Sea turtle conservation benefits from new DNA detection method

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The DNA “fingerprints” left by sea turtles offer scientists a simple and powerful way to track the health and whereabouts of these endangered animals, a key step in their conservation.

A study led by researchers at the University of Florida is the first to sequence the environmental DNA, or eDNA, of sea turtles – the genetic material lost as they travel on beaches and in the water. The research project is also the first to successfully collect animal eDNA from beach sand. The techniques could be used to track and study other types of wildlife, advance research and inform conservation strategies.

Tiny amounts of DNA revealed not only which sea turtle species had recently passed through, but also where they came from and the subpopulation to which they belonged.

“We wanted to test the limits of this technology, which hadn’t really been applied to sea turtles before and certainly not on sand,” said David Duffy, assistant professor at UF of Wildlife Disease Genomics and Associate Professor endowed with the Rising Star Condron family. “It’s a way to survey areas for elusive animals or species that may otherwise be difficult to survey. It’s basically wildlife forensics.

Almost every species of sea turtle on the planet is endangered and faces a myriad of threats, including warming temperatures, habitat destruction and degradation, disease, hunting, and pollutants such as plastics. The conservation of sea turtles is further complicated by the fact that current survey methods rely on tracking them in one of their multiple habitats – on the high seas, in coastal ecosystems or on the beaches where they nest. This makes it difficult to monitor their numbers, genetic diversity and overall health and adapt conservation efforts accordingly, Duffy said.

“Some of these threats are fairly new and even those that have been around longer are getting worse,” said Duffy, who is based at UF. Whitney Laboratory for Marine Biosciences and Sea Turtle Hospital, one of the world’s leading centers for sea turtle rehabilitation, research and education. “That’s why it’s very important for us to have these DNA tools to be able to fully understand 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. Today, however, scientists are harnessing this 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.

Citizen scientist Lucas Meers, Professor David Duffy, and Sea Turtle Program Hospital Director Catherine Eastman collect samples at River to Sea Preserve.

Photo courtesy of Zach Read/University of Florida

Citizen scientist Lucas Meers, Professor David Duffy, and Sea Turtle Program Hospital Director Catherine Eastman collect samples at River to Sea Preserve.

A team led by Duffy and UF graduate students Jessica Farrell and Liam Whitmore have created techniques to identify the presence of green sea turtles, Chelonia mydas and loggerhead sea turtles, Caretta caretta – both endangered species – via the DNA in a small ball of sand or a liter of seawater. Tiny amounts of DNA revealed not only which sea turtle species had recently passed through, but also where they came from and the subpopulation to which they belonged. On the sand, the team was even able to extract viable DNA from an exploration track made by a single loggerhead hatchling, which weighs about as much as a dozen paperclips.

The research project is also the first to successfully collect animal eDNA from beach sand.

Photo courtesy of Dylan Taylor/University of Florida

The project is the first to successfully collect animal eDNA from beach sand.

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

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

The team was also able to determine sea turtle pathogens in the eDNA samples, including the main virus responsible for fibropapillomatosis, an increasingly common cancer that causes cauliflower-like tumors on the skin, the eyes, mouth and internal organs of sea turtles. About 50% of green sea turtles that wash up on Florida beaches have these tumors, which can become so debilitating that they affect the turtles’ ability to grab food and swim. eDNA techniques could identify specific variants of the virus and its concentration in the water column — useful advances for tracking its spread and developing potential treatments in the future, Duffy said.

The next stage of the research project will focus on conservation genetics – using DNA to capture a snapshot of how many individual animals live in an area and their genetic diversity, a crucial predictor of how they will cope threats, Duffy said.

“You can not only tell if the species is present or absent, but you can potentially start measuring how many of those species are present, which is not easy to do for marine animals,” he said. .

Before testing the eDNA methods in the wild, the team refined their techniques in the tanks and sand occupied by recovering turtles at the Whitney Laboratory. Duffy and his team also leveraged the Whitney Laboratory’s statewide network of volunteers to collect sand samples from Florida’s nesting beaches. Scientists found that eDNA from sea turtle nests remained viable for more than a day before collection. Once collected and stored, the DNA in the sand and water samples was stable for weeks or even 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 have to be a highly skilled scientist to collect eDNA, which makes this technology much more democratic,” Duffy said. “It really opens up the possibility of monitoring wildlife non-invasively to a much wider group of people.”

The project would not have been possible without the efforts of a consortium of professors, graduate students, postdoctoral researchers, hospital staff and citizen scientists, Duffy noted. He joined the Whitney Lab in 2020 after setting up his own lab at the University of Limerick, Ireland. The lab is also home to the Research Experience for Undergraduate program, funded by the National Science Foundation.

“It was a great collaboration. We are in a truly unique position in that the Whitney Lab at UF is the only sea turtle hospital in the world that is co-located with a research institute. “We have frontline wildlife rehabilitation and conservation work that goes hand in hand with advanced molecular biology research, allowing us to tackle questions that really can’t be answered anywhere else.”

The study was published in Molecular Ecology Resources.

This article has been republished with permission from the University of Florida. Read the original.

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