Using quantitative eDNA analyses to accurately estimate American bullfrog abundance and to evaluate management efficacy

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.

Experimental assessment of downstream environmental DNA patterns under variable fish biomass and river discharge rates

“…In natural systems, however, such patterns are often exposed to substantial variation resulting from interaction effects with several abiotic factors, such as discharge rate or water volume of the system under study (Rourke et al, 2021;Tillotson et al, 2018). The inclusion of those parameters in prediction models is therefore expected to generate more reliable quantitative eDNA data that better predict the spatial and temporal behavior of aquatic species within and among river systems in the future (Everts et al, 2022;Wilcox et al, 2016;Yates et al, 2021).…”

“…In natural systems, however, such patterns are often exposed to substantial variation resulting from interaction effects with several abiotic factors, such as discharge rate or water volume of the system under study (Rourke et al, 2021; Tillotson et al, 2018). The inclusion of those parameters in prediction models is therefore expected to generate more reliable quantitative eDNA data that better predict the spatial and temporal behavior of aquatic species within and among river systems in the future (Everts et al, 2022; Wilcox et al, 2016; Yates et al, 2021). Large river systems can, on the other hand, be expected to house bigger fish populations too, thereby, at least partly, overcoming dilution effects resulting from increased discharge rates, thereby affecting the quantitative eDNA‐based population estimates and interpretation.…”

“…The use of environmental DNA (eDNA) (allochtonous DNA released by macroorganisms) which can be isolated from environmental samples such as water, sediment or even air (Bedwell & Goldberg, 2019), to detect and quantify the occurrence of organisms in the environment, developed spectacularly in the past decade (Bruce et al, 2021; Everts et al, 2022; Mauvisseau et al, 2021; Wood et al, 2021). Especially in aquatic environments, eDNA‐based methods are applauded as a promising tool to monitor vertebrate species (Curtis et al, 2020; Fremier et al, 2019; Wang et al, 2021) to a point where they can outcompete conventional methods in terms of higher detection sensitivity, lowered sampling effort and associated survey costs (Bruce et al, 2021; Cordier et al, 2021; Wood et al, 2021).…”

Combining multiple markers significantly increases the sensitivity and precision of eDNA‐based single‐species analyses

“…This AIS is listed as one of the 100 worst invasive alien species in the world. Ever since Ficetola et al (2008) developed a species-specific eDNA-based detection protocol that opened up new opportunities for the management of this nuisance species, many studies have focussed on optimizing eDNA-based methods to detect and quantify this species in aquatic environments in order to coordinate management efforts on a region scale (see Everts et al, 2021Everts et al, , 2022Lin et al, 2019). The European weather loach (weather loach hereafter), on the contrary, is a cryptic and poorly known fish, that is listed in the IUCN Red List of Threatened Species (Freyhof, 2011).…”

“…Relying on species‐specific genetic markers serving as a molecular imprint, eDNA‐based methods can reveal the presence of a focal species, even at very low densities (Smart et al, 2016; Wilcox et al, 2016). As a consequence, this approach has proven to be extremely useful for monitoring invasive (Everts et al, 2022; Goldberg et al, 2013) and endangered species (Biggs et al, 2015; Brys, Halfmaerten, et al, 2021; Mauvisseau et al, 2020), especially in aquatic ecosystems. By using thoroughly validated protocols, it is indeed possible to distinguish a single species (barcoding) or entire communities (metabarcoding) within an environmental sample.…”