Data from: Range wide parallel climate-associated genomic clines in Atlantic salmon

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe respectively, with 12 clinal loci in common between continents. Clinal SNPs were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate associated adaptive differentiation. These climate-based clines collectively suggest evidence of large scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.

跨重复环境梯度的渐变变异（clinal variation）可揭示本地适应（local adaptation）的相关证据，为阐明塑造种内多样性（intraspecific diversity）的种群统计与进化过程提供新视角。借助1773个全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）位点，我们对北美与欧洲大西洋鲑（Salmo salar）共134个种群的等位基因频率纬度梯度变异进行了量化评估。我们分别在北美与欧洲种群中检测到84个（占比4.74%）与195个（占比11%）呈现渐变模式的基因座，且两大洲间共有12个渐变基因座。渐变SNP位点在鲑鱼基因组中分布均匀，逻辑回归（logistic regression）分析显示，其与纬度及季节温度存在显著关联，且两大洲的关联均以春季平均温度最为突出。呈现平行渐变模式的基因座与多项代谢及免疫功能相关，这提示了气候关联的适应性分化的潜在遗传基础。这类基于气候的渐变模式整体表明，北大西洋两岸存在大规模环境关联的遗传分化证据。本研究结果支持北大西洋两岸存在平行进化的模式，同时也揭示了其背后遗传结构（genetic architecture）既存在相似性又存在分化的证据。对气候关联的基因组渐变模式的鉴定，阐明了选择与种群统计过程对该物种种内多样性的作用，并为评估气候变化的影响提供了研究框架。