False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)
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Dokumenter
- False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)
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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.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Environmental DNA |
| Vol/bind | 1 |
| Udgave nummer | 4 |
| Sider (fra-til) | 316-328 |
| Antal sider | 13 |
| ISSN | 2637-4943 |
| DOI | |
| Status | Udgivet - 2019 |
Bibliografisk note
Funding Information:
This work was funded by the Irish Research Council & the Marine Institute of Ireland through an Irish Research Council Enterprise Partnership Postgraduate Scholarship Scheme. A Lerner‐Gray Grant for Marine Research was awarded to R.P. from the Richard Gilder Graduate School at the American Museum of Natural History, New York, to purchase the Veggerby eDNA sampler poles. Two Marine Institute Networking and Travel grants were awarded to R.P. to conduct fieldwork with the Icelandic Orca Project in Iceland and to carry out genetic analyses in the laboratories at the Centre for GeoGenetics, University of Copenhagen, Denmark. A.K.W.R. and J.N. were supported by the European Union's Horizon 2020 research and innovation program under grant agreement no. 676154 (ArchSci2020) to conduct the metagenomics data analyses. A.D.F. was supported by the Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment, and from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska‐Curie grant agreement no. 663830. The authors would like to sincerely thank the Irish Pelagic Fishing fleet and Producer's, particularly the Irish skippers and crew for their help and support in providing a platform to take the eDNA samples. Thanks to fieldwork assistant Aoife Foley and Dr Eugene Mullins from the Marine Institute for providing advice and freezer storage between fishing trips. The fieldwork in Iceland was funded by the Icelandic Research Fund (i. Rannsóknasjóður) and in part by the generous support of Earthwatch. We would like to thank everybody who helped with the fieldwork as well as the Earthwatch volunteers.
Funding Information:
This work was funded by the Irish Research Council & the Marine Institute of Ireland through an Irish Research Council Enterprise Partnership Postgraduate Scholarship Scheme. A Lerner-Gray Grant for Marine Research was awarded to R.P. from the Richard Gilder Graduate School at the American Museum of Natural History, New York, to purchase the?Veggerby eDNA sampler poles. Two Marine Institute Networking and Travel grants were awarded to R.P. to conduct fieldwork with the Icelandic Orca Project in Iceland and to carry out genetic analyses in the laboratories at the Centre for GeoGenetics, University of Copenhagen, Denmark. A.K.W.R. and J.N. were supported by the European Union's Horizon 2020 research and innovation program under grant agreement no. 676154 (ArchSci2020) to conduct the metagenomics data analyses. A.D.F. was supported by the Welsh Government and Higher Education Funding Council for Wales through the S?r Cymru National Research Network for Low Carbon, Energy and Environment, and from the European Union's Horizon 2020 research and innovation program under the Marie Sk?odowska-Curie grant agreement no. 663830. The authors would like to sincerely thank the Irish Pelagic Fishing fleet and Producer's, particularly the Irish skippers and crew for their help and support in providing a platform to take the eDNA samples. Thanks to?fieldwork assistant Aoife Foley and Dr Eugene Mullins from the Marine Institute for providing advice and?freezer storage between fishing trips. The fieldwork in Iceland was funded by the Icelandic Research Fund (i. Ranns?knasj??ur) and in part by the generous support of Earthwatch. We would like to thank everybody who helped with the fieldwork as well as the?Earthwatch volunteers.
Publisher Copyright:
© 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd
ID: 283984652