Turtle trackers: Environmental DNA used to detect rare species

URBANA, Ill. — The prehistoric-looking alligator snapping turtle may be the largest freshwater turtle in North America, but that doesn’t make it easy to spot.

The up-to-200-pound armored beasts have only been officially recorded in Illinois 16 times since the late 1800s. But in a recent study, University of Illinois scientists have demonstrated an effective new method to detect the secretive reptiles in the wild.

“You can’t conserve a species or population without knowing where they are. Once we have that foundational information, we can do the nitty gritty of conservation biology: trying to boost populations through habitat restoration, reintroductions, or any number of established conservation tools,” said Ethan Kessler, doctoral student in the Department of Natural Resources and Environmental Sciences and the Illinois Natural History Survey at the University of Illinois.

Kessler is the lead author on the study.

He and his collaborators tested how well an emerging environmental sampling technique known as environmental DNA, or eDNA, could detect alligator snapping turtles in a southern Illinois river system.

The idea is that all organisms shed DNA in the environment as they go about their daily business. Therefore, a simple scoop of soil or water should theoretically contain trace amounts of DNA from all the organisms recently inhabiting or passing through a given area.

“We’re finding that eDNA is really sensitive to the presence of a variety of organisms in both aquatic and terrestrial habitats, and that expands our ability to find hard-to-detect creatures in hard-to-sample environments,” said Eric Larson, assistant professor in NRES and co-author on the study.

The research team knew alligator snapping turtles were in Clear Creek, a southern Illinois stream feeding into the Mississippi River, because they put them there.

A reintroduction program has put 400 to 500 young turtles into the system since 2014 and work is ongoing to determine the introduced population’s viability.

Each turtle is outfitted with a tracking device. To find them, researchers have to walk or kayak around the site with a less-than-waterproof radio receiver, set up and check traps, and interact with potentially dangerous snapping turtles.

“It’s time consuming and a lot of effort. And we’re limited by the number of traps that we can check in a day,” Kessler said. “With eDNA, we can just show up at a location and pull a quick water sample. You can cover a wide geographic area relatively rapidly. That saves money, too, considering the cost of traveling to these remote locations.”

To prove eDNA is capable of detecting alligator snapping turtles, the research team first identified genetic markers that matched all of the subpopulations across the species’ range, but differed from any other turtle species.

After radio-tracking each turtle, they took water samples near the turtles, as well as in dozens of random sites to determine how eDNA travels in a riverine setting.

The eDNA method was able to detect alligator snapping turtles up to a kilometer, or two-thirds of a mile, downstream. Remarkable, considering less than a gallon of water was taken from each sampling location.

“This was a great place to test the performance of eDNA, because there are only so many alligator snapping turtles in Clear Creek, and we know where many of them are. That gave us something like the control of a laboratory experiment, but under very natural conditions in a real ecosystem,” Larson said.

The study also identified shortcomings of the method. For example, the researchers found that stretches of the river that were exposed to more sunlight represented gauntlets of DNA degradation.

“We know ultraviolet light destroys DNA, but we didn’t know how much the sun would affect our ability to detect alligator snapping turtles,” Kessler said.

“We ended up finding that UV exposure does have a slight effect on our ability to detect. It’s reducing the copy number, or the amount of DNA, in our samples.”

Even with reduced copy number in some samples, the researchers were able to detect the elusive species with fairly high fidelity. The results suggest eDNA detection could be used as a first step to find turtles in locations where their status is unknown.

“We developed a tool to rapidly go out and look for this species. This could be used in regions that historically have records for the species, but they either haven’t been found in many years or have really low population levels,” Kessler said.

“But I think just in general, as long as you have a species-specific primer, this is a good tool to use for any rare species. And it’s a way to maximize our time and effort. A lot of animals need help, and conservation biologists have limited resources and time to try to get the most good out of the work that we do.”