Optimising sampling and analysis protocols in environmental DNA studies

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 usin...

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Autores principales:	Andrew Buxton, Eleni Matechou, Jim Griffin, Alex Diana, Richard A. Griffiths
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0e09b70ff6264f2aa91dfcb916c93ebc
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spelling	oai:doaj.org-article:0e09b70ff6264f2aa91dfcb916c93ebc2021-12-02T17:51:29ZOptimising sampling and analysis protocols in environmental DNA studies10.1038/s41598-021-91166-72045-2322https://doaj.org/article/0e09b70ff6264f2aa91dfcb916c93ebc2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91166-7https://doaj.org/toc/2045-2322Abstract 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. (J R Stat Soc Ser C Appl Stat 69: 377–392, 2020), and a second that assumes no false positive error by Stratton et al. (Methods Ecol Evol 11: 1113–1120, 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.Andrew BuxtonEleni MatechouJim GriffinAlex DianaRichard A. GriffithsNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Andrew Buxton Eleni Matechou Jim Griffin Alex Diana Richard A. Griffiths Optimising sampling and analysis protocols in environmental DNA studies
description	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. (J R Stat Soc Ser C Appl Stat 69: 377–392, 2020), and a second that assumes no false positive error by Stratton et al. (Methods Ecol Evol 11: 1113–1120, 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.
format	article
author	Andrew Buxton Eleni Matechou Jim Griffin Alex Diana Richard A. Griffiths
author_facet	Andrew Buxton Eleni Matechou Jim Griffin Alex Diana Richard A. Griffiths
author_sort	Andrew Buxton
title	Optimising sampling and analysis protocols in environmental DNA studies
title_short	Optimising sampling and analysis protocols in environmental DNA studies
title_full	Optimising sampling and analysis protocols in environmental DNA studies
title_fullStr	Optimising sampling and analysis protocols in environmental DNA studies
title_full_unstemmed	Optimising sampling and analysis protocols in environmental DNA studies
title_sort	optimising sampling and analysis protocols in environmental dna studies
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0e09b70ff6264f2aa91dfcb916c93ebc
work_keys_str_mv	AT andrewbuxton optimisingsamplingandanalysisprotocolsinenvironmentaldnastudies AT elenimatechou optimisingsamplingandanalysisprotocolsinenvironmentaldnastudies AT jimgriffin optimisingsamplingandanalysisprotocolsinenvironmentaldnastudies AT alexdiana optimisingsamplingandanalysisprotocolsinenvironmentaldnastudies AT richardagriffiths optimisingsamplingandanalysisprotocolsinenvironmentaldnastudies
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Optimising sampling and analysis protocols in environmental DNA studies

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