Surveying amphibians using environmental DNA: is it worth it?

This week at our QAECO reading group we talked about an exciting new technique for surveying aquatic vertebrates: molecular detection.

Cryptic amphibian species may be hard to spot – is eDNA the solution to the problem of imperfect detection?

We focused on the paper by Goldberg et al. (2011), who used environmental DNA (eDNA) to detect the presence of cryptic amphibians in stream water. They collected between one and three samples at six streams in the Rocky Mountains, and assessed the accuracy of several extraction and PCR protocols in detecting two amphibian species that were known to occur at the sites. They found that the probability of detection was high (> 80%) for both species.

Although eDNA is a relatively new tool for aquatic vertebrate detection, we were excited by the potential that this technique has for sampling both rare and invasive species.  After all, this is what many of us do here at QAECO! So, it got us thinking. How do the costs of eDNA sampling compare to those associated with traditional amphibian survey techniques such as call-playback?

We made a few back-of-the-envelope calculations of the comparative costs of carrying out surveys for frogs in Melbourne with a commonly used method (spotlighting + call-playback surveys) and with eDNA sampling. We made a few assumptions:

  • That fixed costs (e.g. insurance) would be equal and small for both methods. Therefore, we would mainly be comparing variable costs that increase with the number of surveys and sites sampled.
  • An ecological consultant would be paid AU$100 per hour (including all fuel and equipment costs). We estimated that they could survey two sites/hour with the traditional method, and four sites/hour with eDNA sampling. A day’s (night’s) work would last about seven hours, including travel to and from the study area.
  • For the eDNA extraction process, we assumed a laboratory would charge AU$80 for each sample with a “scale economy” effect: for every 10 additional samples, the marginal cost would decrease by AU$10, down to a minimum of AU$30 per sample.

Survey costs for traditional (blue) and eDNA (red) sampling techniques. This assumes that three return visits are required to detect frogs using traditional methods, and only one visit is required to detect frogs using eDNA techniques.

We calculated the total cost of monitoring between 1 and 100 sites, with three surveys for the traditional method and one sample for the eDNA method. We assume that these numbers of surveys would yield a 95% probability of detecting the species if present based on our use of traditional survey techniques in urban Melbourne, and the data presented in Goldberg et al. 2011.

The use of eDNA in detection surveys appears to be a cost effective and exciting new approach for conservation biologists. Our simple calculations suggest that it might be particularly effective for large monitoring programs: processing large numbers of samples will be increasingly cheaper than traditional surveys, where the cost of visiting more sites increases linearly. Much of this advantage depends on exactly how much cheaper the processing of eDNA may become in the future. Traditional survey methods have the obvious advantage that they’ve been intensively scrutinised in the past and well known protocols and models have already been developed. As eDNA is a relatively new method for surveying amphibians, there are still unknowns regarding sensitivity at different densities and across taxa. Therefore, it might be good, at least initially, to approach this problem adaptively, using both methods and cross-validating them.

Interested in amphibians, detectability and conservation? Check out the work of the QAECO team:

Kirsten Parris , Geoff Heard and Stefano Canessa have studied detection methods for amphibians around urban Melbourne and beyond.

Reid Tingley is interested in using detection models to design optimal surveillance strategies for invasive amphibians.

Claire Keely is undertaking a PhD on the conservation genetics of the Growling Grass Frog in an urban landscape.

By Claire, Stefano, Reid, Luke and team

Goldberg et al. (2011) Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders. PLOS ONE.

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One Response to Surveying amphibians using environmental DNA: is it worth it?

  1. Pingback: Seeking student with an interest in genetics and optimal survey design | Reid Tingley

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