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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Online Access: | https://doi.org/10.5061/dryad.3023m |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::f9c3ad702023c78124c5337062e7e51a 2023-05-15T13:43:31+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. 2019-07-15 https://doi.org/10.5061/dryad.3023m undefined unknown Dryad Digital Repository https://dx.doi.org/10.5061/dryad.3023m http://dx.doi.org/10.5061/dryad.3023m lic_creative-commons 10.5061/dryad.3023m oai:easy.dans.knaw.nl:easy-dataset:89603 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89603 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 genotyping-by-sequencing Zooplankton Euphausia superba repetitive DNA RAD sequencing Population Genetics - Empirical Southern Ocean Antarctica Life sciences medicine and health care geo envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2019 fttriple https://doi.org/10.5061/dryad.3023m 2023-01-22T16:51:46Z 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. 1 RAD-seq project info V22_Unique_RAD_TagsSequences of the unique RAD tags3a_BSP_pipeline_logParameters used to generate BAM/SAM files4 Variant call format files V2Variant call format files derived from the RAD ... Dataset Antarc* Antarctic Antarctic Krill Antarctica East Antarctica Euphausia superba Southern Ocean Unknown Antarctic Southern Ocean East Antarctica |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
genotyping-by-sequencing Zooplankton Euphausia superba repetitive DNA RAD sequencing Population Genetics - Empirical Southern Ocean Antarctica Life sciences medicine and health care geo envir |
spellingShingle |
genotyping-by-sequencing Zooplankton Euphausia superba repetitive DNA RAD sequencing Population Genetics - Empirical Southern Ocean Antarctica Life sciences medicine and health care geo envir 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 Euphausia superba repetitive DNA RAD sequencing Population Genetics - Empirical Southern Ocean Antarctica Life sciences medicine and health care geo envir |
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. 1 RAD-seq project info V22_Unique_RAD_TagsSequences of the unique RAD tags3a_BSP_pipeline_logParameters used to generate BAM/SAM files4 Variant call format files V2Variant call format files derived from the RAD ... |
format |
Dataset |
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 |
publisher |
Dryad Digital Repository |
publishDate |
2019 |
url |
https://doi.org/10.5061/dryad.3023m |
geographic |
Antarctic Southern Ocean East Antarctica |
geographic_facet |
Antarctic Southern Ocean East Antarctica |
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_source |
10.5061/dryad.3023m oai:easy.dans.knaw.nl:easy-dataset:89603 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89603 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
https://dx.doi.org/10.5061/dryad.3023m http://dx.doi.org/10.5061/dryad.3023m |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.3023m |
_version_ |
1766189930242899968 |