DOI: 10.5061/dryad.prr4xgxmn
title: Chinook salmon environmental data and allele frequency matrix

description: Many species that undergo long breeding migrations, such as anadromous
 fishes, face highly heterogeneous environments along their migration
 corridors and at their spawning sites. These environmental challenges
 encountered at different life stages may act as strong selective pressures
 and drive local adaptation. However, the relative influence of
 environmental conditions along the migration corridor compared to the
 conditions at spawning sites on driving selection is still unknown. In
 this study, we performed genome-environment associations (GEA) to
 understand the relationship between landscape and environmental conditions
 driving selection in seven populations of the anadromous Chinook salmon
 (Oncorhynchus tshawytscha)–a species of important economic, social,
 cultural and ecological value–in the Columbia River basin. We
 extracted environmental variables for the shared migration
 corridors and at distinct spawning sites for each population, and used a
 Pool-seq approach to perform whole genome resequencing. Bayesian and
 univariate genome-environment association tests with migration-specific
 and spawning site-specific environmental variables indicated many more
 candidate SNPs associated with environmental conditions of the migration
 corridor compared to spawning sites. Specifically, variables associated
 with temperature, precipitation, terrain roughness, and elevation
 variables of the migration corridor were the most significant drivers of
 environmental selection. Additional analyses of neutral loci revealed two
 distinct clusters representing populations from different geographic
 regions of the drainage that also exhibit differences in adult migration
 timing (summer vs. fall). Tests for genomic regions under selection
 revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1
 region that has been identified previously in salmonids as a region
 associated with adult migration timing. Our results show that
 environmental variation experienced throughout migration corridors imposed
 a greater selective pressure on Chinook salmon than environmental
 conditions at spawning sites.
description: <strong>Environmental_data_corr.xlsx</strong> This Exel file contains three sheets. The sheet "140 variables" contains all variable measurments for the seven populations of Chinook salmon. The sheet "Correlation Matrix" shows the correlation values between each variable. Correlations with R value ≥ 0.80 are highlighted in red; correlations with R values ≤ -0.80 are highlighted in yellow. Variables that showed no variation are highlighted in grey. The sheet "Abbreviations" shows the variable name, resolution and geographic resolution, source, and abbreviation for the mean, maximum, minimum, range and point (site).  <strong>env_site.csv</strong> This csv file contains all the environmental variables used in the "Site" dataset <strong>env_migration.csv</strong> This csv file contains all the environmental variables used in the "Migration" dataset <strong>env_combinations.csv</strong> This csv file contains all the environmental variables used in the "Combination" dataset <strong>env_full.csv</strong> This csv file contains all the environmental variables used in the "Full" dataset <strong>allele_freqs_Chinook.RData</strong> This .RData file contains the allele frequency matrix used in GEA analyses