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.

明确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步骤。当景观因素对遗传结构存在相似影响时，对比亲缘关系相近且地理分布重叠的物种往往极具研究价值。不同物种间呈现一致的遗传格局，可凸显景观异质性在塑造遗传结构中的关键作用；而格局差异则提示物种特有的生态特征、生活史差异，或是物种对本地环境的特异性适应的重要性。本研究针对一处原生未受干扰的生境中的两种亲缘关系相近且地理分布重叠的物种，解析了种群动态与适应作用在决定空间遗传结构方面的交互作用。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，对阿拉斯加铜河流域红大马哈鱼（sockeye salmon）的遗传结构进行了解析，并将所得数据与同一区域内已有的大鳞大马哈鱼（Chinook salmon）遗传数据集进行比对分析。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的遗传变异分布。此外，两个物种的种群内与种群间遗传多样性格局整体一致，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固定指数（Fixation Index, FST）异常SNPs位点进行分析时，本研究发现地理距离相近的红大马哈鱼种群间存在潜在的适应性分化。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、历史演化过程与本地适应等议题。