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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fttriple:oai:gotriple.eu:50|dedup_wf_001::5c137605c2504e42312751a787276628 2023-05-15T15:28:42+02:00 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 undefined unknown http://dx.doi.org/10.5061/dryad.463n4v7 https://dx.doi.org/10.5061/dryad.463n4v7 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:103109 10.5061/dryad.463n4v7 oai:easy.dans.knaw.nl:easy-dataset:103109 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 Life sciences medicine and health care sockeye salmon microgeographic adaptation Salmo salar salmonid Atlantic salmon ecotype Holocene local selection Finland Norway Europe envir demo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2018 fttriple https://doi.org/10.5061/dryad.463n4v7 2023-01-22T17:22:58Z 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.tarTar.gz archive containing genotype data in Plink PED format.SsalLocSeln_code.tarTar.gz archive containing code and necessary files for running analyses.SsalLocSeln_results.tarTar.gz archive containing final results for all analyses and all SNPs, including package-specific significance ... Dataset Atlantic salmon Salmo salar Unknown Norway Sockeye ENVELOPE(-130.143,-130.143,54.160,54.160) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care sockeye salmon microgeographic adaptation Salmo salar salmonid Atlantic salmon ecotype Holocene local selection Finland Norway Europe envir demo |
spellingShingle |
Life sciences medicine and health care sockeye salmon microgeographic adaptation Salmo salar salmonid Atlantic salmon ecotype Holocene local selection Finland Norway Europe envir demo 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 |
Life sciences medicine and health care sockeye salmon microgeographic adaptation Salmo salar salmonid Atlantic salmon ecotype Holocene local selection Finland Norway Europe envir demo |
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.tarTar.gz archive containing genotype data in Plink PED format.SsalLocSeln_code.tarTar.gz archive containing code and necessary files for running analyses.SsalLocSeln_results.tarTar.gz archive containing final results for all analyses and all SNPs, including package-specific significance ... |
format |
Dataset |
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 |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.463n4v7 |
long_lat |
ENVELOPE(-130.143,-130.143,54.160,54.160) |
geographic |
Norway Sockeye |
geographic_facet |
Norway Sockeye |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:103109 10.5061/dryad.463n4v7 oai:easy.dans.knaw.nl:easy-dataset:103109 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 |
op_relation |
http://dx.doi.org/10.5061/dryad.463n4v7 https://dx.doi.org/10.5061/dryad.463n4v7 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.463n4v7 |
_version_ |
1766359048453619712 |