Developing eDNA methods to detect Top End animals

Animals leave DNA traces of their presence in hair, skin, urine, faeces, sperm and eggs that are shed into their surrounding environment. This DNA can be found in the environment for a short time even after visible traces have disappeared, and is called eDNA.

This project showed, for the first time, that eDNA can be used to detect the presence of an endangered bird species simply by collecting a cupful of water from the pools where they drink.

The research developed a genetic probe that targets and identifies eDNA of the endangered Gouldian finch (Erythrura gouldiae), a rainbow-coloured grassfinch endemic to the savanna woodlands of northern Australia.

Gouldian finches live in small and mobile groups, making them difficult to find using standard survey methods. This new eDNA test for Gouldian finches will help the Northern Territory Government in their regional wildlife surveys.

Gouldian finches drinking at a waterhole in the Northern Territory.

Gouldian finches drinking at a waterhole in the Northern Territory. Photo: NESP Northern Australia Hub.

The Gouldian finch test is a single-species detection test. This project also aimed to develop a multi-species approach – known as eDNA metabarcoding – to detecting terrestrial animals in northern Australia. Metabarcoding allows the detection of multiple species within a single sample of water, making these tests cheaper and more efficient for surveying general biodiversity.

This project successfully identified species’ DNA from ‘mock’ communities of birds and mammals, using a DNA library. However, the volume of water sampled (250 mL) was insufficient to collect enough DNA when tested in the field.

Given the logistical constraints of collecting and transporting large volumes of water in northern Australia for metabarcoding analysis, single-species detection tests (such as the one developed for Gouldian finches) may be the preferred approach if the goal is to detect particular species of interest – such as threatened or invasive species.

Overview of the eDNA process.

Overview of the eDNA process. Click to enlarge.

August 2021

The Northern Australia Environmental Resources Hub addressed key research questions to come up with practical, on-ground solutions to some of the north’s most complex environmental challenges. A transdisciplinary research approach has been at the heart of the hub. Integrating key research users – policy-makers and land managers including Traditional Owners and ranger groups – into the co-design of research projects has led to rapid uptake of research outcomes into land management practices and decision-making. The hub has produced this wrap-up video outlining these impacts from the perspectives of research users.

January 2019

Project leader, Professor Karen Gibb, provides an update on the Developing eDNA methods to detect Top End animals project at the 2018 TNRM conference.

This project was led by Professor Karen Gibb from Charles Darwin University and Dr Alaric Fisher from the Northern Territory Department of Environment, Parks and Water Security.

Professor Simon Jarman (The University of Western Australia) led the bioinformatics and initial probe design.

Professor Gibb and Dr Fisher were being assisted by researchers from Charles Darwin University and the NT Department of Environment, Parks and Water Security.

This project was completed in December 2021.

Contact

Karen Gibb, Charles Darwin University, [email protected]
Alaric Fisher, Northern Territory Government, [email protected]

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  • Gouldian Finch DNA may be detected in waterholes where they drink or bathe. Minden Pictures/Alamy Stock Photo.
  • Gouldian finch eDNA filter samples. Photo NESP Northern Hub.
  • Gouldian finches moving towards a water hole to drink. Photo NESP Northern Hub.
  • Flock of species that co-occur with gouldian finches departing waterhole. Photo NESP Northern Hub.
  • Environmental DNA has proven to be an efficient way to assess the presence of important species. Photo: Damien Burrows.
  • In aquatic systems, sampling water can provide many insights so now the challenge is to apply this to animals that live on land. Photo: Damien Burrows.
  • This project is developing eDNA methods to specifically detect the Gouldian Finch even when other finch species are present.
  • The Gouldian Finch is the focus of this terrestrial investigation, and field investigations can verify eDNA findings.