Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion
Abstract On the basis of multiple complete mitochondrial DNA genome sequences, we describe the temporal phylogeography of Atlantic cod (Gadus morhua), a lineage that has undergone a complex pattern of vicariant evolution, postglacial demographic shifts, and historic sharp population declines due to...
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Oxford University Press (OUP)
2008
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Online Access: | http://dx.doi.org/10.1534/genetics.108.089730 https://academic.oup.com/genetics/article-pdf/180/1/381/42096162/genetics0381.pdf |
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croxfordunivpr:10.1534/genetics.108.089730 2024-09-09T19:29:45+00:00 Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion Carr, Steven M Marshall, H Dawn 2008 http://dx.doi.org/10.1534/genetics.108.089730 https://academic.oup.com/genetics/article-pdf/180/1/381/42096162/genetics0381.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model Genetics volume 180, issue 1, page 381-389 ISSN 1943-2631 journal-article 2008 croxfordunivpr https://doi.org/10.1534/genetics.108.089730 2024-08-05T04:30:21Z Abstract On the basis of multiple complete mitochondrial DNA genome sequences, we describe the temporal phylogeography of Atlantic cod (Gadus morhua), a lineage that has undergone a complex pattern of vicariant evolution, postglacial demographic shifts, and historic sharp population declines due to fishing and/or environmental shifts. Each of 32 fish from four spawning aggregations from the northwest Atlantic and Norway has a unique mtDNA sequence, which differs by 6–60 substitutions. Phylogenetic analysis identifies six major haplogroups that range in age from 37 to 75 KYA. The widespread haplotype identified by previous single-locus analyses at the center of a “star phylogeny” is shown to be a paraphyletic assemblage of genome lineages. The coalescent that includes all cod occurs 162 KYA. The most basal clade comprises two fish from the western Atlantic. The most recent superclade that includes all fish examined from Norway, and which includes 84% of all fish examined, dates to 128 KYA at the Sangamon/Würm interglacial, when ocean depths on continental shelves would have favored transcontinental movement. The pairwise mismatch distribution dates population expansion of this superclade to the middle of the Wisconsinan/Weichsel glaciation 59 KYA, rather than to a postglacial emergence from a marine refugium 12 KYA, or to more recent historic events. We discuss alternative scenarios for the expansion and distribution of the descendants of the “codmother” in the North Atlantic. Mitochondrial phylogenomic analyses generate highly resolved trees that enable fine-scale tests of temporal hypotheses with an accuracy not possible with single-locus methods. Article in Journal/Newspaper atlantic cod Gadus morhua North Atlantic Northwest Atlantic Oxford University Press Kya ENVELOPE(8.308,8.308,63.772,63.772) Norway Genetics 180 1 381 389 |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
description |
Abstract On the basis of multiple complete mitochondrial DNA genome sequences, we describe the temporal phylogeography of Atlantic cod (Gadus morhua), a lineage that has undergone a complex pattern of vicariant evolution, postglacial demographic shifts, and historic sharp population declines due to fishing and/or environmental shifts. Each of 32 fish from four spawning aggregations from the northwest Atlantic and Norway has a unique mtDNA sequence, which differs by 6–60 substitutions. Phylogenetic analysis identifies six major haplogroups that range in age from 37 to 75 KYA. The widespread haplotype identified by previous single-locus analyses at the center of a “star phylogeny” is shown to be a paraphyletic assemblage of genome lineages. The coalescent that includes all cod occurs 162 KYA. The most basal clade comprises two fish from the western Atlantic. The most recent superclade that includes all fish examined from Norway, and which includes 84% of all fish examined, dates to 128 KYA at the Sangamon/Würm interglacial, when ocean depths on continental shelves would have favored transcontinental movement. The pairwise mismatch distribution dates population expansion of this superclade to the middle of the Wisconsinan/Weichsel glaciation 59 KYA, rather than to a postglacial emergence from a marine refugium 12 KYA, or to more recent historic events. We discuss alternative scenarios for the expansion and distribution of the descendants of the “codmother” in the North Atlantic. Mitochondrial phylogenomic analyses generate highly resolved trees that enable fine-scale tests of temporal hypotheses with an accuracy not possible with single-locus methods. |
format |
Article in Journal/Newspaper |
author |
Carr, Steven M Marshall, H Dawn |
spellingShingle |
Carr, Steven M Marshall, H Dawn Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion |
author_facet |
Carr, Steven M Marshall, H Dawn |
author_sort |
Carr, Steven M |
title |
Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion |
title_short |
Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion |
title_full |
Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion |
title_fullStr |
Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion |
title_full_unstemmed |
Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod ( Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion |
title_sort |
intraspecific phylogeographic genomics from multiple complete mtdna genomes in atlantic cod ( gadus morhua): origins of the “codmother,” transatlantic vicariance and midglacial population expansion |
publisher |
Oxford University Press (OUP) |
publishDate |
2008 |
url |
http://dx.doi.org/10.1534/genetics.108.089730 https://academic.oup.com/genetics/article-pdf/180/1/381/42096162/genetics0381.pdf |
long_lat |
ENVELOPE(8.308,8.308,63.772,63.772) |
geographic |
Kya Norway |
geographic_facet |
Kya Norway |
genre |
atlantic cod Gadus morhua North Atlantic Northwest Atlantic |
genre_facet |
atlantic cod Gadus morhua North Atlantic Northwest Atlantic |
op_source |
Genetics volume 180, issue 1, page 381-389 ISSN 1943-2631 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/genetics.108.089730 |
container_title |
Genetics |
container_volume |
180 |
container_issue |
1 |
container_start_page |
381 |
op_container_end_page |
389 |
_version_ |
1809898862336278528 |