Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water
Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limit...
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ftdryad:oai:v1.datadryad.org:10255/dryad.88630 2023-05-15T14:00:52+02:00 Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water Deagle, Bruce E. Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon N. Southern Ocean Antarctica 2015-09-03T16:43:16Z http://hdl.handle.net/10255/dryad.88630 https://doi.org/10.5061/dryad.3023m unknown doi:10.5061/dryad.3023m/8 doi:10.5061/dryad.3023m/2 doi:10.5061/dryad.3023m/3 doi:10.5061/dryad.3023m/9 doi:10.5061/dryad.3023m/5 doi:10.5061/dryad.3023m/6 doi:10.5061/dryad.3023m/7 doi:10.5061/dryad.3023m/10 doi:10.1111/mec.13370 PMID:26340718 doi:10.5061/dryad.3023m Deagle BE, Faux C, Kawaguchi S, Meyer B, Jarman SN (2015) Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water. Molecular Ecology 24(19): 4943–4959. http://hdl.handle.net/10255/dryad.88630 genotyping-by-sequencing zooplankton RAD sequencing repetitive DNA Population Genetics - Empirical Article 2015 ftdryad https://doi.org/10.5061/dryad.3023m https://doi.org/10.5061/dryad.3023m/8 https://doi.org/10.5061/dryad.3023m/2 https://doi.org/10.5061/dryad.3023m/3 https://doi.org/10.5061/dryad.3023m/9 https://doi.org/10.5061/dryad.3023m/5 https://doi.org/1 2020-01-01T15:20:25Z Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist. Article in Journal/Newspaper Antarc* Antarctic Antarctic Krill Antarctica East Antarctica Euphausia superba Southern Ocean Dryad Digital Repository (Duke University) Antarctic East Antarctica Southern Ocean |
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Open Polar |
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Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
genotyping-by-sequencing zooplankton RAD sequencing repetitive DNA Population Genetics - Empirical |
spellingShingle |
genotyping-by-sequencing zooplankton RAD sequencing repetitive DNA Population Genetics - Empirical Deagle, Bruce E. Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon N. Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
topic_facet |
genotyping-by-sequencing zooplankton RAD sequencing repetitive DNA Population Genetics - Empirical |
description |
Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist. |
format |
Article in Journal/Newspaper |
author |
Deagle, Bruce E. Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon N. |
author_facet |
Deagle, Bruce E. Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon N. |
author_sort |
Deagle, Bruce E. |
title |
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
title_short |
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
title_full |
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
title_fullStr |
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
title_full_unstemmed |
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
title_sort |
data from: antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water |
publishDate |
2015 |
url |
http://hdl.handle.net/10255/dryad.88630 https://doi.org/10.5061/dryad.3023m |
op_coverage |
Southern Ocean Antarctica |
geographic |
Antarctic East Antarctica Southern Ocean |
geographic_facet |
Antarctic East Antarctica Southern Ocean |
genre |
Antarc* Antarctic Antarctic Krill Antarctica East Antarctica Euphausia superba Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Krill Antarctica East Antarctica Euphausia superba Southern Ocean |
op_relation |
doi:10.5061/dryad.3023m/8 doi:10.5061/dryad.3023m/2 doi:10.5061/dryad.3023m/3 doi:10.5061/dryad.3023m/9 doi:10.5061/dryad.3023m/5 doi:10.5061/dryad.3023m/6 doi:10.5061/dryad.3023m/7 doi:10.5061/dryad.3023m/10 doi:10.1111/mec.13370 PMID:26340718 doi:10.5061/dryad.3023m Deagle BE, Faux C, Kawaguchi S, Meyer B, Jarman SN (2015) Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water. Molecular Ecology 24(19): 4943–4959. http://hdl.handle.net/10255/dryad.88630 |
op_doi |
https://doi.org/10.5061/dryad.3023m https://doi.org/10.5061/dryad.3023m/8 https://doi.org/10.5061/dryad.3023m/2 https://doi.org/10.5061/dryad.3023m/3 https://doi.org/10.5061/dryad.3023m/9 https://doi.org/10.5061/dryad.3023m/5 https://doi.org/1 |
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