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eDNA quantification to evaluate bullfrog management

Citation

Everts, Teun et al. (2022), eDNA quantification to evaluate bullfrog management, Dryad, Dataset, https://doi.org/10.5061/dryad.qz612jmhm

Abstract

Biological invasions contribute now more than ever to the global homogenization of fauna and flora. Large-scale monitoring programs are therefore needed to detect incipient invasions and to evaluate management interventions. As conventional monitoring methods are constrained by large costs, environmental DNA (eDNA)-based methods are increasingly recognized as valuable monitoring tools. However, accurately estimating species abundance from eDNA concentrations in natural systems remains challenging and consequently hinders their integration in management applications. Here, we used droplet digital PCR (ddPCR) in eDNA surveys to estimate the abundance of invasive American bullfrogs (Lithobates catesbeianus). We first introduced bullfrog tadpoles in natural ponds to assess the relationship between abundances and eDNA concentrations under field conditions. Next, we combined eDNA sampling with fyke netting in naturally colonized ponds to investigate whether bullfrog eDNA concentrations can estimate bullfrog capture success and conventional abundance measures obtained via depletion sampling. Finally, we evaluated eradication measures by comparing bullfrog eDNA concentrations before and after fyke netting. We found a strong linear relationship between the numbers of introduced tadpoles and eDNA concentrations (r2 = 0.988). Bullfrog eDNA concentrations were not only linearly related to the catch-per-unit-effort (r2 = 0.739), but also to conventional abundance estimates (r2 = 0.716), particularly when eDNA concentrations were standardized for pond area (r2 = 0.834) and volume (r2 = 0.888). Bullfrog tadpoles were only captured when eDNA concentrations exceeded 1.5 copies µL-1, indicating that quantitative eDNA analyses enable the localization of breeding ponds. We found a significant reduction in eDNA concentrations after fyke netting proportional to the number of captured bullfrogs. These results demonstrate that eDNA quantification is a reliable tool that accurately estimates bullfrog abundance in natural lentic systems. We show that quantitative eDNA analyses can complement the toolbox of natural resource managers and facilitate the coordination of eradication campaigns targeting alien invasive species.

Methods

Overview of the collected data types:

  • Experimental ponds
    • Period of collected data: between the 30th of June and the 23rd of July 2021
    • Types of collected data
      • Species-specific environmental DNA data
      • Water quality variables
        • pH
        • Turbidity
        • pH
      • Pond volumes
    • ..
  • Management ponds
    • Period of collected data: between June and September 2021
    • Types of collected data
      • Species-specific environmental DNA data
      • Bullfrog depletion sampling data
      • Water quality variables
        • pH
        • Turbidity
        • pH
      • Pond volumes

Overview of the way the collected data types were acquired

  • Species-specific eDNA data
    • Primer/probe assay validated for western European usage in Everts et al. (2021).
    • Droplet Digital PCR according to protocol described in Everts et al. (2021).
    • Calculation of final eDNA concentrations according to formula in this article.
  • Water quality data
    • pH and conducitivity were measured from the same volume of water as was filtered for eDNA sampling, using a WTW multiLine® Multi 3620 IDS SET KS1 multimeter.
    • Turbidity was measured from the same volume of water as was filtered for eDNA sampling that was deep-frozen and measured afterwards, using a 2100Q Portable Turbidity meter (Hach®)
  • Bullfrog catch data
    • Bullfrogs were caught using double fyke nets with a mesh size of 8mm, consisting of two fykes interconnected with a seven meters long leader net, each with an initial hoop of 80 x 90 cm followed by three narrowing funnels in each fyke
    • The number of fyke nets and period that they were used per pond were given in Table 1 in the Research Article.
    • Catch-per-unit-effort was for all management ponds where bullfrogs were captured
    • Conventional population size estiamtions were obtained via depletion sampling. Subsampling of the data was necessary to comply with the assumptions, which has been reported extensively in the Research Article.
  • Pond volumes (a detailled description is given in the Appendix of the Research Article)
    • Pond volumes were quantified using a 999 CXI HDSI multibeam (Humminbird®) sonar device and the associated software.
    • Pond volumes of extremely shallow ponds (< 50 cm deep) were quantified using a RTK satellite navigation technique using a Trimble® S6 total station with Trimble® R6 receptors.

Funding

Research Foundation Flanders, Award: 1S01822N

Research Institute for Nature and Forest

LIFE 3n-bullfrog, Award: NAT/BE/001016

Sigmaplan