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（Anadromous Atlantic salmon，Salmo salar）是北美地区兼具重要保护与管理价值的物种，过去30年间其种群丰度持续下滑。有效的保护行动需科学划定保护单元，以精准反映种内变异与局部适应的空间尺度。为此，本研究采用了迄今为止最为全面的大西洋鲑遗传与基因组数据库，覆盖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（microsatellite）数据，以及来自50个采样点、可对超过3000个SNP位点进行基因分型的中等密度SNP芯片数据。研究团队借助中性位点与推定受选择位点，在保护单元的界定中整合了适应性信息。基于微卫星数据集与中性SNP位点的贝叶斯聚类分析，所识别的区域集群与此前已发表的区域评估结果基本一致。异常位点SNP的使用并未使区域集群产生显著差异，这表明中性标记即便未受选择压力影响，仍可反映局部适应的地理尺度。本研究还开展了个体遗传归属测试，以对比微卫星、中性SNP与异常位点SNP的分析效能。相较于微卫星标记，使用SNP数据可显著提升分析效能；当使用全部SNP位点时，个体溯源至原生种群的成功率达97%，溯源至原生区域的成功率达100%。仅使用异常位点SNP仅能小幅提升原生种群溯源成功率，但可优化区域归属识别效果。本文探讨了这些全新的遗传资源对北美大西洋鲑保护与管理的启示。