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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Bibliographic Details
Published in:Environmental DNA
Main Authors: 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.
Format: Article in Journal/Newspaper
Language:English
Published: 2019
Subjects:
Orcinus orca
PCR
Scomber scombrus
eDNA
environmental DNA
metagenomics
whole-genome enrichment
Killer Whale
Orca
Killer whale
Online Access:https://pure.au.dk/portal/en/publications/50ac138e-8c57-4e42-9ac8-17312ed37d80
https://doi.org/10.1002/edn3.32
Description
Summary: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.

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