Evaluating the utility of environmental DNA for detecting a large Critically Endangered lizard in tropical northern Australia

Emily P. Hoffmann; Chris J. Jolly; Kathryn L. Dawkins; Kelly M. Dixon; Luke D. Einoder; Graeme R. Gillespie; Brett P. Murphy; Brenton von Takach

doi:10.1071/PC24072

RESEARCH ARTICLE (Open Access)

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Evaluating the utility of environmental DNA for detecting a large Critically Endangered lizard in tropical northern Australia

Emily P. Hoffmann

^A ^B ^* , Chris J. Jolly ^C , Kathryn L. Dawkins ^D , Kelly M. Dixon ^A ^E , Luke D. Einoder ^F , Graeme R. Gillespie ^G , Brett P. Murphy ^E and Brenton von Takach ^H

+ Author Affiliations

- Author Affiliations

^A Territory Natural Resource Management, Darwin, NT, Australia. Email: kelly.dixon@territorynr

^B School of Biological Sciences, University of Western Australia, Perth, WA, Australia.

^C School of Natural Sciences, Macquarie University, Sydney, NSW, Australia. Email: chris.jolly@mq.edu.au

^D eDNA Frontiers, Curtin University, Perth, WA, Australia. Email: kat.dawkins@curtin.edu.au

^E Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, Darwin, NT, Australia. Email: brett.murphy@cdu.edu.au

^F Parks Australia, Darwin, NT, Australia. Email: luke.einoder@dcceew.gov.au

^G School of BioSciences, University of Melbourne, Melbourne, Vic., Australia. Email: graeme.r.gillespie@gmail.com

^H School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia. Email: brenton.vontakach@curtin.edu.au

^* Correspondence to: emily.hoffmann@uwa.edu.au

Handling Editor: Graham Wallis

Pacific Conservation Biology 31, PC24072 https://doi.org/10.1071/PC24072

Submitted: 22 September 2024 Accepted: 19 December 2024 Published: 16 January 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

It can be challenging to reliably detect rare or cryptic species. Environmental DNA (eDNA) is an emerging tool for detecting species and is increasingly being used to detect reptiles in terrestrial environments that are costly or difficult to survey or monitor using traditional methods. Here, we trialled eDNA metabarcoding to detect one of Australia’s most threatened and least known reptile species, the Arnhem rock skink (Bellatorias obiri). At the only site where they were known to persist, we sampled soil from 12 rock crevices, including four with high levels of activity of the target species, as well as water from three adjacent pools. We were unable to identify DNA of B. obiri in any of the soil or water samples, suggesting multiple false-negative errors, despite our successful amplification of B. obiri DNA from an incidental scat sample. We were able to identify 15 non-target vertebrate taxa from our samples. Given that samples were taken from a site where B. obiri was known to be present, the eDNA metabarcoding technique trialled here does not appear to be an effective method for detecting this species. Whilst eDNA metabarcoding is an emerging and powerful tool in ecology and conservation, our pilot study highlights that challenges remain in its application for detecting rare or cryptic terrestrial reptiles.

Keywords: Bellatorias obiri, eDNA, metabarcoding, reptile, soil, species detection, terrestrial, threatened species.

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