Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes
Pritchard, Victoria L., University of Turku
Mäkinen, Hannu, University of Turku, University of Helsinki
Vähä, Juha-Pekka, University of Turku
Erkinaro, Jaakko, Natural Resources Institute Finland
Orell, Panu, Natural Resources Institute Finland
Primmer, Craig R., University of Helsinki, University of Turku
Published Apr 03, 2018 on Dryad.
Cite this dataset
Pritchard, Victoria L. et al. (2018). Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes [Dataset]. Dryad. https://doi.org/10.5061/dryad.463n4v7
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.
Tar.gz archive containing genotype data in Plink PED format.
Tar.gz archive containing code and necessary files for running analyses.
Tar.gz archive containing final results for all analyses and all SNPs, including package-specific significance tests.
Tar.gz archive containing raw output files from analyses.
Tar.gz archive containing ggplot2 code and data files for making the figures in the manuscript.