Environmental DNA for rare and cryptic bromeliad dwelling frogs

by Bela Barata - January 18, 2021

Durrell’s Field Programme Officer, Dr Bela Barata studied the ecology of bromeligenous frogs for four years during her PhD. Her project was looking at population trends and dynamics of a cryptic bromeligenous frog that belongs to a rare genus called Crossodactylodes. There are five species in the genus. All species are endemic to the Atlantic Forest of Brazil, range-restricted and occurring in mountaintops.

There are 99 species of bromeligenous frogs in the world, all endemic to the Neotropical region.

Bromeligenous frogs spend their whole life cycle within bromeliads, where they lay their eggs and develop into adult life. Most species are restricted to single locations, with some occurring only at high elevation sites. We understand very little of species ecology, natural history and distributions. Their dispersal capabilities is still unknown.

During her PhD, Bela studied a single species of bromeligenous frogs: Crossodactylodes itambe.

Crossodactylodes itambe exclusively lives within ground bromeliads, in high elevation outcrops. Both frog and plant occur in a single location in the Espinhaço Mountains of the Atlantic Forest. Species occupancy increases at higher elevation and abundance of individuals is related to bromeliad structure. Plant size and the volume of water retained by the central tank are very important for these frogs. Estimated species extent of occurrence is 0.5 km2. Furthermore, there are worrying signs of a declining population trend at lower elevations where fire is still a pressing threat. The restricted range and habitat requirements for C. itambe make this species highly vulnerable to extinction. Major threats are climate change, wildfires and disease. Given current knowledge and threats, species is classified as Critically Endangered.

Recent eDNA research: advances for bromeligenous frogs

More recently, Bela Barata published a paper in collaboration with researchers from Instituto Biotrópicos, University of Kent, Institute of Zoology, and Amphibian and Reptile Conservation Trust. They aimed to investigate the feasibility of environment DNA (eDNA) for detecting Crossodactylodes itambe (Barata et al. 2021), with a view to applying the method more widely to amphibians that are cryptic and restricted to small water bodies.

In the past years, we saw an increasing use of environmental eDNA analysis to survey species in ponds, rivers, and lakes (ready more about the eDNA method here). However, very few studies have attempted to use eDNA for the detection of species using very small water bodies such as those accumulated in bromeliads. With funds from The Rufford Foundation, the authors collected water samples from 21 bromeliads for which they also had observational data from direct visual surveys. The authors compared results from direct observations with the results from eDNA from bromeliads.

Bela and her team successfully extracted frog DNA from waster samples as small as 120 mL!

Overall, the authors obtained similar estimates using eDNA and visual survey methods. eDNA from bromeliad tanks provided reliable estimates, with very low error levels and improved detection when compared to detectability from direct observation. Therefore, eDNA is a feasible method for species living in small water bodies, from remote locations. In their paper, the authors provide a detailed framework for data collection, DNA extraction and analysis – all applied to small sample sizes.

There are advantages in the use of eDNA to survey cryptic species in remote locations. The method is also good to confirm species presence with high detection rates. The novel eDNA analysis provides an alternative to direct observation methods that require logistically challenging repeated observations. It is also a viable solution to destructive sampling of bromeliads. However, the use of eDNA method for monitoring occupancy of bromeliad dwelling species will likely improve as the method becomes more cost-effective and we better understand of the factors affecting detection in such environments.

Watch this space, as Bela takes us further in understanding bromeligenous frogs from Brazil!