Buxton, A;
Matechou, E;
Griffin, J;
Diana, A;
Griffiths, RA;
(2021)
Optimising sampling and analysis protocols in environmental DNA studies.
Scientific Reports
, 11
(1)
, Article 11637. 10.1038/s41598-021-91166-7.
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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. (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.
| Type: | Article |
|---|---|
| Title: | Optimising sampling and analysis protocols in environmental DNA studies |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1038/s41598-021-91166-7 |
| Publisher version: | http://dx.doi.org/10.1038/s41598-021-91166-7 |
| Language: | English |
| Additional information: | Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
| Keywords: | Conservation biology, Ecological modelling, Freshwater ecology |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Statistical Science |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10129028 |
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