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 toward 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 north eastern 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 (1,956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both range-wide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 – 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 (Range-wide 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 (Range-wide, 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本地适应机制提供了关键视角。奇努克鲑（Chinook salmon，学名*Oncorhynchus tshawytscha*）是分布广泛的太平洋鲑类物种，栖息于东北太平洋的多样生境中，区域环境与气候特征差异显著，但目前对该物种的本地适应机制仍缺乏深入认知。本研究采用多变量方法——冗余分析（Redundancy Analysis, RDA），对覆盖其北美大部分分布范围的46个奇努克鲑采样群体（总计1956个个体）中的19703个SNP位点与一系列环境变量之间的多基因关联进行了鉴定。研究通过将种群分层划分为3个独立遗传谱系，分别开展了全分布范围与区域尺度下的RDA模型构建。结果显示，5.8%~21.8%的基因组变异可由环境特征解释，共鉴定出566个推定适应性位点作为环境适应的靶标。驱动适应性分化的最关键因素包括：最干旱季度降水量（全分布范围与北部沿海谱系，方差分析（ANOVA）p值分别为0.002与0.01）、最湿润季度降水量（哥伦比亚河内陆溪流型谱系，方差分析（ANOVA）p值0.03）、气温日较差均值（南部沿海谱系，方差分析（ANOVA）p值0.005）以及迁移距离（全分布范围，方差分析（ANOVA）p值0.001）。本研究结果表明，环境特征是该物种适应性基因组分化的重要驱动因素，同时为解析奇努克鲑对全球环境变化的响应机制奠定了坚实的研究基础。