Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy 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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ftawi:oai:epic.awi.de:38989 2023-05-15T13:40:27+02:00 Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water Deagle, Bruce Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon 2015-09-01 application/pdf https://epic.awi.de/id/eprint/38989/ https://epic.awi.de/id/eprint/38989/2/Deagleetal.pdf https://hdl.handle.net/10013/epic.46236 https://hdl.handle.net/10013/epic.46236.d002 unknown WILEY-BLACKWELL PUBLISHING https://epic.awi.de/id/eprint/38989/2/Deagleetal.pdf https://hdl.handle.net/10013/epic.46236.d002 Deagle, B. , Faux, C. , Kawaguchi, S. , Meyer, B. orcid:0000-0001-6804-9896 and Jarman, S. (2015) Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water , Molecular Ecology . doi:10.1111/mec.13370 <https://doi.org/10.1111/mec.13370> , hdl:10013/epic.46236 EPIC3Molecular Ecology, WILEY-BLACKWELL PUBLISHING, ISSN: 0962-1083 Article isiRev 2015 ftawi https://doi.org/10.1111/mec.13370 2021-12-24T15:40:51Z 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 Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) Antarctic Southern Ocean East Antarctica Molecular Ecology 24 19 4943 4959 |
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Open Polar |
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Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) |
op_collection_id |
ftawi |
language |
unknown |
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 Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon |
spellingShingle |
Deagle, Bruce Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
author_facet |
Deagle, Bruce Faux, Cassandra Kawaguchi, So Meyer, Bettina Jarman, Simon |
author_sort |
Deagle, Bruce |
title |
Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
title_short |
Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
title_full |
Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
title_fullStr |
Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
title_full_unstemmed |
Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
title_sort |
antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water |
publisher |
WILEY-BLACKWELL PUBLISHING |
publishDate |
2015 |
url |
https://epic.awi.de/id/eprint/38989/ https://epic.awi.de/id/eprint/38989/2/Deagleetal.pdf https://hdl.handle.net/10013/epic.46236 https://hdl.handle.net/10013/epic.46236.d002 |
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 |
EPIC3Molecular Ecology, WILEY-BLACKWELL PUBLISHING, ISSN: 0962-1083 |
op_relation |
https://epic.awi.de/id/eprint/38989/2/Deagleetal.pdf https://hdl.handle.net/10013/epic.46236.d002 Deagle, B. , Faux, C. , Kawaguchi, S. , Meyer, B. orcid:0000-0001-6804-9896 and Jarman, S. (2015) Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water , Molecular Ecology . doi:10.1111/mec.13370 <https://doi.org/10.1111/mec.13370> , hdl:10013/epic.46236 |
op_doi |
https://doi.org/10.1111/mec.13370 |
container_title |
Molecular Ecology |
container_volume |
24 |
container_issue |
19 |
container_start_page |
4943 |
op_container_end_page |
4959 |
_version_ |
1766134726791266304 |