Data from: Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss)

Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long-distance dispersal or migration across larger geographical regions that consist of highly heterogeneous habitats. Therefore, selection may influence adaptive genetic variation associated with landscape features at residing sites and along migration routes in migratory species. We tested for genomic adaptation to landscape features at natal spawning sites and along migration paths to the ocean of anadromous steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin. Results from multivariate ordination, gene-environment association, and outlier analyses using 24,526 single-nucleotide polymorphisms (SNPs) provided evidence that adaptive allele frequencies were more commonly associated with landscape features along migration paths than features at natal sites (91.2% versus 8.8% of adaptive loci, respectively). Among the 45 landscape variables tested, migration distance to the ocean and mean annual precipitation along migration paths were significantly associated with adaptive genetic variation in three distinct genetic clusters. Additionally, variables such as minimum migration water temperature and mean migration slope were significant only in inland stocks of steelhead that migrate up to 1200 km farther than those near the coast, indicating regional differences in migratory selective pressures. This study provides novel approaches for investigating migratory corridors and some of the first evidence that environment along migration paths can lead to substantial divergent selection. Consequently, our approach to understand genetic adaptation to migration conditions can be applied to other migratory species when migration or dispersal paths are generally known.生物通常会展现出对其本地环境特征的适应性演化证据。然而，诸多物种会经历长距离扩散或迁徙，穿越由高度异质性生境构成的广阔地理区域。因此，在迁徙物种中，自然选择可能会影响与栖息位点及迁徙路线沿线景观特征相关的适应性遗传变异。本研究以哥伦比亚河流域的溯河性硬头鳟（Oncorhynchus mykiss）为研究对象，检测其在出生产卵场以及通往海洋的迁徙路径上对景观特征的基因组适应性。基于24526个单核苷酸多态性（single-nucleotide polymorphisms, SNPs）开展的多元排序分析、基因-环境关联分析及异常位点分析结果显示，适应性等位基因频率与迁徙路径沿线景观特征的关联度显著高于其与出生产卵场景观特征的关联度（分别对应91.2%和8.8%的适应性基因座）。在所测试的45个景观变量中，通往海洋的迁徙距离及迁徙路径沿线的年平均降水量，与三个独立遗传聚类群内的适应性遗传变异均呈现显著关联。此外，迁徙途中最低水温、平均迁徙坡度等变量仅在比沿海种群多迁徙多达1200公里的内陆硬头鳟种群中呈现显著关联，这表明迁徙选择压力存在区域差异。本研究为迁徙廊道的相关研究提供了全新方法，同时也是首批证实迁徙路径沿线环境可引发强烈分化选择的研究之一。因此，当迁徙或扩散路径可被明确识别时，本研究用于解析迁徙相关条件下遗传适应性的方法，可推广应用于其他迁徙物种。