Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.解析景观尺度下遗传变异的空间分布特征，是指导物种保护工作的关键基础步骤。当景观因素对不同物种的遗传结构具有相似影响时，比较亲缘关系相近且地理分布重叠的物种往往能获得极具价值的研究结果。不同物种间呈现一致的遗传格局时，可凸显景观异质性对遗传结构塑造的关键作用；反之，若格局存在差异，则提示物种特异性的生态特征、生活史策略差异，或是物种对本地环境的特异性适应所带来的影响。我们以原生未受干扰环境中两种亲缘关系相近且地理分布重叠的物种为研究对象，解析了种群统计过程与适应作用在塑造空间遗传结构中的交互调控机制。本研究利用同时包含中性变异与假定适应性变异的单核苷酸多态性（single nucleotide polymorphism, SNP）位点，对阿拉斯加库珀河（Copper River）内的红鲑（sockeye salmon）种群遗传结构进行了评估，并将所得数据与该区域内已发表的大鳞大麻哈鱼（Chinook salmon）相关数据进行了对比分析。整体而言，两个物种均呈现出距离隔离的遗传格局；种群的空间分布在很大程度上决定了景观尺度下遗传变异的分布特征。此外，两个物种的种群内与种群间遗传多样性格局整体保持一致，进一步凸显了景观异质性与历史演化过程在塑造空间遗传结构中的重要作用。当在景观遗传学框架下对高FST异常值SNP位点进行分析时，我们发现地理邻近的红鲑种群间存在潜在的适应性差异。本研究结果结合物种保护实践进行了讨论，重点关注了生殖隔离、历史演化过程以及本地适应等议题。