Using occupancy modelling to compare environmental DNA to traditional field methods for regional‐scale monitoring of an endangered aquatic species

Abstract

Environmental DNA (eDNA) monitoring approaches promise to greatly improve detection of rare, endangered and invasive species in comparison with traditional field approaches. Herein, eDNA approaches and traditional seining methods were applied at 29 research locations to compare method-specific estimates of detection and occupancy probabilities for endangered tidewater goby (Eucyclogobius newberryi). At each location, multiple paired seine hauls and water samples for eDNA analysis were taken, ranging from two to 23 samples per site, depending upon habitat size. Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance. Compared to traditional field sampling, eDNA provided improved occupancy parameter estimates and can be applied to increase management efficiency across a broad spatial range and within a diversity of habitats.

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

“…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).…”

“…Previous studies have indicated a relationship between eDNA concentrations and animal abundance or biomass Klymus, Richter, Chapman, & Paukert, 2015;Pilliod et al, 2013;Schmelzle & Kinziger, 2016;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012;Thomsen et al, 2012). Previous studies have indicated a relationship between eDNA concentrations and animal abundance or biomass Klymus, Richter, Chapman, & Paukert, 2015;Pilliod et al, 2013;Schmelzle & Kinziger, 2016;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012;Thomsen et al, 2012).…”

“…Additionally, conventional survey methods for freshwater species are often time-and labor-intensive, costly, destructive to habitat, and potentially hazardous to researchers (Nickerson & Krysko, 2003;Pregler, Vokoun, Jensen, & Hagstrom, 2015). Mounting evidence suggests that eDNA sampling methods have a performance, logistical, and detection advantage compared to conventional survey methods (Jerde et al, 2011;Dejean et al, 2012;Pilliod, Goldberg, Arkle, & Waits, 2013;Schmelzle & Kinziger, 2016;Smart, Tingley, Weeks, Rooyen, & McCarthy, 2015;Spear et al, 2015). However, few studies are adequately designed to directly compare the detection probabilities of eDNA and conventional sampling methods (Roussel, Paillisson, Treguier, & Petit, 2015;Smart et al, 2015).…”

Optimal survey designs for environmental DNA sampling

“…Site occupancy detection models (SODMs), which provide an estimate of the number of occupied sites whilst accounting for imperfect detection, have been suggested as one way to overcome the issue of imperfect detection in eDNA studies (Hunter et al., ; Lahoz‐Monfort, Guillera‐Arroita, & Tingley, ; Moyer, Diaz‐Ferguson, Hill, & Shea, ; Schmelzle & Kinziger, ; Schmidt et al., ). For example, Schmidt et al.…”

A probabilistic model for designing and assessing the performance of eDNA sampling protocols

“…They do not address the question of whether positive BC or SC eDNA samples indicate the presence of AC in the CAWS and other sampling locations near the Great Lakes. Occupancy models are used to estimate the probability of target species presence using eDNA sampling results by modelling the probability of detection and amplification (Erickson et al, ; Mize et al, ; Schmelzle & Kinziger, ; Willoughby et al, ). The model in this paper could be incorporated within an occupancy modelling framework by detailing the uncertainties in the detection and amplification steps.…”