Environmental DNA (eDNA) detects the pool frog (Pelophylax lessonae) at times when traditional monitoring methods are insensitive

Abstract

Detection of endangered species is invaluable for conservation efforts, yet many traditional sampling techniques are ineffective at low population abundances or during certain periods of the year. Here, we compared results from a newly developed eDNA approach and the traditional observational method for the endangered pool frog (Pelophylax lessonae). Analysis using an occupancy-modeling framework indicated that the probability of pools being occupied using eDNA (0.93) was higher than for the traditional method of counting calling males and silent observed individuals (0.72). Detailed analysis revealed complementarity among the methods. That is, the traditional method gave a high rate of observation in June, whereas eDNA gave at least as many or more observations during other parts of the year. Discrepancies among the methods depended on the dominant lifecycle stage, and eDNA concentrations were higher when juveniles were present than at times when spawning occurred. eDNA concentrations were also positively related to P. lessonae observations. Our study demonstrates that an eDNA protocol for monitoring of endangered amphibian species can be particularly valuable during periods when individuals are hard to detect by observational methods, and provides guidance to sampling efforts for research and monitoring programs in other regions and systems.

Environmental DNA improves Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) detection over conventional sampling methods

“…Our estimates of 84% detection probability using eDNA compared to 28% for conventional sampling methods suggest that eDNA is a highly effective method to detect hellbender presence. Furthermore, our results are consistent with other eDNA studies that report higher detection estimates than conventional sampling methods (Eiler, Löfgren, Hjerne, Nordén, & Saetre, 2018;Jane et al, 2015;Schmelzle & Kinziger, 2016;Schmidt, Kery, Ursenbacher, Hyman, & Collins, 2013). Thus, the effectiveness of eDNA as a tool for detecting rare, cryptic, or threatened species has wide ranging implications for the monitoring, conservation, and management of these species.…”

“…Our results are consistent with Spear et al (2015), who found that eDNA sampling outperformed conventional surveys for hellbenders. Furthermore, our results are consistent with other eDNA studies that report higher detection estimates than conventional sampling methods (Eiler, Löfgren, Hjerne, Nordén, & Saetre, 2018;Jane et al, 2015;Schmelzle & Kinziger, 2016;Schmidt, Kery, Ursenbacher, Hyman, & Collins, 2013). Estimating detection probabilities from multiple site visits accounts for false negatives (i.e., when the animal is present at a site but goes undetected; MacKenzie et al, 2002).…”

“…Environmental DNA sampling has been widely used and established as a powerful conservation tool (Wilcox et al, 2016). Our study adds to growing evidence suggesting that eDNA methods offer a detection advantage over conventional methods (Eiler et al, 2018;Smart et al, 2015). However, our results counter previous work that detects associations between eDNA concentrations and animal abundance (Pilliod et al, 2013).…”

Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding

“…Our environmental DNA results imply the presence of fish species that have not yet been verified using traditional fishing methods, including a number of non-native species (Table 1 ). This is not surprising given the size of these water bodies, the sensitivity of eDNA surveys 71 , 72 , and the fact that aquaculture 73 and the exotic fish trade 74 are common in China. Two other considerations bear on our results.…”

msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r

“…Environmental DNA (eDNA) surveys continue to gain popularity for detecting invasive, cryptic and rare species (Klymus, Richter, Chapman, & Paukert, 2015; Lodge et al., 2012; Schmelzle & Kinziger, 2016; Sepulveda et al., 2019), as these techniques are often easier, less expensive and more sensitive than non‐molecular detection tools (Eiler, Löfgren, Hjerne, Nordén, & Saetre, 2018; Hunter, Meigs‐Friend, Ferrante, Smith, & Hart, 2019; Sengupta et al., 2019; Sepulveda et al., 2019; Williams, Huyvaert, Vercauteren, Davis, & Piaggio, 2018). These surveys rely on hierarchical sampling techniques to accommodate spatial heterogeneity in the occurrence of DNA within a study region.…”