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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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.

In: Environmental DNA, Vol. 1, No. 4, 2019, p. 316-328.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Pinfield, R, Dillane, E, Runge, AKW, Evans, A, Mirimin, L, Niemann, J, Reed, TE, Reid, DG, Rogan, E, Samarra, FIP, Sigsgaard, EE & Foote, AD 2019, 'False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)', Environmental DNA, vol. 1, no. 4, pp. 316-328. https://doi.org/10.1002/edn3.32

APA

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., & 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), 316-328. https://doi.org/10.1002/edn3.32

Vancouver

Pinfield R, Dillane E, Runge AKW, Evans A, Mirimin L, Niemann J et al. False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca). Environmental DNA. 2019;1(4):316-328. https://doi.org/10.1002/edn3.32

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. / False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca). In: Environmental DNA. 2019 ; Vol. 1, No. 4. pp. 316-328.

Bibtex

@article{dc00853cae6c4941badeedc804629458,

title = "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 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.",

keywords = "eDNA, environmental DNA, metagenomics, Orcinus orca, PCR, Scomber scombrus, whole-genome enrichment",

author = "R{\'o}is{\'i}n Pinfield and Eileen Dillane and Runge, {Anne Kathrine W.} and Alice Evans and Luca Mirimin and Jonas Niemann and Reed, {Thomas E.} and Reid, {David G.} and Emer Rogan and Samarra, {Filipa I. P.} and Sigsgaard, {Eva Egelyng} and Foote, {Andrew D.}",

note = "Publisher Copyright: {\textcopyright} 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd",

year = "2019",

doi = "10.1002/edn3.32",

language = "English",

volume = "1",

pages = "316--328",

journal = "Environmental DNA",

issn = "2637-4943",

publisher = "Wiley",

number = "4",

}

RIS

TY - JOUR

T1 - False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

AU - Pinfield, Róisín

AU - Dillane, Eileen

AU - Runge, Anne Kathrine W.

AU - Evans, Alice

AU - Mirimin, Luca

AU - Niemann, Jonas

AU - Reed, Thomas E.

AU - Reid, David G.

AU - Rogan, Emer

AU - Samarra, Filipa I. P.

AU - Sigsgaard, Eva Egelyng

AU - Foote, Andrew D.

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - eDNA

KW - environmental DNA

KW - metagenomics

KW - Orcinus orca

KW - PCR

KW - Scomber scombrus

KW - whole-genome enrichment

U2 - 10.1002/edn3.32

DO - 10.1002/edn3.32

M3 - Journal article

AN - SCOPUS:85106272930

VL - 1

SP - 316

EP - 328

JO - Environmental DNA

JF - Environmental DNA

SN - 2637-4943

IS - 4

ER -

ID: 283984652

Globe Institute