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 sa...
Published in: | Molecular Ecology |
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Format: | Article in Journal/Newspaper |
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Online Access: | http://hdl.handle.net/10138/326500 |
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/326500 2024-01-07T09:42:10+01:00 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. Makinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. Biosciences Organismal and Evolutionary Biology Research Programme Evolution, Conservation, and Genomics Helsinki Institute of Sustainability Science (HELSUS) Doctoral Programme in Wildlife Biology 2021-02-16T08:53:01Z 16 application/pdf http://hdl.handle.net/10138/326500 eng eng Wiley 10.1111/mec.14705 Suomen Akatemia, Grant/Award Number: 284941, 314254; Suomen Kulttuurirahasto Pritchard , V L , Makinen , H , Vähä , J-P , Erkinaro , J , Orell , P & Primmer , C R 2018 , ' Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes ' , Molecular Ecology , vol. 27 , no. 11 , pp. 2560-2575 . https://doi.org/10.1111/mec.14705 ORCID: /0000-0002-3687-8435/work/47430067 85051777368 7388b976-8225-433b-b6f7-6fe5bfbace90 http://hdl.handle.net/10138/326500 000434152100006 openAccess info:eu-repo/semantics/openAccess Atlantic salmon ecotype local selection microgeographic adaptation sockeye salmon MAJOR HISTOCOMPATIBILITY COMPLEX HOMEODOMAIN PROTEIN SIX6 CLASS-II COMBINATIONS MHC CLASS-I SOCKEYE-SALMON ONCORHYNCHUS-TSHAWYTSCHA STRUCTURED POPULATIONS EVOLUTIONARY ECOLOGY POSITIVE SELECTION WILD POPULATIONS 1181 Ecology evolutionary biology Article acceptedVersion 2021 ftunivhelsihelda 2023-12-14T00:02:20Z 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 subdrainage, 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 colocalized 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 covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research. Peer reviewed Article in Journal/Newspaper Atlantic salmon Salmo salar HELDA – University of Helsinki Open Repository Sockeye ENVELOPE(-130.143,-130.143,54.160,54.160) Molecular Ecology 27 11 2560 2575 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
Atlantic salmon ecotype local selection microgeographic adaptation sockeye salmon MAJOR HISTOCOMPATIBILITY COMPLEX HOMEODOMAIN PROTEIN SIX6 CLASS-II COMBINATIONS MHC CLASS-I SOCKEYE-SALMON ONCORHYNCHUS-TSHAWYTSCHA STRUCTURED POPULATIONS EVOLUTIONARY ECOLOGY POSITIVE SELECTION WILD POPULATIONS 1181 Ecology evolutionary biology |
spellingShingle |
Atlantic salmon ecotype local selection microgeographic adaptation sockeye salmon MAJOR HISTOCOMPATIBILITY COMPLEX HOMEODOMAIN PROTEIN SIX6 CLASS-II COMBINATIONS MHC CLASS-I SOCKEYE-SALMON ONCORHYNCHUS-TSHAWYTSCHA STRUCTURED POPULATIONS EVOLUTIONARY ECOLOGY POSITIVE SELECTION WILD POPULATIONS 1181 Ecology evolutionary biology Pritchard, Victoria L. Makinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes |
topic_facet |
Atlantic salmon ecotype local selection microgeographic adaptation sockeye salmon MAJOR HISTOCOMPATIBILITY COMPLEX HOMEODOMAIN PROTEIN SIX6 CLASS-II COMBINATIONS MHC CLASS-I SOCKEYE-SALMON ONCORHYNCHUS-TSHAWYTSCHA STRUCTURED POPULATIONS EVOLUTIONARY ECOLOGY POSITIVE SELECTION WILD POPULATIONS 1181 Ecology evolutionary biology |
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 subdrainage, 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 colocalized 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 covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research. Peer reviewed |
author2 |
Biosciences Organismal and Evolutionary Biology Research Programme Evolution, Conservation, and Genomics Helsinki Institute of Sustainability Science (HELSUS) Doctoral Programme in Wildlife Biology |
format |
Article in Journal/Newspaper |
author |
Pritchard, Victoria L. Makinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. |
author_facet |
Pritchard, Victoria L. Makinen, Hannu Vähä, Juha-Pekka Erkinaro, Jaakko Orell, Panu Primmer, Craig R. |
author_sort |
Pritchard, Victoria L. |
title |
Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes |
title_short |
Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes |
title_full |
Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes |
title_fullStr |
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 |
Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes |
title_sort |
genomic signatures of fine-scale local selection in atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes |
publisher |
Wiley |
publishDate |
2021 |
url |
http://hdl.handle.net/10138/326500 |
long_lat |
ENVELOPE(-130.143,-130.143,54.160,54.160) |
geographic |
Sockeye |
geographic_facet |
Sockeye |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
10.1111/mec.14705 Suomen Akatemia, Grant/Award Number: 284941, 314254; Suomen Kulttuurirahasto Pritchard , V L , Makinen , H , Vähä , J-P , Erkinaro , J , Orell , P & Primmer , C R 2018 , ' Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes ' , Molecular Ecology , vol. 27 , no. 11 , pp. 2560-2575 . https://doi.org/10.1111/mec.14705 ORCID: /0000-0002-3687-8435/work/47430067 85051777368 7388b976-8225-433b-b6f7-6fe5bfbace90 http://hdl.handle.net/10138/326500 000434152100006 |
op_rights |
openAccess info:eu-repo/semantics/openAccess |
container_title |
Molecular Ecology |
container_volume |
27 |
container_issue |
11 |
container_start_page |
2560 |
op_container_end_page |
2575 |
_version_ |
1787423089804443648 |