Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes

Elucidating the genetic basis of adaptation to the local environment can
improve our understanding of how the diversity of life has evolved. In
this study we used a dense SNP array to identify candidate loci
potentially underlying fine-scale local adaptation within a large Atlantic
salmon (Salmo salar) population. By combining outlier, gene–environment
association, and haplotype homozygosity analyses, we identified multiple
regions of the genome with strong evidence for diversifying selection.
Several of these candidate regions had previously been identified in other
studies, demonstrating that the same loci could be adaptively important in
Atlantic salmon at sub-drainage, regional and continental scales. Notably,
we identified signals consistent with local selection around genes
associated with variation in sexual maturation, energy homeostasis, and
immune defence. These included the large-effect age-at-maturity gene
vgll3, the known obesity gene mc4r, and major histocompatibility complex
II. Most strikingly, we confirmed a genomic region on Ssa09 that was
extremely differentiated among subpopulations, and that is also a
candidate for local selection over the global range of Atlantic salmon.
This region co-localized with a haplotype strongly associated with
spawning ecotype in sockeye salmon (Oncorhynchus nerka), with
circumstantial evidence that the same gene (six6) may be the selective
target in both cases. The phenotypic effect of this region in Atlantic
salmon remains cryptic, although allelic variation is related to upstream
catchment area and co-varies with timing of the return spawning migration.
Our results further inform management of Atlantic salmon and open multiple
avenues for future research.