变异模式。研究在全基因组范围内共鉴定出4104个单核苷酸多态性位点（single-nucleotide polymorphisms，SNPs），其中通过FST离群值检测筛选得到193个候选适应性SNPs。基于候选适应性SNPs的细齿鲑种群结构估算结果，与基于3911个中性SNPs位点组或此前采用14个微卫星标记（microsatellites）得到的分析结果相近，但前者的种群分辨率更高。在候选适应性SNPs位点组中，研究发现遗传多样性指标自南向北呈现逐步升高的梯度模式，而中性标记（SNPs或微卫星）中未观察到此现象。该结果表明，不同区域的细齿鲑种群在淡水与海洋生境中面临差异化的选择压力；同时，在制定保护工作中的遗传边界划分方案时，中性标记无法捕捉的适应性多样性模式可作为重要参考依据。基于中性SNPs位点组与微卫星标记得到的有效种群大小（effective population size，Ne）估算结果一致，该方法可应用于难以开展种群数量普查的细齿鲑种群的种群状态监测。相较于中性SNPs位点组或微卫星标记，候选适应性SNPs位点组展现出更强的种群分化能力，因此在种群识别应用中可实现更高的个体归群准确率。本研究首次开发了适用于太平洋细齿鲑的SNPs标记，基于该类标记的分析结果凸显了整合全基因组中性与适应性遗传变异在物种保护与渔业管理中的重要价值。