False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca )
While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture follow...
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Online Access: | https://pure.au.dk/portal/en/publications/50ac138e-8c57-4e42-9ac8-17312ed37d80 https://doi.org/10.1002/edn3.32 |
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ftuniaarhuspubl:oai:pure.atira.dk:publications/50ac138e-8c57-4e42-9ac8-17312ed37d80 2024-02-11T10:05:30+01:00 False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) Pinfield, Roisin Dillane, Eileen Wiborg Runge, Anne Kathrine Evans, Alice Mirimin, Luca Niemann, Jonas Reed, Thomas E. Reid, David G. Rogan, Emer Samarra, Filipa I. P. Sigsgaard, Eva Egelyng Foote, Andrew D. 2019-11 https://pure.au.dk/portal/en/publications/50ac138e-8c57-4e42-9ac8-17312ed37d80 https://doi.org/10.1002/edn3.32 eng eng https://pure.au.dk/portal/en/publications/50ac138e-8c57-4e42-9ac8-17312ed37d80 info:eu-repo/semantics/openAccess Pinfield , R , Dillane , E , Wiborg Runge , A K , Evans , A , Mirimin , L , Niemann , J , Reed , T E , Reid , D G , Rogan , E , Samarra , F I P , Sigsgaard , E E & Foote , A D 2019 , ' False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) ' , Environmental DNA , vol. 1 , no. 4 , pp. 316-328 . https://doi.org/10.1002/edn3.32 Orcinus orca PCR Scomber scombrus eDNA environmental DNA metagenomics whole-genome enrichment article 2019 ftuniaarhuspubl https://doi.org/10.1002/edn3.32 2024-01-18T00:00:22Z While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions. Article in Journal/Newspaper Killer Whale Orca Orcinus orca Killer whale Aarhus University: Research Environmental DNA 1 4 316 328 |
institution |
Open Polar |
collection |
Aarhus University: Research |
op_collection_id |
ftuniaarhuspubl |
language |
English |
topic |
Orcinus orca PCR Scomber scombrus eDNA environmental DNA metagenomics whole-genome enrichment |
spellingShingle |
Orcinus orca PCR Scomber scombrus eDNA environmental DNA metagenomics whole-genome enrichment Pinfield, Roisin Dillane, Eileen Wiborg Runge, Anne Kathrine Evans, Alice Mirimin, Luca Niemann, Jonas Reed, Thomas E. Reid, David G. Rogan, Emer Samarra, Filipa I. P. Sigsgaard, Eva Egelyng Foote, Andrew D. False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) |
topic_facet |
Orcinus orca PCR Scomber scombrus eDNA environmental DNA metagenomics whole-genome enrichment |
description |
While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions. |
format |
Article in Journal/Newspaper |
author |
Pinfield, Roisin Dillane, Eileen Wiborg Runge, Anne Kathrine Evans, Alice Mirimin, Luca Niemann, Jonas Reed, Thomas E. Reid, David G. Rogan, Emer Samarra, Filipa I. P. Sigsgaard, Eva Egelyng Foote, Andrew D. |
author_facet |
Pinfield, Roisin Dillane, Eileen Wiborg Runge, Anne Kathrine Evans, Alice Mirimin, Luca Niemann, Jonas Reed, Thomas E. Reid, David G. Rogan, Emer Samarra, Filipa I. P. Sigsgaard, Eva Egelyng Foote, Andrew D. |
author_sort |
Pinfield, Roisin |
title |
False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) |
title_short |
False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) |
title_full |
False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) |
title_fullStr |
False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) |
title_full_unstemmed |
False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) |
title_sort |
false‐negative detections from environmental dna collected in the presence of large numbers of killer whales ( orcinus orca ) |
publishDate |
2019 |
url |
https://pure.au.dk/portal/en/publications/50ac138e-8c57-4e42-9ac8-17312ed37d80 https://doi.org/10.1002/edn3.32 |
genre |
Killer Whale Orca Orcinus orca Killer whale |
genre_facet |
Killer Whale Orca Orcinus orca Killer whale |
op_source |
Pinfield , R , Dillane , E , Wiborg Runge , A K , Evans , A , Mirimin , L , Niemann , J , Reed , T E , Reid , D G , Rogan , E , Samarra , F I P , Sigsgaard , E E & Foote , A D 2019 , ' False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca ) ' , Environmental DNA , vol. 1 , no. 4 , pp. 316-328 . https://doi.org/10.1002/edn3.32 |
op_relation |
https://pure.au.dk/portal/en/publications/50ac138e-8c57-4e42-9ac8-17312ed37d80 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1002/edn3.32 |
container_title |
Environmental DNA |
container_volume |
1 |
container_issue |
4 |
container_start_page |
316 |
op_container_end_page |
328 |
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1790602548077395968 |