Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9,142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3,000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite dataset and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.溯河洄游大西洋鲑（Salmo salar）是北美地区备受保护与管理关注的物种，其种群丰度在过去30年间持续下滑。有效的保护行动需要划定保护单元，以精准反映该物种种内变异与本地适应的空间尺度。为达成这一目标，本研究采用了目前为止最为全面的大西洋鲑遗传与基因组数据库，覆盖了该物种在北美的全部分布范围。该数据库包含来自149个采样点的9142个个体的微卫星数据，以及针对50个采样点、可检测超过3000个单核苷酸多态性（SNP）位点基因型的中等密度SNP芯片数据。我们选取中性位点与推定受选择位点，将适应性信息整合至保护单元的界定流程中。基于微卫星数据集与中性SNP位点的贝叶斯聚类分析所得到的区域聚类群，与此前已发表的区域评估结果大体一致。使用异常SNP位点并未对区域聚类群造成显著差异，这表明中性标记即便未处于选择压力之下，仍可反映本地适应的地理尺度。本研究同时开展了个体归属测试，以对比微卫星、中性SNP以及异常SNP位点的个体识别效能。相较于微卫星数据，使用SNP数据可大幅提升个体识别效能：当使用全部SNP位点时，个体溯源至原种群的成功率可达97%，溯源至原生境区域的成功率更是达到100%。仅使用异常SNP位点仅能小幅提升个体溯源至原种群的成功率，但可优化区域归属识别结果。最后，我们讨论了这些全新的遗传资源对北美大西洋鲑的保护与管理工作的重要意义。