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.
Highlights
Biodiversity assessments are increasingly carried out by indirect survey methodologies, such as the targeting of environmental DNA
All survey methods suffer from imperfect detection: the target organism—or its DNA—may be present but not be detected, or the target may be detected when it is absent, a misidentification[5,27]
M, S and K are all important in reducing the bias and mean posterior credible interval (PCI) widths for all or some of occupancy (ψ), stage 1 false positive ( θ10), stage 1 true positive ( θ11), stage 2 false positive ( p10) and stage 2 true positive ( p11) (Figs. 2, 3 and 4)
Summary
Biodiversity assessments are increasingly carried out by indirect survey methodologies, such as the targeting of environmental DNA (eDNA). The level of error and detectability, in a study targeting eDNA, will be influenced by several factors, relating to the s pecies[8], survey timing 9, concentration of DNA within the waterbody[9], sample volume[10], strategy used to collect a sample[11], protocols used for DNA extraction[12] and DNA amplification and identification p rotocols[4] Taking these into consideration and refining the methodologies used will reduce error, but it would be naïve to assume this would be sufficient to ensure it was zero in all c ases[7]. The probabilities of false positive and negative errors and the probability of site occupancy may be influenced by a variety of covariates that relate to environmental conditions, which could act at either Stage 1 or Stage 2 5
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