Concurrent visual encounter sampling validates eDNA selectivity and sensitivity for the endangered wood turtle (Glyptemys insculpta)

Abstract

Environmental DNA (eDNA) has been used to record the presence of many different organisms in several different aquatic and terrestrial environments. Although eDNA has been demonstrated as a useful tool for the detection of invasive and/or cryptic and declining species, this approach is subject to the same considerations that limit the interpretation of results from traditional survey techniques (e.g. imperfect detection). The wood turtle is a cryptic semi-aquatic species that is declining across its range and, like so many chelonian species, is in-need of a rapid and effective method for monitoring distribution and abundance. To meet this need, we used an eDNA approach to sample for wood turtle presence in northern Virginia streams. At the same time, we used repeat visual encounter surveys in an occupancy-modelling framework to validate our eDNA results and reveal the relationship of detection and occupancy for both methods. We sampled 37 stream reaches of varying size within and beyond the known distribution of the wood turtle across northern Virginia. Wood turtle occupancy probability was 0.54 (0.31, 0.76) and while detection probability for wood turtle occupancy was high (0.88; 0.58, 0.98), our detection of turtle abundance was markedly lower (0.28; 0.21, 0.37). We detected eDNA at 76% of sites confirmed occupied by VES and at an additional three sites where turtles were not detected but were known to occur. Environmental DNA occupancy probability was 0.55 (0.29, 0.78); directly comparable to the VES occupancy estimate. Higher probabilities of detecting wood turtle eDNA were associated with higher turtle densities, an increasing number of days since the last rainfall, lower water temperatures, and lower relative discharges. Our results suggest that eDNA technology holds promise for sampling aquatic chelonians in some systems, even when discharge is high and biomass is relatively low, when the approach is validated and sampling error is quantified.

Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

“…The eDNA method has been described as more sensitive (Biggs et al, 2015;Dejean et al, 2012;Fernández et al, 2019;Hinlo et al, 2017;Jerdeet al, 2011;Pilliod et al, 2013;Schneider et al, 2016) and cheaper (Akre et al, 2019;Miya et al, 2015;Stoeckle et al, 2016) than traditional survey methods. Environmental DNA surveys are, therefore, recognized as a powerful tool for monitoring endangered species (Akamatsu et al, 2020;Brozio et al, 2017;Day et al, 2019;Laramie et al, 2015;Schmelzle & Kinziger, 2016;Thomsen et al, 2012) with the advantage of being nondestructive (Grealy et al, 2015;Hunter et al, 2015;Knudsen et al, 2019;Li et al, 2019).…”

High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability

“…the hydrograph or flow regime; Poff et al., 1997) may strongly affect the performance of this method (Stoeckle et al., 2017). Yet the effects of stream flow on eDNA remain understudied (but see Akre et al., 2019; Jane et al., 2015; Shogren et al., 2018). High stream flows or floods may affect eDNA concentrations and the overall detectability of target organisms through multiple, potentially opposing mechanisms.…”

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

“…Increasing the number of DNA extracts per sample or the number of amplifications per DNA extract does not necessarily increase the probability of detection but will require more laboratory reagents, time, and effort. However, collecting biological samples from sites where the target species is most likely to be detected-based on knowledge of the target species' ecology-can enhance the detection probability (Ficetola et al 2015;Akre et al 2019;Wineland et al 2019;Wood et al 2019;Bedwell & Goldberg 2020;Vimercati et al 2020).…”