False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca)
Abstract 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 captu...
Published in: | Environmental DNA |
---|---|
Main Authors: | , , , , , , , , , , , |
Other Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2019
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1002/edn3.32 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fedn3.32 https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.32 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/edn3.32 |
id |
crwiley:10.1002/edn3.32 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1002/edn3.32 2024-10-13T14:08:45+00:00 False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales ( Orcinus orca) Pinfield, Róisín Dillane, Eileen Runge, Anne Kathrine W. Evans, Alice Mirimin, Luca Niemann, Jonas Reed, Thomas E. Reid, David G. Rogan, Emer Samarra, Filipa I. P. Sigsgaard, Eva Egelyng Foote, Andrew D. Earthwatch Institute H2020 Marie Skłodowska-Curie Actions Horizon 2020 Framework Programme Marine Institute Irish Research Council 2019 http://dx.doi.org/10.1002/edn3.32 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fedn3.32 https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.32 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/edn3.32 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Environmental DNA volume 1, issue 4, page 316-328 ISSN 2637-4943 2637-4943 journal-article 2019 crwiley https://doi.org/10.1002/edn3.32 2024-09-27T04:17:12Z Abstract 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 Wiley Online Library Environmental DNA 1 4 316 328 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
Abstract 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. |
author2 |
Earthwatch Institute H2020 Marie Skłodowska-Curie Actions Horizon 2020 Framework Programme Marine Institute Irish Research Council |
format |
Article in Journal/Newspaper |
author |
Pinfield, Róisín Dillane, Eileen Runge, Anne Kathrine W. Evans, Alice Mirimin, Luca Niemann, Jonas Reed, Thomas E. Reid, David G. Rogan, Emer Samarra, Filipa I. P. Sigsgaard, Eva Egelyng Foote, Andrew D. |
spellingShingle |
Pinfield, Róisín Dillane, Eileen Runge, Anne Kathrine W. 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) |
author_facet |
Pinfield, Róisín Dillane, Eileen Runge, Anne Kathrine W. 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, Róisín |
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) |
publisher |
Wiley |
publishDate |
2019 |
url |
http://dx.doi.org/10.1002/edn3.32 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fedn3.32 https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.32 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/edn3.32 |
genre |
Killer Whale Orca Orcinus orca Killer whale |
genre_facet |
Killer Whale Orca Orcinus orca Killer whale |
op_source |
Environmental DNA volume 1, issue 4, page 316-328 ISSN 2637-4943 2637-4943 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
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 |
_version_ |
1812815510018981888 |