Date Published: April 24, 2019
Publisher: Public Library of Science
Author(s): Thomas S. Akre, Lillian D. Parker, Ellery Ruther, Jesus E. Maldonado, Lorien Lemmon, Nancy Rotzel McInerney, Hideyuki Doi.
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.
Environmental DNA (eDNA) technology has emerged over the last decade as an important method for the detection of both invasive and declining species that are cryptic or difficult to detect in freshwater, marine, and even terrestrial ecosystems [1–5]. What began as a means of detection for pathogenic microorganisms in water [6–9], quickly emerged as a method for detecting invasive, exotic species [10–16]. More recently, it has been used extensively for detecting cryptic, rare and declining species [17–22]. The rapid adoption of this technique is the result of 1) the high selectivity and increased sensitivity of eDNA [11, 16, 23–26], 2) an overall reduction in time and expenses compared to traditional sampling approaches [3, 27], and 3) the capacity for multi-species sampling approaches that come with emergent meta-genomic technology [28–30].
Due to its high selectivity and sensitivity, and time and cost efficiency, eDNA has been demonstrated to be a powerful tool for the detection and management of invasive and declining or rare species. Our study validates the utility and potential of eDNA sampling for the detection and monitoring of wood turtles in Virginia. Further, it does so with the identification of best practices for eDNA sampling of wood turtles and the verification of reduced costs compared to VES. Stream discharge and extremely low turtle densities were a limitation in our system; however, we have developed a procedure that would improve detection and sensitivity in the future. Therefore, we recommend the use of eDNA for wood turtle detection and monitoring programs in Virginia and beyond as part of conservation management plans. All told, the results of this study also confirm the great potential for application of the eDNA approach to threatened and endangered freshwater turtle species across the world. We suggest the use of eDNA as part of a toolbox for rapid detection and/or robust monitoring of cryptic, hard to detect, and endangered turtle species. Now that there is a broader understanding of both how to parameterize the environmental factors that affect eDNA detection and the use of statistical models that account for imperfect detection, the eDNA approach can readily be used to complement many conservation management programs for endangered turtles. This is especially true given rapid advances and reduction in costs of in high-throughput sequencing/genomic techniques [29–30].