Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

By T. Wilcox, Kevin S. McKelvey, M. Young, Adam J. Sepulveda, B. Shepard, Stephen F. Jane, Andrew R Whiteley, W. Lowe, M. D. Schwartz. 2015

394 citations recorded by the source corpus.

Abstract Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout ( Salvelinus fontinalis ) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.

Subfields: Ecology, Molecular Biology, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/cdd77cfbe01da5bbd2a0efc74fb87bf762e219b7

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Citations in the corpus

Critical considerations for the application of environmental DNA methods to detect aquatic species (2016, background): “10% commercial bleach solution, quaternary ammonia) may be insufficient (Kemp & Smith 2005; Wilcox et al. 2016).”
Efficacy of Environmental DNA to Detect and Quantify Brook Trout Populations in Headwater Streams of the Adirondack Mountains, New York (2017, background): “Relative eDNA concentrations or the number of copies of the mitochondrially encoded cytochrome-c oxidase I gene complex have been observed to be correlated with the density and/or biomass of aquatic species (Takahara et al. 2012; Wilcox et al. 2016; present study).”
Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys (2021, background): “Consequently, different- sized individuals of the same species can exhibit different DNA shedding rates (Klymus et al., 2015; Maruyama et al., 2014; Wilcox et al., 2016), potentially influencing the interpretation of eDNA quantification for some species.”
Downstream transport and seasonal variation in freshwater pearl mussel ( Margaritifera margaritifera ) eDNA concentration (2019, background): “While some of the existing studies concluded that eDNA concentrations primarily reflect local abundance (Doi et al., 2017; Tillotson et al., 2018; Wilcox et al., 2016), Spear et al. (2015) found extensive downstream transport and accumulation of eDNA.”
Meta‐analysis supports further refinement of eDNA for monitoring aquatic species‐specific abundance in nature (2019, background): “However, what environmental variables are im‐ portant to include are likely to be dependent on both species (e.g., body size/age distributions, temperature, diurnal period, season, etc.) and system (e.g., upstream eDNA input in lotic systems (Wilcox et al., 2016).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “General considerations A key issue with the extraction and amplification of DNA from water is low DNA concentration, which can require the filtration of many litres of water to obtain sufficient DNA from a single sample (Wilcox et al. 2016).”
Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation (2018, background): “Clearly, the biological, physical, and chemical factors responsible for the origin, movement, degradation, or persistence of eDNA need much more investigation (Barnes et al. 2014, Barnes & Turner 2016, Wilcox et al. 2016).”