eDNA for indirect detection

Many threatened and rare aquatic and semi-aquatic species call northern Australia home – but remote locations and challenging habitats make it difficult to locate many of these species using traditional survey methods.

We are refining environmental DNA (eDNA) approaches to indirectly detect threatened species in remote northern Australian habitats using water samples. Our team is developing assays to identify tropical species of interest for conservation and testing user-friendly field methods, increasing the range of applications for this innovative ecological monitoring technique. These projects are supporting targeted conservation and management to protect northern Australia’s biodiversity.

Threatened freshwater fish

Extensive flooding after Tropical Cyclone Jasper in late 2023 had major impacts on waterways across the Wet Tropics World Heritage Area. The effects of this flooding on the rare and threatened native freshwater fish in the region – species already at risk from habitat degradation and competition from non-native fish – are currently unknown.

We are using eDNA analysis alongside traditional survey methods to assess how recent flood events have impacted endangered populations of Bloomfield River cod. Our team will also investigate the preferred habitat, tropic relationships, life history, and genetics of this poorly understood species to identify potential risks for targeted management.

Rare rainforest frogs

Finding endangered rainforest frog populations presents a challenge for researchers; these frogs live in mountainous areas of dense vegetation, criss-crossed by rivers, creeks, and streams where frogs might be found.

We developed assays to detect three frog species of interest – the lace-eyed tree frog, armoured mist frog, and waterfall frog – using eDNA. Our team also trialled the collection and analysis of unfiltered water samples, removing the need to filter large amounts of water on site.

We successfully identified a small population of just 1,000 individual Litoria lorica frogs in the Carbine Tablelands from a sample collected over 20 kilometres downstream. Locating these endangered frog populations is an important first step for effective conservation planning. These results were published in PeerJ here.

Elusive freshwater turtle

Irwin’s turtle was first recorded in the Burdekin River catchment in the early 1990s, but a lack of formal sightings for 25 years cast doubt on whether these turtles could still be found in the region.

Environmental DNA methods were ideally suited for detecting this species, as the turtles are not easily trapped and live in murky waters in remote areas, making access difficult and underwater cameras ineffective. We partnered with Traditional Owners, government, and industry to survey the Burdekin, Bowen, and Broken Rivers in search of Irwin’s turtle in 2020-2021.

The team collected water samples for eDNA analysis from 37 sites across the three river catchments, with some remote sites accessible only by helicopter. They successfully detected the turtle at several sites along the lower Burdekin, suggesting Irwin’s turtles may be able to survive in more turbid waters than previously thought. These results were published in BMC Ecology and Evolution here.

Endangered sawfish

Sawfish are endangered worldwide, but difficult to survey using traditional methods as they live in turbid, murky waters and remote habitats, requiring specialist equipment and highly trained staff. Environmental DNA offers a cost-effective alternative with the potential for simpler field methods, allowing Indigenous Rangers and communities to collect samples themselves.

Historical sightings suggested sawfish could be living in a saltwater lake on Groote Eylandt in the Northern Territory. We collaborated with Anindilyakwa Land and Sea Rangers to collect water samples at four sites around the lake for eDNA analysis to identify large-toothed and dwarf sawfish. Samples were also collected by Mimal Land Management in Arnhem Land.

Although no sawfish were detected at the lake on Groote Eylandt, this project demonstrated a user-friendly method for eDNA sample collection by non-specialists that has been used for other monitoring projects.

Project details

These projects are led by Professor Damien Burrows and Dr Cecilia Villacorta-Rath with funding from the National Environmental Science Program. The Bloomfield River cod project is led by Professor Mark Kennard of Griffith University.