Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range
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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）是快速发展的研究领域，近年来基因分型效率与统计分析技术的双重进步，为解析不同环境与选择压力下种群的局部适应性机制提供了全新视角。奇努克鲑（Oncorhynchus tshawytscha）是分布广泛的太平洋鲑属物种，栖息于东北太平洋的多样生境中，该区域环境与气候特征差异显著，但目前对该物种的局部适应性研究仍较为匮乏。本研究采用多元分析方法——冗余分析（RDA），对分布于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个单核苷酸多态性（SNP）位点与一系列环境变量之间的多基因关联进行了鉴定。研究通过将种群层级划分为三个独立的遗传谱系，分别在全分布范围与区域尺度下构建冗余分析模型。研究结果显示，环境特征可解释5.8%至21.8%的基因组变异，共鉴定出566个推定适应性位点作为环境适应性的靶标。驱动适应性分化的最关键影响因素包括：年度最干旱季度降水量（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）、年度最湿润季度降水量（内陆哥伦比亚河溪流型谱系，方差分析（ANOVA）P值为0.03）、日均气温日较差（南部沿海谱系，方差分析（ANOVA）P值为0.005）以及迁移距离（全分布范围，方差分析（ANOVA）P值为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提供了坚实的研究基础。
