New technology detects snake DNA in the environment and allows researchers to determine if invasive snakes such as the Burmese python are in the area.
Pioneered by the University of Florida, the technology, known as a tetraplex digital PCR assay, allows researchers to detect trace amounts of an animal’s DNA, also known as eDNA, in water and soil samples.
Animals, including humans, shed DNA constantly. A sneeze sets loose a cloud of DNA. A snake flicking its tongue in the water, or shedding its skin, or defecating, also releases DNA.
Previous tests could detect eDNA, but the new digital technology is far more precise, and it can detect up to four species in a single sample. Currently, researchers are working with a test that detects four invasive constrictor snake species, all of which have established populations in Florida: Burmese pythons, North African pythons, boa constrictors and rainbow boas.
University of Florida invasion ecology specialist Melissa Miller, lead author of , said that they were able to detect Burmese python DNA in a soil sample two weeks after the snake was removed from an outdoor enclosure.
They did similar tests with captive pythons in water at different time intervals. In the field, variables such as weather and current flow are at play, so they’re still looking into such effects before launching the technology.
The test does not find individual snakes, but shows that a species exists in a given area.
The de facto method for detecting pythons in Florida is a visual survey. But the snakes are nearly invisible, and often live far from roads, where the surveys are conducted. Studies find that visual surveys typically find less than 5% of Burmese pythons in a given area.
“With this new method, we increase our ability to detect these cryptic species tremendously, no matter how many there are,” said co-author and research assistant scientist at UF, Sergio Balaguera-Reina.
The eDNA advancements allow wildlife officials to detect invasive snakes whether they can see them or not.
In order to detect minute amounts of DNA, researchers start with, say, a water sample, filter it, then put it in a solvent that they ֱ over a plate about the size of a smartphone.
That plate has 20,000 very small dimples on its surface. The equipment then analyzes each of the dimples. “By doing that you can detect very trace amounts of nucleic acids, or DNA,” Miller said.
All this micro technology is devoted to a macro problem – invasive species that are thriving in Florida and undermining native wildlife. There are 500 or so invasive species in Florida, 50 of which are reptiles. Burmese pythons, which were brought to Florida primarily through the exotic pet trade of the 1970s and ’80, have expanded their range from the southern tip of the Everglades up to areas surrounding Lake Okeechobee.
In areas were they dominate, mammal sightings drop by 98%. The longest ever captured in Florida measured 19 feet, and biologists have documented a 16-foot snake swallowing a 77-pound deer.
Miller said that when wildlife officials are trying to slow or contain an invasive species, it’s all about rapid detection and rapid response. These new tests would allow wildlife officials to quickly know where pythons or other destructive reptiles, such as Argentine tegu lizards, are showing up, and then focus efforts to remove them.
“Say you’re trying to remove pythons from around a bird rookery where there are spoonbills. You still have to go back and monitor and make sure you’ve removed the snakes,” she said. This can be costly. The eDNA tests offer a cost-effective way to monitor an area over a long period of time.
MIller said the Loxahatchee Wildlife Refuge, which sits between the Everglades Agricultural Area and the western suburbs of Palm Beach County, is a good example of how and where this technology could be used.
She said there is currently not an established python population there. But periodic soil and water sampling by land managers could tip them off if the snakes show up. Or they could do DNA collection anywhere they think they had a sighting.
She said the UF lab can run the eDNA analysis in a day, so land managers from all over the state could send them staples.
She plans to create a grid eDNA testing effort through the interior regions of the Loxahatchee Wildlife Refuge, among the very remote tree islands, and sample systematically to see if they invasive DNA. At some point in the future, she hopes to use drones to reach the most remote spots. If they find a python hot spot, they can concentrate removal efforts.
She currently has camera traps out among the tree islands to get a baseline of population densities of mammals such as bobcats, raccoons and opossums — all prime python meals. If mammals drop off, she can then use the eDNA tests to confirm a python invasion and beef up removal efforts.
Miller said that wildlife managers could customize the tests to look for other species, including native species. Testing over a wide area might show a broad area of egg-eating tegu lizards and a shrinking presence of birds.
Frank Mazzotti, co-author and professor of wildlife ecology at UF, said that they plan to add other species to the detection roster, including fish such as Asian swamp eels and bullseye snakeheads. He said UF also plans on creating a regional multi-species sampling network that will allow early detection of invasive species.
The goal would be rapid response to new invasions. The next step is testing in the field. Miller has tagged snakes in the eastern Everglades that she can locate via telemetry. They’ll use the eDNA kits around those snakes to see how close they have to be to a snake to pick up DNA, or how weather and time affect the tests.
Once those refinements are done, they’ll implement the technology in the field with the South Florida Water Management District.
He said they also want to evaluate removal efforts, especially in areas of the Comprehensive Everglades Restoration Plan, where the state and federal government have spent billions to restore Everglades water flow and ecosystems to a more natural state.
The presence of pythons raises the question: Is it really restoration if pythons dominate the ecosystem? “That depends on your view of restoration,” Miller said. “But to me, no it’s not. It doesn’t help to have it pristine for a species that was never intended to be here.”
Bill Kearney covers the environment, the outdoors and tropical weather. He can be reached at bkearney@sunsentinel.com. Follow him on Instagram or on X .
