A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut
Abstract Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commer...
Published in: | ICES Journal of Marine Science |
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Language: | English |
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Oxford University Press (OUP)
2021
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Online Access: | http://dx.doi.org/10.1093/icesjms/fsab061 http://academic.oup.com/icesjms/article-pdf/78/7/2371/40535636/fsab061.pdf |
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croxfordunivpr:10.1093/icesjms/fsab061 2024-09-15T18:26:19+00:00 A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut Kess, Tony Einfeldt, Anthony L Wringe, Brendan Lehnert, Sarah J Layton, Kara K S McBride, Meghan C Robert, Dominique Fisher, Jonathan Le Bris, Arnault den Heyer, Cornelia Shackell, Nancy Ruzzante, Daniel E Bentzen, Paul Bradbury, Ian R Hauser, Lorenz Ocean Frontier Institute and the Department of Fisheries and Oceans Canada Genomics Research and Development Initiative 2021 http://dx.doi.org/10.1093/icesjms/fsab061 http://academic.oup.com/icesjms/article-pdf/78/7/2371/40535636/fsab061.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model ICES Journal of Marine Science volume 78, issue 7, page 2371-2384 ISSN 1054-3139 1095-9289 journal-article 2021 croxfordunivpr https://doi.org/10.1093/icesjms/fsab061 2024-08-27T04:18:00Z Abstract Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species. Article in Journal/Newspaper Northwest Atlantic Oxford University Press ICES Journal of Marine Science 78 7 2371 2384 |
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Oxford University Press |
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croxfordunivpr |
language |
English |
description |
Abstract Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species. |
author2 |
Hauser, Lorenz Ocean Frontier Institute and the Department of Fisheries and Oceans Canada Genomics Research and Development Initiative |
format |
Article in Journal/Newspaper |
author |
Kess, Tony Einfeldt, Anthony L Wringe, Brendan Lehnert, Sarah J Layton, Kara K S McBride, Meghan C Robert, Dominique Fisher, Jonathan Le Bris, Arnault den Heyer, Cornelia Shackell, Nancy Ruzzante, Daniel E Bentzen, Paul Bradbury, Ian R |
spellingShingle |
Kess, Tony Einfeldt, Anthony L Wringe, Brendan Lehnert, Sarah J Layton, Kara K S McBride, Meghan C Robert, Dominique Fisher, Jonathan Le Bris, Arnault den Heyer, Cornelia Shackell, Nancy Ruzzante, Daniel E Bentzen, Paul Bradbury, Ian R A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut |
author_facet |
Kess, Tony Einfeldt, Anthony L Wringe, Brendan Lehnert, Sarah J Layton, Kara K S McBride, Meghan C Robert, Dominique Fisher, Jonathan Le Bris, Arnault den Heyer, Cornelia Shackell, Nancy Ruzzante, Daniel E Bentzen, Paul Bradbury, Ian R |
author_sort |
Kess, Tony |
title |
A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut |
title_short |
A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut |
title_full |
A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut |
title_fullStr |
A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut |
title_full_unstemmed |
A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut |
title_sort |
putative structural variant and environmental variation associated with genomic divergence across the northwest atlantic in atlantic halibut |
publisher |
Oxford University Press (OUP) |
publishDate |
2021 |
url |
http://dx.doi.org/10.1093/icesjms/fsab061 http://academic.oup.com/icesjms/article-pdf/78/7/2371/40535636/fsab061.pdf |
genre |
Northwest Atlantic |
genre_facet |
Northwest Atlantic |
op_source |
ICES Journal of Marine Science volume 78, issue 7, page 2371-2384 ISSN 1054-3139 1095-9289 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1093/icesjms/fsab061 |
container_title |
ICES Journal of Marine Science |
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78 |
container_issue |
7 |
container_start_page |
2371 |
op_container_end_page |
2384 |
_version_ |
1810466792981659648 |