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

Simple item page
dc.contributor.authorPinfield, Róisín
dc.contributor.authorDillane, Eileen
dc.contributor.authorRunge, Anne Kathrine W.
dc.contributor.authorEvans, Alice
dc.contributor.authorMirimin, Luca
dc.contributor.authorNiemann, Jonas
dc.contributor.authorReed, Thomas E.
dc.contributor.authorReid, David G.
dc.contributor.authorRogan, Emer
dc.contributor.authorSamarra, Filipa I. P.
dc.contributor.authorSigsgaard, Eva Egelyng
dc.contributor.authorFoote, Andrew D.
dc.contributor.funderEarthwatch Instituteen
dc.contributor.funderHorizon 2020en
dc.contributor.funderIcelandic Research Funden
dc.contributor.funderIrish Research Councilen
dc.contributor.funderMarine Instituteen
dc.contributor.funderAmerican Museum of Natural Historyen
dc.contributor.funderHigher Education Funding Council for Walesen
dc.contributor.funderWelsh Governmenten
dc.contributor.funderEuropean Research Councilen
dc.contributor.funderHorizon 2020en
dc.date.accessioned2019-10-16T06:01:02Z
dc.date.available2019-10-16T06:01:02Z
dc.date.issued2019-09-12
dc.description.abstractWhile 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.sponsorshipIrish 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.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationPinfield, 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. (2019) 'False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)', Environmental DNA, 1(4), pp. 316-328. doi: 10.1002/edn3.32en
dc.identifier.doi10.1002/edn3.32en
dc.identifier.endpage328en
dc.identifier.issn2637-4943
dc.identifier.journaltitleEnvironmental DNAen
dc.identifier.startpage316en
dc.identifier.urihttps://hdl.handle.net/10468/8785
dc.identifier.volume1
dc.language.isoenen
dc.publisherJohn Wiley & Sons, Inc.en
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-FP/663830/EU/Strengthening International Research Capacity in Wales/SIRCIWen
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-ITN-EJD/676154/EU/Archaeology on the Edge: Northern Europe and the Circumpolar World/ArchSci2020en
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::ERC::ERC-STG/639192/EU/Alternative life histories: linking genes to phenotypes to demography/ALHen
dc.relation.urihttps://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.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjecteDNAen
dc.subjectEnvironmental DNAen
dc.subjectMetagenomicsen
dc.subjectOrcinus orcaen
dc.subjectPCRen
dc.subjectScomber scombrusen
dc.subjectWhole-genome enrichmenten
dc.titleFalse‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)en
dc.typeArticle (peer-reviewed)en
Files
Original bundle
Now showing 1 - 3 of 3
Thumbnail Image
Name:
Pinfield_et_al-2019-Environmental_DNA.pdf
Size:
1.37 MB
Format:
Adobe Portable Document Format
Description:
Published version
Download
Thumbnail Image
Name:
edn332-sup-0001-supinfo.docx
Size:
607.6 KB
Format:
Microsoft Word XML
Description:
Supplementary file 1
Download
Thumbnail Image
Name:
edn332-sup-0002-appendixs1.docx
Size:
608.11 KB
Format:
Microsoft Word XML
Description:
Supplementary file 2
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
2.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Biological, Earth and Environmental Sciences - Journal Articles