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）是一个快速发展的研究领域，近年来基因型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新的认知。奇努克鲑（Chinook salmon，Oncorhynchus tshawytscha）是分布范围广泛的太平洋鲑类物种，栖息于东北太平洋区域的多样生境中，其环境与气候特征存在显著差异，但目前对该物种的局部适应性机制仍知之甚少。本研究采用多元分析方法——冗余分析（redundancy analysis, RDA），对分布于北美大部分分布区的46个奇努克鲑采样群（总计1956个个体）中的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进行了鉴定。我们通过将种群划分为三个独立的遗传谱系，在全分布区与区域两个尺度上开展了冗余分析建模。研究结果显示，环境特征可解释5.8%至21.8%的基因组变异，同时鉴定出566个推定的适应性位点作为环境适应性的靶标。影响适应性分化的最关键驱动因子包括：最干旱季度的降水量（全分布区与北沿海谱系，方差分析[Analysis of Variance, ANOVA] P值分别为0.002与0.01）、最湿润季度的降水量（哥伦比亚河内陆溪流型谱系，ANOVA P=0.03）、温度昼夜温差的变异（南沿海谱系，ANOVA P=0.005）以及迁移距离（全分布区，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子，同时为探究奇努克鲑如何响应全球环境变化奠定了研究基础。

搜集汇总

背景与挑战

背景概述

该数据集聚焦于北美洲奇努克鲑鱼的环境适应性研究，通过冗余分析（RDA）方法，整合了46个种群、1956个体的19,703个SNP位点与多种环境变量数据，揭示了环境因素（如降水、温度变化和迁移距离）对基因组变异的显著影响，识别出566个潜在适应性位点，为理解物种对环境变化的响应提供了基因组学基础。数据集包含基因型、等位基因频率和环境数据文件，适用于景观基因组学和进化生物学分析。