Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)
DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, t...
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ftdryad:oai:v1.datadryad.org:10255/dryad.53364 2023-05-15T17:57:49+02:00 Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) Heintzman, Peter D. Elias, Scott A. Moore, Karen Paszkiewicz, Konrad Barnes, Ian Scandinavia North America Russia Canada Sweden Quaternary Late Pleistocene Holocene Recent 2013-11-27T16:33:28Z http://hdl.handle.net/10255/dryad.53364 https://doi.org/10.5061/dryad.0179t unknown doi:10.5061/dryad.0179t/8 doi:10.5061/dryad.0179t/10 doi:10.5061/dryad.0179t/12 doi:10.5061/dryad.0179t/14 doi:10.5061/dryad.0179t/16 doi:10.5061/dryad.0179t/18 doi:10.5061/dryad.0179t/19 doi:10.5061/dryad.0179t/20 doi:10.5061/dryad.0179t/21 doi:10.5061/dryad.0179t/7 doi:10.5061/dryad.0179t/9 doi:10.5061/dryad.0179t/11 doi:10.5061/dryad.0179t/13 doi:10.5061/dryad.0179t/15 doi:10.5061/dryad.0179t/17 doi:10.5061/dryad.0179t/1 doi:10.5061/dryad.0179t/2 doi:10.5061/dryad.0179t/3 doi:10.5061/dryad.0179t/4 doi:10.5061/dryad.0179t/5 doi:10.5061/dryad.0179t/6 doi:10.5061/dryad.0179t/22 doi:10.5061/dryad.0179t/23 doi:10.5061/dryad.0179t/24 doi:10.5061/dryad.0179t/25 doi:10.5061/dryad.0179t/26 doi:10.5061/dryad.0179t/27 doi:10.1111/1755-0998.12205 PMID:24266987 doi:10.5061/dryad.0179t Heintzman PD, Elias SA, Moore K, Paszkiewicz K, Barnes I (2013) Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera). Molecular Ecology Resources 14(3): 606–615. http://hdl.handle.net/10255/dryad.53364 DNA preservation ancient DNA museum DNA shotgun sequencing Metagenomics Article 2013 ftdryad https://doi.org/10.5061/dryad.0179t https://doi.org/10.5061/dryad.0179t/8 https://doi.org/10.5061/dryad.0179t/10 https://doi.org/10.5061/dryad.0179t/12 https://doi.org/10.5061/dryad.0179t/14 https://doi.org/10.5061/dryad.0179t/16 https://doi.o 2020-01-01T15:03:32Z DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we explored DNA preservation in specimens of the ground beetle Amara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiable DNA, with the maximum amplifiable fragment length decreasing with age. Amplification of DNA was only possible in 45% of ancient specimens. Preserved mitochondrial DNA fragments were significantly longer than those of nuclear DNA in both museum and ancient specimens. Metagenomic characterisation of extracted DNA demonstrated that parasite-derived sequences, including Wolbachia and Spiroplasma, are recoverable from museum beetle specimens. Ancient DNA extracts contained beetle DNA in amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient beetle specimens in future genetic studies. Article in Journal/Newspaper permafrost Dryad Digital Repository (Duke University) Canada |
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Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
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unknown |
topic |
DNA preservation ancient DNA museum DNA shotgun sequencing Metagenomics |
spellingShingle |
DNA preservation ancient DNA museum DNA shotgun sequencing Metagenomics Heintzman, Peter D. Elias, Scott A. Moore, Karen Paszkiewicz, Konrad Barnes, Ian Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) |
topic_facet |
DNA preservation ancient DNA museum DNA shotgun sequencing Metagenomics |
description |
DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we explored DNA preservation in specimens of the ground beetle Amara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiable DNA, with the maximum amplifiable fragment length decreasing with age. Amplification of DNA was only possible in 45% of ancient specimens. Preserved mitochondrial DNA fragments were significantly longer than those of nuclear DNA in both museum and ancient specimens. Metagenomic characterisation of extracted DNA demonstrated that parasite-derived sequences, including Wolbachia and Spiroplasma, are recoverable from museum beetle specimens. Ancient DNA extracts contained beetle DNA in amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient beetle specimens in future genetic studies. |
format |
Article in Journal/Newspaper |
author |
Heintzman, Peter D. Elias, Scott A. Moore, Karen Paszkiewicz, Konrad Barnes, Ian |
author_facet |
Heintzman, Peter D. Elias, Scott A. Moore, Karen Paszkiewicz, Konrad Barnes, Ian |
author_sort |
Heintzman, Peter D. |
title |
Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) |
title_short |
Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) |
title_full |
Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) |
title_fullStr |
Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) |
title_full_unstemmed |
Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera) |
title_sort |
data from: characterizing dna preservation in degraded specimens of amara alpina (carabidae: coleoptera) |
publishDate |
2013 |
url |
http://hdl.handle.net/10255/dryad.53364 https://doi.org/10.5061/dryad.0179t |
op_coverage |
Scandinavia North America Russia Canada Sweden Quaternary Late Pleistocene Holocene Recent |
geographic |
Canada |
geographic_facet |
Canada |
genre |
permafrost |
genre_facet |
permafrost |
op_relation |
doi:10.5061/dryad.0179t/8 doi:10.5061/dryad.0179t/10 doi:10.5061/dryad.0179t/12 doi:10.5061/dryad.0179t/14 doi:10.5061/dryad.0179t/16 doi:10.5061/dryad.0179t/18 doi:10.5061/dryad.0179t/19 doi:10.5061/dryad.0179t/20 doi:10.5061/dryad.0179t/21 doi:10.5061/dryad.0179t/7 doi:10.5061/dryad.0179t/9 doi:10.5061/dryad.0179t/11 doi:10.5061/dryad.0179t/13 doi:10.5061/dryad.0179t/15 doi:10.5061/dryad.0179t/17 doi:10.5061/dryad.0179t/1 doi:10.5061/dryad.0179t/2 doi:10.5061/dryad.0179t/3 doi:10.5061/dryad.0179t/4 doi:10.5061/dryad.0179t/5 doi:10.5061/dryad.0179t/6 doi:10.5061/dryad.0179t/22 doi:10.5061/dryad.0179t/23 doi:10.5061/dryad.0179t/24 doi:10.5061/dryad.0179t/25 doi:10.5061/dryad.0179t/26 doi:10.5061/dryad.0179t/27 doi:10.1111/1755-0998.12205 PMID:24266987 doi:10.5061/dryad.0179t Heintzman PD, Elias SA, Moore K, Paszkiewicz K, Barnes I (2013) Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera). Molecular Ecology Resources 14(3): 606–615. http://hdl.handle.net/10255/dryad.53364 |
op_doi |
https://doi.org/10.5061/dryad.0179t https://doi.org/10.5061/dryad.0179t/8 https://doi.org/10.5061/dryad.0179t/10 https://doi.org/10.5061/dryad.0179t/12 https://doi.org/10.5061/dryad.0179t/14 https://doi.org/10.5061/dryad.0179t/16 https://doi.o |
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