Developing eDNA methods to detect Top End animals

It can be difficult to detect animals in remote, data-poor environments like much of northern Australia where many logistical challenges and safety hazards also hamper monitoring. Conventional techniques such as trapping and visual counting are resource intensive and logistically challenging, and many target species are rare or shy, so survey intensity is very high. To better support planning, management and impact assessments we need to better monitor the presence or absence of animals such as threatened species, pest species and species of high cultural value.

Gouldian map

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. Early studies have demonstrated that eDNA from terrestrial animals can be detected in soil or in waterbodies where they drink or bathe. More research is required to determine which terrestrial species can be readily detected, to develop species-specific probes, to identify practical sampling and analytic methods and to know how to appropriately interpret results.

This project is investigating the use of eDNA to detect a key terrestrial animal species in the Top End. The approach is being trialled on the endangered Gouldian Finch with field validation using water samples from sites where the abundance of finches is closely monitored. After a successful trial for the Gouldian Finch, stage two of the project will compare eDNA test performance against existing survey methods under a major government program assessing biodiversity values in remote, data-poor regions. This will allow both validation and an assessment of cost-effectiveness and potential complementarity.

This project is:

  • developing and validating eDNA probes for the endangered Gouldian Finch
  • improving our understanding of the distribution and local occurrence of this threatened species
  • developing eDNA sampling protocols that are informing protocols for regional environmental assessments
  • testing the extent to which this eDNA method can be used to detect terrestrial animals by comparing its utility and cost-effectiveness with traditional sampling methods. If the eDNA method performs well, it will significantly improve monitoring of key species in remote, data-poor areas.

Project activities

  • Analyse existing data to identify whether a suitable probe exists for the Gouldian Finch and if not, develop a suitable probe through DNA sequencing and bioinformatics
  • Optimise eDNA probe markers using DNA from other finch species and aviary water samples to ensure the method only detects the Gouldian Finch
  • Develop detailed protocols for field sampling, sample preservation, DNA extraction and analysis and data management
  • Sample for eDNA in waterholes where finch populations are intensively monitored and validate results against finch monitoring data
  • Develop a workplan to test the extent to which the eDNA method can be applied in a regional-scale biodiversity assessment program
  • Implement the plan (stage two).

Anticipated outputs

  • Report on the potential for eDNA methods to detect key terrestrial species
  • Report assessing the use of eDNA for detecting Gouldian Finch, and for other species if stage two goes ahead
  • Protocols and training manual for sampling design, sample collection and transport, analysis and interpretation
  • Workshops, video, presentations and summary reports
  • Scientific publications.
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 is being 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) is leading the bioinformatics and initial probe design.

Professor Gibb and Dr Fisher are being assisted by researchers from Charles Darwin University and the Department of Environment and Natural Resources.

This project is due for completion in June 2021.


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

     NT government logo      UWA Logo

  • 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.