Data from: Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

Little is known about the genetic basis differentiating resident and anadromous forms found in many salmonid species. Using a medium-density SNP array, we documented genomic diversity and divergence at 2336 genetically mapped loci among three pairs of North American anadromous and freshwater Atlantic salmon populations. Our results show that across the genome, freshwater populations have lower diversity and a smaller proportion of private polymorphism relative to anadromous populations. Moreover, differentiation was more pronounced among freshwater than among anadromous populations at multiple spatial scales, suggesting a large effect of genetic drift in these isolated freshwater populations. Using nonhierarchical and hierarchical genome scans, we identified hundreds of markers spread across the genome that are potentially under divergent selection between anadromous and freshwater populations, but few outlier loci were repeatedly found in all three freshwater–anadromous comparisons. Similarly, a sliding window analysis revealed numerous regions of high divergence that were nonparallel among the three comparisons. These last results show little evidence for the parallel evolution of alleles selected for in freshwater populations, but suggest nonparallel adaptive divergence at many loci of small effects distributed through the genome. Overall, this study emphasizes the important role of genetic drift in driving genome-wide reduction in diversity and divergence in freshwater Atlantic salmon populations and suggests a complex multigenic basis of adaptation to resident and anadromous strategies with little parallelism.

目前学界对诸多鲑科鱼类中定居型与溯河洄游型种群间的遗传分化基础仍知之甚少。本研究采用中等密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）阵列，对3组北美溯河洄游型与淡水定居型大西洋鲑种群的2336个遗传定位基因座开展了基因组多样性与分化特征分析。结果显示，全基因组范围内，淡水定居种群的遗传多样性更低，且私有多态性位点的占比显著低于溯河洄游种群。此外，在多种空间尺度下，淡水种群间的遗传分化程度均高于溯河洄游种群，提示遗传漂变在这些孤立淡水种群中发挥了较强作用。通过非层级与层级基因组扫描方法，本研究鉴定出数百个分布于全基因组、可能在溯河洄游与淡水种群间受到歧化选择的分子标记，但在3组淡水-溯河种群对比中均被重复检出的异常位点寥寥无几。类似地，滑动窗口分析揭示了大量高分化区域，但这些区域在3组对比中并不具有平行性。上述结果表明，淡水种群中受选择等位基因的平行进化证据极少，提示基因组内大量小效应基因座上存在非平行的适应性分化。总体而言，本研究强调了遗传漂变在驱动淡水大西洋鲑种群全基因组多样性降低与分化中的关键作用，并表明适应定居与溯河洄游生存策略的遗传基础具有复杂的多基因特性，且平行性极低。