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Whale shark

Scientists have estimated the number of reproducing female whale sharks in part of the Arabian Gulf using nothing but DNA floating in the ocean.

Steffen Sanvig Bach, Maersk Oil Research and Technology Centre, Qatar

DNA collected from seawater may solve mysteries about world’s largest fish

Using only the DNA from sloughed-off cells floating in the ocean, scientists have been able to determine the population size and genetic properties of one of the world’s largest and most mysterious animals: the whale shark. The work marks the first time researchers have been able to use so-called environmental DNA (eDNA) to estimate the genetic characteristics of an aquatic species, and it could help scientists study the population and health of a wide range of marine animals without ever setting foot in the water.

The results are a “conceptual advance,” says marine biologist Ryan Kelly of the University of Washington (UW) in Seattle, who was not involved with the research. They “push the boundaries of what is possible to do with environmental DNA.”

The research traces its origins to one summer day in 2007, when a worker on a Maersk Oil platform in the Al Shaheen oil field off the coast of Qatar saw a surprising sight: a group of roughly 100 whale sharks feeding near the surface. Scientists hadn’t realized that the fish—the world’s largest at roughly the size of a school bus—frequented these waters, and the gas field soon became a hotbed for studying this endangered species.

Whale sharks can be difficult to locate, however, because they are often far out at sea. Those at the Al Shaheen oil field were more than 80 kilometers from the coast in the Arabian Gulf. Biologist Eva Egelyng Sigsgaard at the Natural History Museum of Denmark at the University of Copenhagen and her team collected seawater containing skin cells—along with cells from urine and feces—naturally shed by the whale sharks and other animals. The researchers isolated the cells, extracted and sequenced the DNA within them, and then used software to assign some of the DNA to whale sharks, based on the presence of certain gene groups. Sigsgaard and her team also showed that the cells were a good indicator of recent fish activity. Because ultraviolet light and microbes break whale shark eDNA into undetectably small pieces within only a few days, their samples likely traced whale sharks that had passed by recently. 

The researchers then used the DNA to estimate the number of reproductive female whale sharks—roughly 71,000. Whale sharks appear to be genetically split between two groups, and this estimate reflects the female population of whale sharks in the Indo-Pacific Ocean group. This number was broadly consistent with estimates from actual tissue samples, the team reports online today in Nature Ecology & Evolution.

In a related study published this month in PLOS ONE, scientists showed that eDNA collected off Greenland revealed which fish were most likely to be caught by deep-water trawling, a finding that could revolutionize how marine species are studied. That’s because using eDNA is a cheaper, easier option than dragging nets across the ocean bottom to collect tissue samples. “We can get a quite detailed and precise picture of fish fauna using only environmental DNA,” says team member Peter Rask Møller, fish curator at the Natural History Museum of Denmark.

In the future, scientists like UW’s Kelly envision using eDNA to determine marine biodiversity in difficult-to-sample habitats like rocky ocean bottoms that cannot be trawled. “Does environmental DNA give us useful information about the world that we could not have gotten otherwise?” he asks. “I think the answer is yes.”

*Correction, 22 November, 12:19 p.m.: The story has been changed to reflect that the population estimate of whale sharks corresponded to individuals in one genetically similar group.