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 sal...
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ftzenodo:oai:zenodo.org:4977794 2024-09-15T17:55:50+00:00 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. Mäkinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. 2018-04-03 https://doi.org/10.5061/dryad.463n4v7 unknown Zenodo https://doi.org/10.1111/mec.14705 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.463n4v7 oai:zenodo.org:4977794 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode sockeye salmon microgeographic adaptation Salmo salar Holocene info:eu-repo/semantics/other 2018 ftzenodo https://doi.org/10.5061/dryad.463n4v710.1111/mec.14705 2024-07-26T13:59:58Z 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. SsalLocSeln_genotypes.tar Tar.gz archive containing genotype data in Plink PED format. SsalLocSeln_code.tar Tar.gz archive containing code and necessary files for running analyses. SsalLocSeln_results.tar Tar.gz archive containing final results for all analyses and all SNPs, including package-specific ... Other/Unknown Material Atlantic salmon Salmo salar Zenodo |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
sockeye salmon microgeographic adaptation Salmo salar Holocene |
spellingShingle |
sockeye salmon microgeographic adaptation Salmo salar Holocene Pritchard, Victoria L. Mäkinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
topic_facet |
sockeye salmon microgeographic adaptation Salmo salar Holocene |
description |
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. SsalLocSeln_genotypes.tar Tar.gz archive containing genotype data in Plink PED format. SsalLocSeln_code.tar Tar.gz archive containing code and necessary files for running analyses. SsalLocSeln_results.tar Tar.gz archive containing final results for all analyses and all SNPs, including package-specific ... |
format |
Other/Unknown Material |
author |
Pritchard, Victoria L. Mäkinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. |
author_facet |
Pritchard, Victoria L. Mäkinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. |
author_sort |
Pritchard, Victoria L. |
title |
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
title_short |
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
title_full |
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
title_fullStr |
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
title_full_unstemmed |
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
title_sort |
data from: genomic signatures of fine‐scale local selection in atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes |
publisher |
Zenodo |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.463n4v7 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
https://doi.org/10.1111/mec.14705 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.463n4v7 oai:zenodo.org:4977794 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.463n4v710.1111/mec.14705 |
_version_ |
1810432068116545536 |