If you lean over the side of a boat and scoop up some water with a jug, you have just taken a census of the ocean. That water contains traces of the animals that swim below your boat—flecks of skin and scales, fragments of mucus and waste, tiny cells released from their bodies. All of these specks contain DNA. And by sequencing that DNA gathered from the environment—which is known as environmental DNA, or eDNA—scientists can work out exactly what’s living in a patch of water, without ever having to find, spot, or identify a single creature.
And that helps, even when the creature in question is 18 meters long.
In August 2007, an oil worker named Soren Stig looked over the side of a rig in the middle of the Persian Gulf, and saw a horde of giants. They were whale sharks—the world’s largest fish, with a cavernous mouth and a back that looks like a field of stars. They live throughout the tropical oceans and often gather en masse to feed on plankton and fish eggs. But scientists believed that they were rare in the Persian Gulf, unable to tolerate its superlatively hot waters. And yet, when Stig looked into those waters, he saw huge numbers of them.
He took a photo and uploaded them to an online database of whale-shark sightings. Within a few years, the Qatar Whale Shark Project was born, and scientists were studying the animals with help from the oil workers. By towing nets amid the feeding shoals, they showed that the sharks had gathered to eat the eggs of spawning mackerel tuna. By fitting the sharks with satellite tags and photographing them, they could identify and track individuals—more than 300 to date.
Many of these traditional methods rely on spotting the sharks—a tricky task when water is clouded by fish eggs. “I’ve been there three times now,” says Eva Egelyng Sigsgaard, from the University of Copenhagen. “The first time, the visibility was really poor, and then out of the blue, this huge mouth comes out at you. They’re completely harmless, but it’s still pretty scary.” But Sigsgaard and her colleagues have now shown that they can use eDNA to study the titanic fish without having to see them at all.
In most eDNA studies, scientists focus on small sections of DNA that vary between species. These act like barcodes, allowing the researchers to work out which animals are present. But Sigsgaard’s team took a different approach: They focused on bits of DNA that vary between individuals. “Rather than just saying there’s whale sharks here, we could go to the next level and look at individuals within the population,” she says.
For example, the team showed that the Persian Gulf whale sharks are part of a population that spans across the entire Indo-Pacific, and are genetically distinct from those in the Atlantic. Then, based on the number of sharks observed in the Gulf and the diversity of their DNA, the team could estimate the size of the entire Indo-Pacific population—around 75,500 females, with a possible range of 54,700 to 96,400. And all of this came from scooping up just 30 liters of seawater.
These estimates are vital. Whale sharks are endangered, and to protect them properly, conservationists first need to know how many there are. But they are so big and so widespread that it’s “close to impossible to get good population estimates from field surveys,” says Al Dove, from the Georgia Aquarium. “There’s always a place for tagging and photographic identification. Those methods give you things that eDNA does not, like the ability to track specific individuals from place to place. But it’s great to have a new tool to help us unravel the biology of the world’s biggest fish. We need all the help we can get.”
Most of the well-studied whale shark populations “are heavily dominated by juvenile male sharks, so we have little knowledge on the pups, adults, or the majority of the females,” adds Simon Pierce, from the Marine Megafauna Foundation. “It's hard to take samples from animals we can't find [but] eDNA is a promising means of learning more about these underrepresented life stages.”
Using eDNA also means that scientists don’t have to take tissue samples from living sharks. “It’s not that doing so is especially harmful to the sharks, but it’s preferable if you don’t have to come into contact with them,” says Sigsgaard. “It’s also less dependent on weather. In principle, you could put out a machine that captured water samples every week. It wouldn’t matter if it was stormy, or if the sharks were visible.”
This ability to monitor hard-to-find animals in hard-to-reach places makes eDNA extremely compelling to conservationists. Philip Francis Thomsen, who led the new whale shark study, recently used eDNA to catalogue the deep-water fish that live off Greenland, which would otherwise be hard to study without dragging a net through the water. The DNA doesn’t have to come from the sea, either. Blood-sucking parasites like leeches take up the DNA of their hosts when they feed; recently, Thomas Gilbert and Douglas Yu used DNA from leeches to make an inventory of the animals that live in Vietnamese rainforests.
And now, Sigsgaard and Thomsen have shown that they can use eDNA not just to catalogue an area’s animals, but to count them too. They did so for whale sharks, but the water they collected also contains DNA from every other animal in that patch of the Persian Gulf. They could do population-wide genetic studies for all kinds of species. “The main limitation is the amount of resources you have to analyze the samples,” says Sigsgaard. “Everything’s basically in there.”