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

Environmental DNA (eDNA) monitoring approaches promise to greatly improve detection of rare, endangered, and invasive aquatic species. Although research has shown eDNA to be a sensitive monitoring tool, rigorous comparisons to traditional field sampling methods have not been fully explored. Few studies have specifically examined the application of eDNA within a statistical framework that explicitly allows for direct comparison between eDNA and traditional field sampling approaches while simultaneously accounting for imperfect detection of both methods. An eDNA approach was compared to traditional seining methods for determining site occupancy and relative abundance of endangered tidewater goby (Eucyclogobius newberryi) within insularized lagoon and estuary habitats across approximately 400 kilometers of coastline. At 29 research locations, paired samples were collected at sub-sampling replicates consisting of one traditional seine haul and a water sample for eDNA analysis. The number of paired collections at each location depended on habitat size and site characteristics, ranging from two to 23 samples. Each water sample was tested for tidewater goby DNA using six replicate qPCR assays. A multi-method occupancy modeling framework was used to estimate method specific detection probabilities and site occupancy. The probability of detection using eDNA methods was nearly double (0.72) 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 despite past field surveys and one location considered to be locally extirpated based upon prior field surveys. 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. The results indicate that eDNA is a highly sensitive monitoring technique. Compared to traditional field sampling it provided improved detectability and therefore estimates of site occupancy, and can be used to increase management efficiency across a broad spatial range and within a diversity of habitats.