Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy analysis (RDA), to identify polygenic correlations between 19 703 SNP loci and a suite of environmental variables in 46 collections of Chinook salmon (1956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both rangewide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 and 21.8% of genomic variation can be accounted for by environmental features, and 566 putatively adaptive loci were identified as targets of environmental adaptation. The most influential drivers of adaptive divergence included precipitation in the driest quarter of the year (Rangewide and North Coastal Lineage, anova P = 0.002 and 0.01, respectively), precipitation in the wettest quarter of the year (Interior Columbia River Stream-Type Lineage, anova P = 0.03), variation in mean diurnal range in temperature (South Coastal Lineage, anova P = 0.005), and migration distance (Rangewide, anova P = 0.001). Our results indicate that environmental features are strong drivers of adaptive genomic divergence in this species, and provide a foundation to investigate how Chinook salmon might respond to global environmental change.

景观基因组学（Landscape genomics）是一门快速发展的学科，近年来基因分型效率与统计分析方法的双重进步，为解析不同环境与选择压力下种群的局部适应性提供了全新视角。奇努克鲑（Chinook salmon，Oncorhynchus tshawytscha）是分布广泛的太平洋鲑鱼物种，栖息于东北太平洋的多样生境中，环境与气候特征差异显著，但目前对该物种的局部适应性仍知之甚少。本研究采用多元分析方法冗余分析（Redundancy analysis, RDA），在覆盖北美大部分分布区的46个奇努克鲑采样群体（共计1956个个体）中，鉴定了19703个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点与一系列环境变量之间的多基因关联。通过将种群分层划分为三个独立的遗传谱系，本研究在全域与区域两个尺度上开展了RDA模型分析。研究结果显示，5.8%至21.8%的基因组变异可由环境特征解释，同时共鉴定出566个推定的适应性位点，作为环境适应性的作用靶点。驱动适应性分化的关键环境因子包括：最干季度降水量（全域谱系与北沿海谱系，方差分析（Analysis of Variance, ANOVA）P值分别为0.002与0.01）、最湿季度降水量（哥伦比亚河内陆溪流型谱系，ANOVA P=0.03）、气温昼夜温差变异（南沿海谱系，ANOVA P=0.005）以及迁徙距离（全域谱系，ANOVA P=0.001）。本研究结果证实，环境特征是该物种适应性基因组分化的重要驱动因素，同时为探究奇努克鲑如何响应全球环境变化奠定了坚实的研究基础。