Shark DNA in the Water? Cue Music from Jaws

Sharks aren’t any more interested in hunting people than they’ve ever been, but they may be cruising our coasts in larger numbers, raising the odds, however slightly, that sharks may attack surfers, ocean swimmers, and beachgoers. Nearby sharks can be tracked, offering the public some security. For example, sharks can be followed visually or tagged in various ways. And now an even better technique may become available: an environmental DNA (eDNA) assay.

The eDNA assay emerged from a scientific collaboration researchers from UC Santa Barbara and the U.S. Geological Survey (USGS), with colleagues from California State University Long Beach (CSULB) and Central Michigan University (CMU). According to these researchers, eDNA in water samples can be analyzed for shark-specific genes. The researchers demonstrated their technology by detecting DNA left behind by white sharks.

eDNA is genetic material collected from the environment, as opposed to within a living organism. Things animals may leave behind – such as mucus, feces, or shed skin – contain their genetic signatures, which can be parsed out and identified through genetic sequencing. Scientists can extract and amplify specific genes within the DNA fragments found in water samples. Then the scientists can determine if the DNA contained in those samples is from a specific species.

“One of the goals of [our] research is for a lifeguard to be able to walk down to the shore, scoop up some water, shake it, and see if white sharks are around,” says Kevin Lafferty, a USGS ecologist and researcher with UCSB’s Marine Science Institute (MSI).

Lafferty is lead author of a new paper (“Detecting southern California’s white sharks with environmental DNA”) that appeared in the journal Frontiers in Marine Science. The article describes a species-specific eDNA assay that targets a 163 bp fragment of the white shark (Carcharodon carcharias) mitochondrial cytochrome B gene on a digital droplet PCR (ddPCR) platform.

“We used this marker to detect white shark DNA in 250 mL water samples taken from across two sites in Santa Barbara, CA, frequented by juvenile white sharks,” wrote the article’s authors. “We did not detect white shark DNA in samples from two neighboring sites where sharks are presumably absent, suggesting that eDNA can indicate nearby white sharks.”

The team’s results add to a growing body of evidence that white sharks, which had been declining in numbers due to overfishing, have for the last several years been experiencing a comeback along the California coast.

According to CSULB professor, white shark expert, and study co-author Chris Lowe, the resurgence is due to the success of state and federal protections from fishing, recovery of marine mammal populations and better fisheries management.

“However, white shark population recovery has co-occurred during a period when more people than ever before are using the coastal ocean for recreation, ultimately increasing the likelihood of interactions,” he says. “While sightings of juvenile white sharks have risen considerably along California over the last eight years, there has been no dramatic increase in shark bites on people.”

In Carpinteria, down the coast from UC Santa Barbara, Lowe had been acoustic- and satellite-tracking tagged juvenile sharks at one of several summer/fall nurseries along southern California. Lafferty and Lowe wondered if these sharks were leaving a detectable eDNA plume. Lafferty had little success using eDNA to sample for sharks until eDNA expert and MSI researcher Chris Jerde shared a new protocol he developed with CMU’s Andrew Mahon.

“Ten years ago, we started working on eDNA,” says Jerde, who is a co-author of the paper. “The advances in technology since then have dramatically improved the reliability, portability, and widespread application of the method.”

Because eDNA can drift with currents, and sharks can swim long distances in the time it takes eDNA to degrade, the new approach only gives a rough idea about where sharks actually are at a particular moment. Still, “Chris Lowe can now add eDNA to his new white shark monitoring program, which includes real-time acoustic tracking and drone flights,” Lafferty says.

“We can now sample eDNA along the coast to make better maps and seasons for white sharks,” he adds. “And if we can do it for white sharks, we can do it for other marine species, too.”

The authors of the paper concluded that marker development, testing, and opportunistic application in a region with known distributions of white sharks could be further developed to improve the monitoring of white sharks, thereby informing conservation planning and public safety. “With the potential increase in white shark populations due to decades of protection, there is a need for fishery-independent methods for assessing white shark distributions,” the authors noted, “and eDNA may provide be an ideal, non-intrusive tool for coastal assessments.”

“We can use eDNA not only to determine whether white sharks have been present at a beach, but also to determine if their favorite food is there as well, such as stingrays,” states Lowe. “Once we are able to better refine and calibrate the methods, another goal will be to integrate eDNA technology into autonomous surface vehicles that can be programmed to move along the coast sampling water and send data into the cloud, along with text alerts to local lifeguards, of the presence of white sharks at a particular location. This technology holds great promise for future, near real-time monitoring.”