Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting

Abstract

The potential of environmental DNA (eDNA) methods to enhance the detection of invasive species during routine monitoring is of interest to management agencies. Here we applied the eDNA methodology concurrent with conventional detection techniques during two routine monitoring seasons to detect the presence of three invasive fish in Australia with contrasting spatial distributions (benthopelagic, pelagic and benthic): common carp (Cyprinus carpio), redfin perch (Perca fluviatilis) and Oriental weatherloach (Misgurnus anguillicaudatus). Our objectives were to compare the seasonal detection of the target species using eDNA and conventional detection (fyke nets), determine the relationship between catch per unit effort (CPUE) and DNA copy number and ascertain the best water location (surface vs. subsurface) for eDNA detection. Our results show that eDNA had a higher detection rate than fyke nets for Oriental weatherloach and redfin perch during both the autumn and spring surveys. Common carp was detected at all sites for both seasons using fyke nets and eDNA with the exception of one site during the autumn survey where common carp was captured using fyke nets but no carp eDNA was detected. Season had a significant effect on DNA concentration for common carp (P<.005) and Oriental weatherloach (P=.002) but sampling location (surface vs. subsurface) had no significant effect on DNA concentration for all three species. We found a positive correlation between CPUE and DNA copy number for Oriental weatherloach (rs = .718, α = .045) and redfin perch (rs = .756, α = .030) during spring but a non-significant, negative trend was observed for common carp in both seasons (rs = −.357, α = .385 spring; ρ = −.539, α = .168 autumn). Our results show that eDNA is an effective tool for the detection of single or multiple species to complement the traditional approaches using physical capture. As with all survey methods, the eDNA approach suffers from imperfect detection. We conclude that eDNA survey results are more powerful when used in conjunction with other survey methods as a way to enhance detection rates and increase confidence in the monitoring results.