Media Release

Ocean detectives in search for whale shark’s genetic fingerprint

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29 August 2019


A whale shark cruises over the reef at Ningaloo, Western Australia. Image: Andre Rerekura


Researchers from Australia’s tropical marine research agency the Australian Institute of Marine Science, are developing new ways to study the world’s largest fish in the ocean, using the smallest of clues.

A team of researchers has been leading a study in the waters off Western Australia during this year’s whale shark season, trialling the latest methods to monitor their movements.

AIMS fish biologist Dr Mark Meekan said even at Ningaloo Reef, one of Australia’s whale shark ‘hotspots’, the animals were challenging to study.

“Despite their size, whale sharks are difficult to study because they do not have to surface for air like whales, and they swim large distances,” Dr Meekan said.

“Traditionally, aerial searches are used to find the gentle giants, but a trial is looking to next-generation genetic sequencing to detect a whale shark’s DNA in the water column.”

Dr Meekan said this new form of environmental DNA (eDNA) sequencing was an emerging technique, that promises to be a vital tool for monitoring and conservation, and in this case could give researchers the tools to detect individual whale sharks.

“These huge animals shed DNA from their skin, or small amounts of mucus, leaving behind tiny clues like genetic fingerprints that reveal they were in an area,” Dr Meekan said.

“We are using a way of separating and identifying individual DNA from many organisms in a water sample using a process called DNA metabarcoding.

“This process allows us to collect water samples in an area of reef where we know whale sharks gather, and we can determine which individual whale sharks were there, and at what time of year they show up.”


Researchers collecting samples of eDNA in their search for genetic fingerprints of whale sharks at Ningaloo Reef

Dr Mark Meekan said endangered whale sharks were an integral part of the ecology at Ningaloo and its $20 million ecotourism industry.

“Whale sharks share the Exmouth Basin region with shipping and other industry players in the same marine space, so it is important to also understand the impacts of activities on these animals,” Dr Meekan said.

AIMS and UWA Oceans Institute molecular ecologist Dr Luke Thomas, said with eDNA metabarcoding thousands of species can be profiled simultaneously from a single water sample.

“We are constantly coming up with new technology to monitor marine populations and one approach is coupling next-generation sequencing with environmental DNA,” Dr Thomas said.

“It is an alternate monitoring tool to those currently available that can give us really powerful data.”

Dr Thomas said AIMS collaborated with Curtin University researchers to develop a floating next-generation sequencing laboratory onboard AIMS Research Vessel Solander to allow researchers to monitor whale shark populations in real-time.

This AIMS whale shark research project is supported by Santos Limited.

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