Chinook salmon environmental data and allele frequency matrix

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.