False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

Show simple item record

dc.contributor.author Pinfield, Róisín
dc.contributor.author Dillane, Eileen
dc.contributor.author Runge, Anne Kathrine W.
dc.contributor.author Evans, Alice
dc.contributor.author Mirimin, Luca
dc.contributor.author Niemann, Jonas
dc.contributor.author Reed, Thomas E.
dc.contributor.author Reid, David G.
dc.contributor.author Rogan, Emer
dc.contributor.author Samarra, Filipa I. P.
dc.contributor.author Sigsgaard, Eva Egelyng
dc.contributor.author Foote, Andrew D.
dc.date.accessioned 2019-10-16T06:01:02Z
dc.date.available 2019-10-16T06:01:02Z
dc.date.issued 2019-09-12
dc.identifier.citation Pinfield, R., Dillane, E., Runge, A. K. W., Evans, A., Mirimin, L., Niemann, J., Reed, T. E., Reid, D. G., Rogan, E., Samarra, F. I. P., Sigsgaard, E. E. and Foote, A. D. 'False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)', Environmental DNA, (13pp.) DOI: 10.1002/edn3.32 en
dc.identifier.startpage 1 en
dc.identifier.endpage 13 en
dc.identifier.issn 2637-4943
dc.identifier.uri http://hdl.handle.net/10468/8785
dc.identifier.doi 10.1002/edn3.32 en
dc.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. en
dc.description.sponsorship Irish Research Council (Enterprise Partnership Scheme Postgraduate Scholarship (Grant Number: EPSPG/2015/158)); Marine Institute (Networking and Travel Grant Numbers: NT‐17‐55, NT‐18‐49; Enterprise Partnership Scheme Postgraduate Scholarship); American Museum of Natural History (Lerner‐Gray Fund for Marine Research) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher John Wiley & Sons, Inc. en
dc.relation.uri https://onlinelibrary.wiley.com/doi/full/10.1002/edn3.32
dc.rights ©2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.subject eDNA en
dc.subject Environmental DNA en
dc.subject Metagenomics en
dc.subject Orcinus orca en
dc.subject PCR en
dc.subject Scomber scombrus en
dc.subject Whole-genome enrichment en
dc.title False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca) en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Thomas Reed, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland. +353-21-490-3000 Email:treed@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Earthwatch Institute en
dc.contributor.funder Horizon 2020 en
dc.contributor.funder Icelandic Research Fund en
dc.contributor.funder Irish Research Council en
dc.contributor.funder Marine Institute en
dc.contributor.funder American Museum of Natural History en
dc.contributor.funder Higher Education Funding Council for Wales en
dc.contributor.funder Welsh Government en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Environmental DNA en
dc.internal.IRISemailaddress treed@ucc.ie en
dc.internal.bibliocheck Check, vol, issue and article ID en
dc.relation.project info:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-FP/663830/EU/Strengthening International Research Capacity in Wales/SIRCIW en
dc.relation.project info:eu-repo/grantAgreement/EC/H2020::MSCA-ITN-EJD/676154/EU/Archaeology on the Edge: Northern Europe and the Circumpolar World/ArchSci2020 en


Files in this item

This item appears in the following Collection(s)

Show simple item record

©2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd  This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as ©2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
This website uses cookies. By using this website, you consent to the use of cookies in accordance with the UCC Privacy and Cookies Statement. For more information about cookies and how you can disable them, visit our Privacy and Cookies statement