Abstract
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.
Highlights
Determining the distribution of an introduced species is an important step for planning control and eradication efforts
Using alignments of the limited available mitochondrial sequence data for these species from GenBank and BOLD, supplemented with additional, de novo mitochondrial sequence data we obtained for the control region, ND2 and CO1 regions from these species, as well as two less closely related snake species, Pituophis catenifer and Lampropeltis getula, we identified a 173 bp sequence across tRNA-GLN, tRNA-MET and the 5’ end of the ND2 gene that was shared between N. fasciata and N. sipedon, but not Thamnophis elegans, T. gigas, or T. sirtalis (Fig 3)
All five lab-positive control water samples tested positive for Nerodia environmental DNA (eDNA) in our qPCR assay
Summary
Determining the distribution of an introduced species is an important step for planning control and eradication efforts. For a widely distributed introduced species, effort might be focused on limiting its further spread. For an introduced species currently restricted to a small area in its non-native range, effort might be expended to eradicate the nascent population. A survey method that has a high probability of detecting the introduced species while requiring the least effort is highly desirable. EDNA can be more effective at documenting the presence of aquatic species than traditional survey methods [1,4], many studies have not accounted for the imperfect detection of eDNA assays using modern statistical methods ([5,6] but see [7,8])
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