Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data
Cultivated bivalves are hugely important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for...
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ftzenodo:oai:zenodo.org:4957246 2023-05-15T14:13:31+02:00 Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data Vendrami, David L.J. Houston, Ross D. Gharbi, Karim Telesca, Luca Gutierrez, Alejandro P. Gurney-Smith, Helen Hasegawa, Natsuki Boudry, Pierre Hoffman, Joseph I. Vendrami, David L. J. 2018-11-07 https://zenodo.org/record/4957246 https://doi.org/10.5061/dryad.6d778b6 unknown doi:10.1111/eva.12736 https://zenodo.org/communities/dryad https://zenodo.org/record/4957246 https://doi.org/10.5061/dryad.6d778b6 oai:zenodo.org:4957246 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode restriction site associated DNA (RAD) sequencing Pacific oyster single nucleotide polymorphism (SNP) high density genotyping array 2014 - 2016 Inbreeding Crassostrea gigas Aquaculture info:eu-repo/semantics/other dataset 2018 ftzenodo https://doi.org/10.5061/dryad.6d778b610.1111/eva.12736 2023-03-10T17:27:49Z Cultivated bivalves are hugely important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large-scale comparison of wild and hatchery populations to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the hatchery populations. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of invasive populations, while also providing a novel window on how hatchery propagation may influence inbreeding, with important economic and management implications. Cgigas_SNPArray_genotypesGenotypes for 232 oyster samples in PED format obtained from the medium density SNP array described in Gutierrez et al. (2017).Cgigas_SNPArray.pedCgigas_SNPArray_map_fileSNPs identifiers in MAP format relative to the PED file containing genotypes based on the SNP array.Cgigas_SNPArray.mapCgigas_RADseq_map_filesSNPs identifiers in PED format relative to the PED file containing genotypes ... Dataset Antarc* Antarctica Crassostrea gigas Pacific oyster Zenodo Canada Norway Pacific |
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ftzenodo |
language |
unknown |
topic |
restriction site associated DNA (RAD) sequencing Pacific oyster single nucleotide polymorphism (SNP) high density genotyping array 2014 - 2016 Inbreeding Crassostrea gigas Aquaculture |
spellingShingle |
restriction site associated DNA (RAD) sequencing Pacific oyster single nucleotide polymorphism (SNP) high density genotyping array 2014 - 2016 Inbreeding Crassostrea gigas Aquaculture Vendrami, David L.J. Houston, Ross D. Gharbi, Karim Telesca, Luca Gutierrez, Alejandro P. Gurney-Smith, Helen Hasegawa, Natsuki Boudry, Pierre Hoffman, Joseph I. Vendrami, David L. J. Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data |
topic_facet |
restriction site associated DNA (RAD) sequencing Pacific oyster single nucleotide polymorphism (SNP) high density genotyping array 2014 - 2016 Inbreeding Crassostrea gigas Aquaculture |
description |
Cultivated bivalves are hugely important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large-scale comparison of wild and hatchery populations to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the hatchery populations. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of invasive populations, while also providing a novel window on how hatchery propagation may influence inbreeding, with important economic and management implications. Cgigas_SNPArray_genotypesGenotypes for 232 oyster samples in PED format obtained from the medium density SNP array described in Gutierrez et al. (2017).Cgigas_SNPArray.pedCgigas_SNPArray_map_fileSNPs identifiers in MAP format relative to the PED file containing genotypes based on the SNP array.Cgigas_SNPArray.mapCgigas_RADseq_map_filesSNPs identifiers in PED format relative to the PED file containing genotypes ... |
format |
Dataset |
author |
Vendrami, David L.J. Houston, Ross D. Gharbi, Karim Telesca, Luca Gutierrez, Alejandro P. Gurney-Smith, Helen Hasegawa, Natsuki Boudry, Pierre Hoffman, Joseph I. Vendrami, David L. J. |
author_facet |
Vendrami, David L.J. Houston, Ross D. Gharbi, Karim Telesca, Luca Gutierrez, Alejandro P. Gurney-Smith, Helen Hasegawa, Natsuki Boudry, Pierre Hoffman, Joseph I. Vendrami, David L. J. |
author_sort |
Vendrami, David L.J. |
title |
Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data |
title_short |
Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data |
title_full |
Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data |
title_fullStr |
Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data |
title_full_unstemmed |
Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data |
title_sort |
data from: detailed insights into pan-european population structure and inbreeding in wild and hatchery pacific oyster (crassostrea gigas) populations revealed by genome-wide snp data |
publishDate |
2018 |
url |
https://zenodo.org/record/4957246 https://doi.org/10.5061/dryad.6d778b6 |
geographic |
Canada Norway Pacific |
geographic_facet |
Canada Norway Pacific |
genre |
Antarc* Antarctica Crassostrea gigas Pacific oyster |
genre_facet |
Antarc* Antarctica Crassostrea gigas Pacific oyster |
op_relation |
doi:10.1111/eva.12736 https://zenodo.org/communities/dryad https://zenodo.org/record/4957246 https://doi.org/10.5061/dryad.6d778b6 oai:zenodo.org:4957246 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.6d778b610.1111/eva.12736 |
_version_ |
1766285984191741952 |