Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)
High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel o...
Published in: | Molecular Ecology |
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2012
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Online Access: | https://pure.qub.ac.uk/en/publications/66378246-92cf-4a6f-9f2c-788b8eb8e969 https://doi.org/10.1111/j.1365-294X.2012.05639.x |
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ftqueensubelpubl:oai:pure.qub.ac.uk/portal:publications/66378246-92cf-4a6f-9f2c-788b8eb8e969 2024-09-15T18:23:02+00:00 Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) Limborg, Morten T Helyar, Sarah J De Bruyn, Mark Taylor, Martin I Nielsen, Einar E Ogden, Rob Carvalho, Gary R Bekkevold, Dorte 2012-08 https://pure.qub.ac.uk/en/publications/66378246-92cf-4a6f-9f2c-788b8eb8e969 https://doi.org/10.1111/j.1365-294X.2012.05639.x eng eng https://pure.qub.ac.uk/en/publications/66378246-92cf-4a6f-9f2c-788b8eb8e969 info:eu-repo/semantics/restrictedAccess Limborg , M T , Helyar , S J , De Bruyn , M , Taylor , M I , Nielsen , E E , Ogden , R , Carvalho , G R , Bekkevold , D & FPT Consortium 2012 , ' Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) ' , Molecular Ecology , vol. 21 , no. 15 , pp. 3686-703 . https://doi.org/10.1111/j.1365-294X.2012.05639.x Animals Atlantic Ocean Cluster Analysis Environment Fishes Gene Flow Genetic Loci Genotyping Techniques North Sea Polymorphism Single Nucleotide Salinity Selection Genetic Sequence Analysis DNA Temperature Transcriptome /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water article 2012 ftqueensubelpubl https://doi.org/10.1111/j.1365-294X.2012.05639.x 2024-07-22T23:44:20Z High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12 °C) and two salinity clines (5-35‰). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity. Article in Journal/Newspaper North Atlantic Northeast Atlantic Queen's University Belfast Research Portal Molecular Ecology 21 15 3686 3703 |
institution |
Open Polar |
collection |
Queen's University Belfast Research Portal |
op_collection_id |
ftqueensubelpubl |
language |
English |
topic |
Animals Atlantic Ocean Cluster Analysis Environment Fishes Gene Flow Genetic Loci Genotyping Techniques North Sea Polymorphism Single Nucleotide Salinity Selection Genetic Sequence Analysis DNA Temperature Transcriptome /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
spellingShingle |
Animals Atlantic Ocean Cluster Analysis Environment Fishes Gene Flow Genetic Loci Genotyping Techniques North Sea Polymorphism Single Nucleotide Salinity Selection Genetic Sequence Analysis DNA Temperature Transcriptome /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water Limborg, Morten T Helyar, Sarah J De Bruyn, Mark Taylor, Martin I Nielsen, Einar E Ogden, Rob Carvalho, Gary R Bekkevold, Dorte Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) |
topic_facet |
Animals Atlantic Ocean Cluster Analysis Environment Fishes Gene Flow Genetic Loci Genotyping Techniques North Sea Polymorphism Single Nucleotide Salinity Selection Genetic Sequence Analysis DNA Temperature Transcriptome /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
description |
High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12 °C) and two salinity clines (5-35‰). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity. |
format |
Article in Journal/Newspaper |
author |
Limborg, Morten T Helyar, Sarah J De Bruyn, Mark Taylor, Martin I Nielsen, Einar E Ogden, Rob Carvalho, Gary R Bekkevold, Dorte |
author_facet |
Limborg, Morten T Helyar, Sarah J De Bruyn, Mark Taylor, Martin I Nielsen, Einar E Ogden, Rob Carvalho, Gary R Bekkevold, Dorte |
author_sort |
Limborg, Morten T |
title |
Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) |
title_short |
Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) |
title_full |
Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) |
title_fullStr |
Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) |
title_full_unstemmed |
Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) |
title_sort |
environmental selection on transcriptome-derived snps in a high gene flow marine fish, the atlantic herring (clupea harengus) |
publishDate |
2012 |
url |
https://pure.qub.ac.uk/en/publications/66378246-92cf-4a6f-9f2c-788b8eb8e969 https://doi.org/10.1111/j.1365-294X.2012.05639.x |
genre |
North Atlantic Northeast Atlantic |
genre_facet |
North Atlantic Northeast Atlantic |
op_source |
Limborg , M T , Helyar , S J , De Bruyn , M , Taylor , M I , Nielsen , E E , Ogden , R , Carvalho , G R , Bekkevold , D & FPT Consortium 2012 , ' Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus) ' , Molecular Ecology , vol. 21 , no. 15 , pp. 3686-703 . https://doi.org/10.1111/j.1365-294X.2012.05639.x |
op_relation |
https://pure.qub.ac.uk/en/publications/66378246-92cf-4a6f-9f2c-788b8eb8e969 |
op_rights |
info:eu-repo/semantics/restrictedAccess |
op_doi |
https://doi.org/10.1111/j.1365-294X.2012.05639.x |
container_title |
Molecular Ecology |
container_volume |
21 |
container_issue |
15 |
container_start_page |
3686 |
op_container_end_page |
3703 |
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1810463144734097408 |