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To track sea turtles, get DNA from the sand

"You don't need to be a highly trained scientist to collect eDNA, which makes this technology a lot more democratic," David Duffy says. "This really opens up the ability to monitor wildlife non-invasively to a much wider pool of people." (Credit: ericdalecreative/Flickr)

The DNA “fingerprints” that sea turtles leave behind offer scientists a way to track the health and whereabouts of the endangered animals, say researchers.

The study is the first to sequence sea turtles’ environmental DNA, or eDNA—genetic material shed as they travel over beaches and in water. The research project is also the first to successfully collect animal eDNA from beach sand. Scientists could use the techniques to trace and study other kinds of wildlife, advancing research, and informing conservation strategies.

“We wanted to test the boundaries of this technology, which hadn’t really been applied to sea turtles before and certainly not on sand,” says David Duffy, assistant professor of wildlife disease genomics at the University of Florida. “This is a way to survey areas for elusive animals or species that can be hard to study otherwise. It’s essentially wildlife forensics.”

Nearly all of the planet’s sea turtle species are endangered and face a multitude of threats, including warming temperatures, habitat destruction and degradation, disease, hunting, and pollutants such as plastics. Conserving sea turtles is also complicated because current survey methods rely on spotting them in one of their multiple habitats—in the open sea, coastal ecosystems, or on beaches where they nest. This makes it difficult to monitor their numbers, genetic diversity, and overall health and tailor conservation efforts accordingly, Duffy says.

“Some of these threats are quite new and even ones that existed for a longer time are getting worse,” says Duffy, who is based at the university’s Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital. “That’s why it’s very important for us to have these DNA tools to be able to get a proper handle on what’s happening to the population in real time.”

eDNA techniques were originally developed to extract and analyze DNA from microbes in soil and water. Now, however, scientists are using the technology to detect the presence of much larger animals, which regularly leave behind small amounts of genetic material via skin, hair, scales, feces, or bodily fluids.

A team led by Duffy and graduate students Jessica Farrell and Liam Whitmore created techniques that can identify the presence of green turtles, Chelonia mydas, and loggerheads, Caretta caretta—both endangered species—via DNA in a small scoop of sand or a liter of seawater. Minuscule amounts of DNA revealed not only which species of sea turtles had recently passed through, but also their place of origin and the subpopulation to which they belonged. On sand, the team was even able to extract viable DNA from a crawl track made by a single loggerhead hatchling, which weighs about as much as a dozen paperclips.

The methods could help scientists verify where sea turtles are living and how their range and numbers are shifting over time, Duffy says. eDNA also omits the need to take tissue and blood samples, which can be stressful for turtles, particularly nesting females.

“By optimizing eDNA practices for sea turtles, we had a much better success rate of identifying them in an area than with traditional survey methods,” Duffy says. “We were surprised at how sensitive it was.”

The team could also ascertain sea turtle pathogens in eDNA samples, including the main virus that causes fibropapillomatosis, an increasingly common cancer that causes cauliflower-like tumors on sea turtles’ skin, eyes, mouth, and internal organs. About 50% of green turtles that strand on Florida beaches are afflicted with these tumors, which can become so debilitating that they affect turtles’ ability to catch food and swim. eDNA techniques could pinpoint specific variants of the virus and its concentration in the water column—helpful advancements in following its spread and developing potential treatments in the future, Duffy says.

The next step in the research project will focus on conservation genetics—using DNA to capture a snapshot of how many individual animals live in an area and how genetically diverse they are, a crucial predictor in how they will weather threats, Duffy says.

“You can say not only whether the species is present or absent, but you can potentially start to measure how many of those species are present, which is not easy to do for marine animals,” he says.

Before testing eDNA methods in the wild, the team refined their techniques in the tanks and sand occupied by recuperating turtles at the Whitney Laboratory. Duffy and his team also used Whitney Laboratory’s statewide network of volunteers to collect sand samples from nesting beaches across Florida. The scientists found that eDNA from sea turtle nests remained viable for more than a day before collection. Once collected and stored, DNA in sand and water samples was stable for weeks to months, allowing time for citizen scientists as far away as the Florida Keys to obtain and ship samples to the Whitney Lab for processing.

“You don’t need to be a highly trained scientist to collect eDNA, which makes this technology a lot more democratic,” Duffy says. “This really opens up the ability to monitor wildlife non-invasively to a much wider pool of people.”

The study appears in Molecular Ecology Resources. Funding for the research came from the National Save The Sea Turtle Foundation, Inc.’s Fibropapillomatosis Training and Research Initiative; a Welsh Government Sêr Cymru II; European Union’s Horizon 2020 research and innovation program; the Gumbo Limbo Nature Center; and an Irish Research Council Government of Ireland Postgraduate Scholarship.

Source: University of Florida