Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes

• Published in: PloS one 2019-07, Vol.14 (7), p.e0219244-e0219244
• Main Authors: Rose, Jonathan P, Wademan, Cara, Weir, Suzanne, Wood, John S, Todd, Brian D
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Biodiversity; Biology and Life Sciences; California; Colubridae - genetics; Comparative analysis; Conservation biology; Corridors (Ecology); Deoxyribonucleic acid; Distribution; DNA; DNA sequencing; Earth Sciences; Ecology; Ecology and Environmental Sciences; Endangered & extinct species; Environmental DNA; Environmental DNA - analysis; Environmental Monitoring - methods; Environmental protection; Genetic testing; Geography; Habitats; Introduced animals; Introduced species; Invasive species; Methods; Native species; Nerodia sipedon; Nonnative species; Occupancy; Polls & surveys; Polymerase Chain Reaction; Probabilistic methods; Probability; Reptiles & amphibians; Research and Analysis Methods; Sampling; Sampling methods; Snakes; Studies; Surveillance; Trapping; Traps; Varieties; Water; Water analysis; Water sampling; Water shortages; Wildlife conservation
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0219244

Given limited resources for managing invasive species, traditional survey methods may not be feasible to implement at a regional scale. Environmental DNA (eDNA) sampling has proven to be an effective method for detecting some invasive species, but comparisons between the detection probability of eDNA and traditional survey methods using modern occupancy modeling methods are rare. We developed a qPCR assay to detect two species of watersnake (Nerodia fasciata and Nerodia sipedon) introduced to California, USA, and we compared the efficacy of eDNA and aquatic trapping. We tested 3-9 water samples each from 30 sites near the known range of N. fasciata, and 61 sites near the known range of N. sipedon. We also deployed aquatic funnel traps at a subset of sites for each species. We detected N. fasciata eDNA in three of nine water samples from just one site, but captured N. fasciata in traps at three of ten sites. We detected N. sipedon eDNA in five of six water samples from one site, which was also the only site of nine at which this species was captured in traps. Traditional trapping surveys had a higher probability of detecting watersnakes than eDNA surveys, and both survey methods had higher detection probability for N. sipedon than N. fasciata. Occupancy models that integrated both trapping and eDNA surveys estimated that 5 sites (95% Credible Interval: 4-10) of 91 were occupied by watersnakes (both species combined), although snakes were only detected at four sites (three for N. fasciata, one for N. sipedon). Our study shows that despite the many successes of eDNA surveys, traditional sampling methods can have higher detection probability for some species. We recommend those tasked with managing species invasions explicitly compare eDNA and traditional survey methods in an occupancy framework to inform their choice of the best method for detecting nascent populations.