How to identify a whale shark with a bottle of water

What’s in a bottle of seawater? A simple sample can hold information about the presence of marine creatures in the local area – and may help conserve whale sharks.

eDNA is a non-invasive method of identifying species. DNA is sloughed off the skin cells and bodily waste of marine animals and remains in the water. eDNA tracking identifies these markers, and provides a window into the local ecosystem.

Typically, eDNA is used to identify the presence of members of a general species, but a study in Molecular Ecology Resources, has identified a new technique – eDNA haplotyping – which allows researchers from the Australian Institute of Marine Science (AIMS) and UWA Oceans Institute to identify individual whale sharks.

“Our new method has taken this incredible leap to detect the genetic signature of individual whale sharks just by analysing the seawater,” says Laurence Dugal, PhD researcher and lead author. “We have moved beyond species detection and into the realm of population genetics – we’ve opened a new door in what is possible with eDNA.”

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Giant whale sharks are huge but elusive, and are considered endangered. Image credit: Andre Rerekura/Whale Shark Research WA

Despite being enormous – the species averages out at about 12 metres long – whale sharks are elusive and listed as endangered by the IUCN, thought to be a victim of bycatch, international markets that prize them for meat and offshore drilling among other human factors.

Researchers visited whale shark ‘hot spots’ at Ningaloo Reef in Western Australia, swimming behind whale sharks and filling small bottles with seawater. They then analysed the seawater samples using eDNA haplotyping. 

They also collected tissue samples and compared the results. 

“The tissue biopsies successfully matched, with high accuracy, to all the individual whale sharks’ eDNA,” says Dugal. “Up until now, we have only been able to get DNA samples through tissue biopsies, which is logistically difficult, expensive to collect and require invasive sampling techniques.”

Now, the team can take a sample of seawater proximate to a whale shark and tell whether it’s a known individual, and if so, which individual it is. This allows researchers to understand more about the animals’ movements and population dynamics.

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eDNA haplotyping can identify the genetic signatures of individual animals in a single bottle of ocean water. Image credit: Andre Rerekura, Whale Shark Research WA

According to AIMS and UWA Oceans Institute scientist Luke Thomas, the method could be applied to other vulnerable or endangered species. 

“This new method is faster, cheaper, highly accurate, easier to scale up and minimally invasive,” he says. “It has the potential to radically change the way we monitor and track megafauna species. It could help answer global population-level questions for other megafauna, such as sharks, rays, marine turtles or dugongs.”

AIMS Principal Research Scientist Mark Meekan says endangered whale sharks are a key part of the ecology at Ningaloo World Heritage Area, and bring in $20 million per year in ecotourism.

“AIMS has been leading the research on whale sharks for decades at Ningaloo – a known hot spot for these majestic giants,” he says. “It is important our marine environments are responsibly managed to ensure we can use the ocean and its resources sustainably while preserving the future of whale sharks.”

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