Genomic differentiation in Pacific cod using Pool‐ Seq
Abstract Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible...
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crwiley:10.1111/eva.13488 2024-06-02T07:54:44+00:00 Genomic differentiation in Pacific cod using Pool‐ Seq Spies, Ingrid Tarpey, Carolyn Kristiansen, Trond Fisher, Mary Rohan, Sean Hauser, Lorenz 2022 http://dx.doi.org/10.1111/eva.13488 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13488 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13488 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Evolutionary Applications volume 15, issue 11, page 1907-1924 ISSN 1752-4571 1752-4571 journal-article 2022 crwiley https://doi.org/10.1111/eva.13488 2024-05-03T11:29:30Z Abstract Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod ( Gadus macrocephalus ) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence ( F ST ) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence ( d XY ) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence ( d XY ) but roughly double the relative divergence ( F ST ) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species. Article in Journal/Newspaper Aleutian Island atlantic cod Bering Sea Aleutian Islands Wiley Online Library Bering Sea Pacific Evolutionary Applications 15 11 1907 1924 |
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Wiley Online Library |
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English |
description |
Abstract Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod ( Gadus macrocephalus ) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence ( F ST ) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence ( d XY ) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence ( d XY ) but roughly double the relative divergence ( F ST ) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species. |
format |
Article in Journal/Newspaper |
author |
Spies, Ingrid Tarpey, Carolyn Kristiansen, Trond Fisher, Mary Rohan, Sean Hauser, Lorenz |
spellingShingle |
Spies, Ingrid Tarpey, Carolyn Kristiansen, Trond Fisher, Mary Rohan, Sean Hauser, Lorenz Genomic differentiation in Pacific cod using Pool‐ Seq |
author_facet |
Spies, Ingrid Tarpey, Carolyn Kristiansen, Trond Fisher, Mary Rohan, Sean Hauser, Lorenz |
author_sort |
Spies, Ingrid |
title |
Genomic differentiation in Pacific cod using Pool‐ Seq |
title_short |
Genomic differentiation in Pacific cod using Pool‐ Seq |
title_full |
Genomic differentiation in Pacific cod using Pool‐ Seq |
title_fullStr |
Genomic differentiation in Pacific cod using Pool‐ Seq |
title_full_unstemmed |
Genomic differentiation in Pacific cod using Pool‐ Seq |
title_sort |
genomic differentiation in pacific cod using pool‐ seq |
publisher |
Wiley |
publishDate |
2022 |
url |
http://dx.doi.org/10.1111/eva.13488 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13488 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13488 |
geographic |
Bering Sea Pacific |
geographic_facet |
Bering Sea Pacific |
genre |
Aleutian Island atlantic cod Bering Sea Aleutian Islands |
genre_facet |
Aleutian Island atlantic cod Bering Sea Aleutian Islands |
op_source |
Evolutionary Applications volume 15, issue 11, page 1907-1924 ISSN 1752-4571 1752-4571 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/eva.13488 |
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Evolutionary Applications |
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15 |
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11 |
container_start_page |
1907 |
op_container_end_page |
1924 |
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1800743205094817792 |