Scientists have created a groundbreaking tool that helps locate invasive species to support eradication efforts.
Researchers at the University of Florida have created an innovative tool designed to enhance the protection of Florida against invasive species: a DNA-based environmental monitoring test that can accurately identify their past locations, facilitating eradication measures.
When a nonnative species infiltrates an ecosystem, it often becomes too late for removal, leading to a focus on containment or long-term management solutions. Both options incur significant costs in terms of the impact on native wildlife and required funding, according to Melissa Miller, the lead author of the study and an invasion ecologist at the UF/IFAS Fort Lauderdale Research and Education Center (UF/IFAS FLREC).
“Our aim with this innovative eDNA sampling tool is to enhance the effectiveness of invasive species management by enabling early detection and swift removal of nonnative species,” she stated.
This testing method, known as a tetraplex digital PCR assay, allows scientists to analyze water or soil samples for the rapid and accurate identification of invasive snakes, including Burmese pythons, northern African pythons, boa constrictors, and rainbow boas, utilizing environmental DNA—referred to as eDNA—collected from natural habitats. The test is capable of detecting four invasive snake species at once.
Environmental DNA (eDNA) is the genetic material released by organisms into their surroundings. In a study published in the journal Ecology and Evolution, researchers from UF’s Institute of Food and Agricultural Sciences (UF/IFAS) highlight this as a major advancement in the detection of invasive snakes and a valuable tool for preserving Florida’s ecosystems.
“Cryptic species, like most snakes, present challenges when they are introduced outside their natural range due to their low detectability, even when present in high numbers. This new method significantly enhances our ability to detect them, regardless of their population density,” stated Sergio Balaguera-Reina, co-author and research assistant scientist at UF/IFAS FLREC.
Florida hosts over 500 nonnative species, predominantly reptiles. Over 50 nonnative reptile species have become established in the state, many of which pose substantial threats to agriculture, native ecosystems, public safety, and the economy.
Current monitoring techniques rely on visual inspections by researchers, which frequently overlook elusive and secretive invasive constrictors. It is estimated that traditional surveys identify fewer than 5% of Burmese pythons. In contrast, the newly developed tetraplex assay enables the detection of DNA traces from these snakes even weeks after they have vacated an area.
This innovation provides wildlife managers with an essential tool to confirm the presence of these hidden species and evaluate the effectiveness of removal operations. “While eDNA sampling has been used previously to detect non-native wildlife, the advantage of our approach is that it allows for the sampling of multiple target species in one go, helping natural resource managers save costs linked to surveying multiple non-native species in affected ecosystems,” Miller explained.
“Thanks to the high accuracy and specificity of this invasive constrictor snake detection method, resource managers can promptly and confidently apply effective management strategies like removal operations,” Miller added.
The test is designed to work efficiently in Florida’s diverse and challenging environments, from the thick habitats of the Everglades to urban areas where nonnative constrictors are found. This DNA-based strategy enables wildlife managers to run programs that monitor several species simultaneously, prioritize response actions, and ultimately reduce the ecological impact of these snakes on Florida’s ecosystems and efforts for Everglades restoration.
The creation of this tool required extensive work and significant technical advancements to ensure accurate identification of each targeted snake species’ DNA.
“The first step was to create the molecular test, which essentially combines four tests into one,” said Brian Bahder, a senior author of the study who developed the eDNA methodology and is an associate professor of vector entomology at UF/IFAS FLREC. “Each test focuses on a different snake species and is carefully designed to detect DNA from the Burmese python, northern African rock python, rainbow boa, and boa constrictor, ensuring there is no overlap in detection among the species.”
Bahder, whose expertise mainly involves detecting lethal bronzing in palm trees, clarified that the basic process of molecular testing is consistent across various organisms, with the primary difference being the DNA sequences, making many of these techniques easily adaptable.
After the researchers successfully developed the molecular test, they conducted controlled experiments using known DNA concentrations in water samples. They utilized a vacuum pump to concentrate the DNA onto a filter, subsequently testing it to confirm they could extract the DNA successfully and achieve accurate results.
Next, an experiment involved placing a Burmese python in water and collecting samples at different time intervals to validate the method’s effectiveness. The data helped estimate the amount of snake DNA that would be detected in the water if sampled close by. A field experiment further demonstrated that snake DNA could be found in soil where a snake had rested, even two weeks after its departure.
“These concentration estimates represent initial steps in a broader monitoring endeavor, with further tests needed to understand how time, distance, and environmental factors influence DNA detection rates,” stated Bahder. “Ultimately, this technology aims to assist in monitoring and locating these invasive snakes, validating removal actions undertaken.”
The new assay is consistent with ongoing efforts from state and federal agencies, which have allocated over $10 million to manage Burmese pythons from 2004 to 2021.
“For successful detection and monitoring of invasive wildlife, quick recognition and accurate identification of nonnative species are crucial,” emphasized Miller.
The UF team intends to investigate the tool’s potential further, planning to expand the assay to include more invasive species and applications for monitoring ecological restoration outcomes.
“Two significant next steps are essential for maximizing the benefits of this eDNA analysis. First, we aim to include more species conducive to identification through the tetraplex digital PCR assay, particularly fish species like Asian swamp eels and bullseye snakeheads,” remarked Frank Mazzotti, co-author and wildlife ecology professor at UF/IFAS FLREC. “Secondly, to fully utilize this innovative methodology, we plan to create a regional multi-species sampling network aimed at early detection and rapid response to new invasions, as well as assessing the success of removal efforts within the framework of the Comprehensive Everglades Restoration Plan.”
