CSIRO creates DNA test to better manage wild fish populations

DNA test

The CSIRO, Australia’s national science agency, has developed a DNA test to determine a fish’s age, improving management of wild fish populations for conservation or harvest. This will help maintain sustainability in fishery supply chains. 

The test is a non-lethal alternative to counting growth rings in fishes’ otoliths, or ear bones, CSIRO Environomics Future Science Platform postdoctoral fellow Dr Ben Mayne said. 

“We developed a fast, cost-effective DNA test for use with three threatened Australian freshwater species, the Australian lungfish, the Murray cod and the Mary River cod, which can also be adapted for other fish species,” Mayne said. 

“Knowing the ages of fish in a population is vital for their management, such as setting sustainable harvests or determining whether a species is at risk of extinction as well as understanding growth and reproduction of a species. 

“We’re now hoping to share this test with fisheries managers to support conservation projects and sustainable fisheries worldwide,” he said. 

Until now, most animals including fish didn’t have a practical and non-lethal method to determine age. Seqwater senior research scientist Dr David T. Roberts has been conducting research on lungfish for over a decade. 

“The search for a method to age Australian lungfish has been costly and technologically challenging,” Roberts said.  

“This breakthrough DNA-based ageing method will advance our understanding of lungfish population dynamics, providing a low cost, accurate and simple method that will improve conservation efforts long into the future.” 

Working on water planning that balances multiple stakeholders’ needs and key aquatic species in Queensland for 15 years is Queensland Department of Regional Development, Manufacturing and Water aquatic ecologist Tom Espinoza. 

“Australian lungfish, Murray cod and Mary River cod are iconic species in Australia due to their economic, scientific and cultural value,” Espinoza said.  

“Non-lethal ageing provides an important platform from which to develop this technique across more species and improve management of the fisheries and natural resources that support them.” 

To develop the DNA test, Mayne’s team first worked with zebrafish, long used to study fish biology, before calibrating the technique for threatened species. Here they used fish of known ages, bomb radiocarbon dating of scales and ages determined from otoliths. 

The result is a rapid and cost-effective method to determine the age of a fish, based on methylation of DNA at places in the genome, known as CpG sites. 

Despite the zebrafish and the Australian lungfish being separated by more than 100 million years of evolution, this system is conserved and works in both species. 

This work is part of CSIRO’s ongoing research to develop ways to use DNA to measure and monitor the environment, including estimating the lifespan of vertebrate species using DNA and surveying biodiversity in seawater using eDNA. 

“We are continuing to work with lungfish and cod in southeast Queensland by ageing historic genetic libraries, to provide detailed demographic profiles to help conserve these species,” Mayne said. 

The relevant paper, “Non-lethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod” was published in Molecular Ecology Resources by authors from CSIRO, Seqwater, Queensland government, NSW Department of Primary Industries, University of Queensland and University of Western Australia. 

An earlier paper is also available: “A DNA methylation age predictor for zebrafish.” 


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