Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Abstract

Surveys of rare or cryptic species may miss individuals or populations that are actually present. Despite the increasing use of environmental DNA (eDNA) analysis to survey species in ponds, rivers, and lakes, very few studies have attempted to use eDNA for the detection of species using very small water bodies such as those accumulated within plants. Our aim was to investigate the feasibility of an eDNA sampling method for detecting Crossodactylodes itambe, an endemic bromeliad-dwelling frog from a remote location in Brazil. We collected water samples from 19 bromeliads for which we had observational data from direct visual surveys. We compared occupancy estimated from direct observations with the results from quantitative real-time PCR based eDNA assays. For observational surveys, we used a single season occupancy model. We applied a novel Bayesian occupancy model to estimate occupancy from eDNA samples, as well as false positives and false negatives at different stages of the workflow. eDNA from bromeliad tanks provided reliable estimates, with very low error levels and improved detection when compared to detectability from direct observation. Estimated occupancies using eDNA and visual survey methods were similar. The method is feasible for species restricted to small water bodies and exposed to direct UV radiation, and particularly useful to survey remote locations and confirm species presence. eDNA analysis provides a viable alternative to destructive sampling of bromeliads or direct observation methods that require logistically challenging repeated observations. Therefore, eDNA methods may be widely applicable to sampling programmes of other amphibians that live in plants.

First extraction of eDNA from tree hole water to detect tree frogs: a simple field method piloted in Madagascar

“…Many filtering methods were considered to ensure a toolkit which did not need electricity for the pump, and which was lightweight for carrying long distances in the field. We adapted the method Barata et al (2021) used for bromeliad water sampling, using similar equipment and adding a clear polyethylene round tube to be put down the tree hole (Table 1). This kit can be procured inexpensively in comparison to others that contains, for example, a pump.…”

“…The 60 ml syringe was aspirated to pull water up the tubing. As in Barata et al (2021) we planned on collecting 120 ml of water (2 × 60 ml full syringe), however the tree holes did not contain sufficient amounts of water, such that just 20 ml was collected. As a reduced volume of water was used, the surveyor had to remove the tubing and use gravity to get the remaining water into the syringe.…”

“…This piloted method should be applied more widely and in much greater sample numbers to determine whether this method could indeed be used to monitor the species more efficiently, complimenting acoustic surveys which are thought to perform better than VES (Barata et al in press). Based on previous datasets, the eDNA method could be trialled alongside VES and acoustic surveys to test its accuracy and efficiency for target species (as in Takahara et al 2020 andBarata et al 2021), together with a cost-effective analysis to compare feasibility of different methods. Beyond Ambohitantely, we recommend trialling this method on the other two Endangered Anodonthyla species using the primers developed, and other tree frogs using metabarcoding.…”

“…It has been used to detect whole communities (Lopes et al 2017;Sasso et al 2017), but also cryptic (Torresdal et al 2017;Bálint et al 2018), threatened (Thomsen et al 2012) and invasive species (Dejean et al 2012), even when a species may be present at low population densities (Sasso et al 2017). eDNA is becoming an increasingly popular tool for amphibian surveying and there is growing evidence that detection rates may be as efficient as more traditional visual encounter and acoustic surveying (Lopes et al 2017;Bálint et al 2018;Barata et al 2021).…”

“…Small terrestrial water sources such as inside bromeliads have been surveyed for frog eDNA, and three studies have successfully used the method to survey for endangered species (Brozio et al 2017;Torresdal et al 2017;Barata et al 2021). Barata et al (2021) compared eDNA results with visual encounter surveys and found eDNA to provide reliable estimates with very low error, and the estimated occupancies were very similar between the two methods. They concluded that this eDNA method is an alternative to destructive bromeliad searching when conducting presenceabsence studies.…”