Enigmatic whale shark’s genetic secrets

The colossal yet elusive whale shark holds its genetic secrets close. But bits of its DNA floating in the oceans can help us understand these gentle giants, a new study shows.

Eva Sigsgaard from the University of Copenhagen in Denmark and colleagues collected seawater to study a group of whale sharks off the coast of Qatar in the Arabian Gulf.

Traces of DNA in the seawater allowed them to estimate the genetic variation in a population without invasive techniques. They published their method in Nature Ecology & Evolution.

Whale sharks are endangered, but understanding their genetics can help with conservation. Declining genetic diversity is a danger for small populations, which might not be able to adapt to or cope with shifts in the environment.

To get reliable genetic information, scientists usually have to take tissue samples or stick tags in individual animals. Shark after shark must be prodded and poked – a stress that scientists would prefer to avoid, especially with endangered species.

And finding the animals is not always easy. Whale sharks spend a lot of time out in the open ocean and their migratory routes are largely a mystery.

So aquatic eDNA can be a useful “additional tool” to gain genetic insights, says Luciano Beheregaray, a molecular ecologist from Flinders University in Australia who was not involved in the study.

Living organisms leave traces of their DNA in the environment. For instance, you shed skin cells; a whale shark sloughs off tough scale-like structures called “dermal denticles”. 

Testing seawater where whale sharks congregate picks up their genetic remnants to create a basic blueprint of the population.

Aquatic eDNA has been used to detect which organisms are present in an area of water. But this is the first study to delve into the genetic composition of a population.

The general technique is fairly simple. Sigsgaard and her team extracted DNA from seawater and amplified certain fragments specific to whale sharks.

From these fragments, the researchers could estimate whale shark genetic diversity. And to cross check, they compared their results with DNA from whale shark flesh samples. 

The genetic information was similar – and the eDNA picked up even more genetic diversity than the tissue.

Relationships between eDNA concentrations of whale sharks and their tuna prey also showed that a water sample could provide insights into their feeding habits.

So while aquatic eDNA sampling is sensitive and non-invasive, it’s not the answer to all sampling problems, Beheregaray says.

One of the biggest issues is that the genetic information is based only on mitochondrial DNA.

Found on a short chromosome in the mitochondria – the powerhouses of the cell – mitochondrial DNA codes only for specific metabolic proteins. It is also inherited directly from the maternal line, “so it’s half the story”, Beheregaray says.

“To actually be able to make strong inferences about populations you would need nuclear DNA. And eDNA is not there yet”.

The researchers used mitochondrial DNA because it seems to preserve better in the ocean than nuclear DNA, which is the genetic information found in the nucleus of the cell.

This might be because each cell contains just two copies of nuclear DNA, whereas mitochondria can number in the thousands.

Another drawback is eDNA can’t identify individuals – it simply shows a range of DNA that exists in the population in general.

And of course, ocean currents constantly sweep material across the world. It’s possible to detect DNA from populations that don’t actually live in the area.

Despite limitations, its sensitivity, cost-efficiency and non-invasiveness means eDNA is a promising method to study animal dynamics and patterns and manage biodiversity.

Although he considers it an interesting advance, Beheregaray stresses that eDNA is unlikely to replace other methods, but instead might complement them to help uncover genetic patterns in rare animals.