Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Distribution of ecotypic variation in natural populations is influenced by
neutral and adaptive evolutionary forces that are challenging to
disentangle without understanding of genomic architecture for phenotypic
traits. This study provides a high-resolution portrait of genomic
variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a
region of major effect for ecotypic variation in migration timing. With a
filtered dataset of ~13 million SNPs from low coverage whole genome
resequencing of 53 populations (3,566 barcoded individuals), we contrasted
patterns of genomic variation within and among major lineages and examined
the extent of a selective sweep at a major effect region underlying
migration timing (GREB1L/ROCK1). Allele frequency variation in
GREB1L/ROCK1 was highly correlated with mean migration timing for early-
and late-run populations within each of the lineages (r2 between
0.58–0.95; P < 0.001). However, the extent of selection within the
genomic region controlling migration timing was much narrower in one
lineage (interior stream-type) compared to the other two major lineages
which corresponded to the breadth of phenotypic variation in migration
timing observed among lineages. Evidence of a duplicated block within
GREB1L/ROCK1 may be responsible for reduced recombination in this portion
of the genome and contributes to phenotypic variation within and across
lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for
their utility in discriminating migration timing among lineages, and we
recommend multiple markers nearest the duplication to provide highest
accuracy in conservation applications such as those that aim to protect
early migrating Chinook salmon. These results highlight the need to
investigate variation throughout the genome and the effects of structural
variants on ecologically relevant phenotypic variation in natural species.