Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between...
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ftzenodo:oai:zenodo.org:4963077 2024-09-15T17:55:21+00:00 Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions Berg, Paul R. Star, Bastiaan Pampoulie, Christophe Bradbury, Ian R. Bentzen, Paul Hutchings, Jeffrey A. Jentoft, Sissel Jakobsen, Kjetill S. 2017-08-11 https://doi.org/10.5061/dryad.b20ps unknown Zenodo https://doi.org/10.1038/hdy.2017.54 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.b20ps oai:zenodo.org:4963077 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Genomic adaptation Inversion polymorphism Chromosomal rearrangement ecological divergence SNPs info:eu-repo/semantics/other 2017 ftzenodo https://doi.org/10.5061/dryad.b20ps10.1038/hdy.2017.54 2024-07-26T23:57:44Z Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the more than 100,000 years old trans-Atlantic separation of Atlantic cod. The long-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by co-evolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions - each containing hundreds of genes – likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean. BergEtAl2017_AtlanticCod_TransatlanticDataset_PLINK-format SNP array data for 316 individuals of Atlantic cod (Gadus morhua), genotyped at 8,165 loci in standard PLINK file format. The PLINK file format consists of two files, a map file and a ped file. In the map file, the first column defines the linkage group, the second column contains the loci names (dbSNP accession numbers), the third line describes the position within the linkage groups (here all are set to 0) and the fourth column defines the order of the SNPs within each linkage group. In the ped file, column one is used to separate the populations (pop-1 to pop-9), column 2 defines the individuals within each population (denoted as the population abbreviation followed by the individual number) where the populations are abbreviated as follows: Can-N_PB = Placentia Bay, Can-N_SG = Southern Gulf of St. Lawrence, ... Other/Unknown Material atlantic cod Gadus morhua Northeast Atlantic Northwest Atlantic Zenodo |
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Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Genomic adaptation Inversion polymorphism Chromosomal rearrangement ecological divergence SNPs |
spellingShingle |
Genomic adaptation Inversion polymorphism Chromosomal rearrangement ecological divergence SNPs Berg, Paul R. Star, Bastiaan Pampoulie, Christophe Bradbury, Ian R. Bentzen, Paul Hutchings, Jeffrey A. Jentoft, Sissel Jakobsen, Kjetill S. Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions |
topic_facet |
Genomic adaptation Inversion polymorphism Chromosomal rearrangement ecological divergence SNPs |
description |
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the more than 100,000 years old trans-Atlantic separation of Atlantic cod. The long-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by co-evolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions - each containing hundreds of genes – likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean. BergEtAl2017_AtlanticCod_TransatlanticDataset_PLINK-format SNP array data for 316 individuals of Atlantic cod (Gadus morhua), genotyped at 8,165 loci in standard PLINK file format. The PLINK file format consists of two files, a map file and a ped file. In the map file, the first column defines the linkage group, the second column contains the loci names (dbSNP accession numbers), the third line describes the position within the linkage groups (here all are set to 0) and the fourth column defines the order of the SNPs within each linkage group. In the ped file, column one is used to separate the populations (pop-1 to pop-9), column 2 defines the individuals within each population (denoted as the population abbreviation followed by the individual number) where the populations are abbreviated as follows: Can-N_PB = Placentia Bay, Can-N_SG = Southern Gulf of St. Lawrence, ... |
format |
Other/Unknown Material |
author |
Berg, Paul R. Star, Bastiaan Pampoulie, Christophe Bradbury, Ian R. Bentzen, Paul Hutchings, Jeffrey A. Jentoft, Sissel Jakobsen, Kjetill S. |
author_facet |
Berg, Paul R. Star, Bastiaan Pampoulie, Christophe Bradbury, Ian R. Bentzen, Paul Hutchings, Jeffrey A. Jentoft, Sissel Jakobsen, Kjetill S. |
author_sort |
Berg, Paul R. |
title |
Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions |
title_short |
Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions |
title_full |
Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions |
title_fullStr |
Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions |
title_full_unstemmed |
Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions |
title_sort |
data from: trans-oceanic genomic divergence of atlantic cod ecotypes is associated with large inversions |
publisher |
Zenodo |
publishDate |
2017 |
url |
https://doi.org/10.5061/dryad.b20ps |
genre |
atlantic cod Gadus morhua Northeast Atlantic Northwest Atlantic |
genre_facet |
atlantic cod Gadus morhua Northeast Atlantic Northwest Atlantic |
op_relation |
https://doi.org/10.1038/hdy.2017.54 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.b20ps oai:zenodo.org:4963077 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.b20ps10.1038/hdy.2017.54 |
_version_ |
1810431640561778688 |