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

PLoS One. 2019 Jul 2;14(7):e0219244. doi: 10.1371/journal.pone.0219244. eCollection 2019.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • California
  • Colubridae / genetics*
  • DNA, Environmental / analysis*
  • Environmental Monitoring / methods*
  • Geography
  • Polymerase Chain Reaction
  • Probability

Substances

  • DNA, Environmental

Grants and funding

BDT received Cooperative Agreement award #F14AC01074 from the United States Fish and Wildlife Service (https://www.fws.gov) and award #MB704 from the Center for Natural Lands Management (https://cnlm.org) to support this study. The U.S. Fish and Wildlife Service and Center for Natural Lands Management provided feedback on high priority areas for surveying for the presence of non-native watersnakes in California. Other than that contribution during the study design stage, the funders had no role in data collection and analysis, decision to publish, or preparation of the manuscript. Pisces Molecular, LLC provided support in the form of salaries for authors JSW and SW, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.