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Optimising sampling and analysis protocols in environmental DNA studies

Buxton, Andrew S., Matechou, Eleni, Griffin, Jim, Diana, Alex, Griffiths, Richard A. (2021) Optimising sampling and analysis protocols in environmental DNA studies. Scientific Reports, 11 . Article Number 11637. ISSN 2045-2322. (doi:10.1038/s41598-021-91166-7) (KAR id:88280)

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Abstract

Ecological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al. (2020), and a second that assumes no false positive error by Stratton et al. (2020). Additionally, we apply the Griffin et al. (2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al. (2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al. (2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of >1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis.

Item Type: Article
DOI/Identification number: 10.1038/s41598-021-91166-7
Uncontrolled keywords: Occupancy, False Positive, False Negative, environmental DNA, eDNA, qPCR, great crested newt; Replication
Subjects: Q Science > QH Natural history > QH541 Ecology
Divisions: Divisions > Division of Computing, Engineering and Mathematical Sciences > School of Mathematics, Statistics and Actuarial Science
Divisions > Division of Human and Social Sciences > School of Anthropology and Conservation > DICE (Durrell Institute of Conservation and Ecology)
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Andrew Buxton
Date Deposited: 20 May 2021 10:14 UTC
Last Modified: 29 Jun 2021 13:18 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/88280 (The current URI for this page, for reference purposes)
Buxton, Andrew S.: https://orcid.org/0000-0002-0555-2491
Matechou, Eleni: https://orcid.org/0000-0003-3626-844X
Griffin, Jim: https://orcid.org/0000-0002-4828-7368
Griffiths, Richard A.: https://orcid.org/0000-0002-5533-1013
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