Using Environmental DNA for Burmese Python Detection Probabilities and Range-Delimitation in Southern Florida

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Current tools for detection of Burmese pythons in South Florida have resulted in low detection rates. Environmental DNA - eDNA - has shown to be effective at detecting these invasive snakes, and can help to determine range limits for the species, information that is critical for management and control efforts. 

 

Burmese Python are difficult to detect
Due to their cryptic nature, Burmese Python are difficult to detect.

The Science Issue and Relevance:  Improving the probability of detecting invasive giant snakes is vital for the management of emerging or established populations. Detecting invasive species at low densities or prior to establishment as a population is critical for successful control and eradication. Burmese pythons occupy thousands of square kilometers of habitats that are difficult to access. Current tools for detection and control of Burmese pythons in Florida, e.g., detector dogs, remote sensing, attractant traps, “Judas snakes”, etc., have yielded low detection rates with varying degrees of success. Estimation of detection probabilities have been inadequate using traditional tools such as visual searching or trapping. This is problematic because large constrictor snakes are detrimental to native species, especially imperiled or at risk wading birds in the Everglades.

Environmental DNA (eDNA) has been shown to be effective at detecting Burmese pythons where traditional and novel detection methods have failed. Environmental DNA originates from cellular material shed by organisms (via skin, excrement, etc.) into water and can be used for species identification. Environmental DNA methods have been shown to be time and cost effective in a number of systems and may be preferable to traditional detection methods for constrictor snakes. Determining the species’ true range-limits would be beneficial for management and control before they are able to significantly impact additional native species and systems.

Environmental DNA (eDNA) has been shown to be effective at detecting Burmese pythons
Environmental DNA (eDNA) has been shown to be effective at detecting Burmese pythons.

 Methodology for Addressing the Issue: To address the true range-limits and provide occurrence and detection estimates for the invasive Burmese python population, comprehensive surveys will be conducted across the northern limit of the range and in invaded habitats to gather more accurate detection and occurrence estimates. A droplet digital PCR platform (ddPCR) will be used to detect a single molecule of DNA from an environmental sample, which significantly enhances accuracy and precision compared to traditional eDNA detection methods. To detect individual species, three species-specific markers (two primers and a fluorescently labelled probe) are developed and added to the samples. Filtered surface water samples are then split into ~20,000 PCR droplets, each containing the markers and, if present, a copy of the target species’ DNA. The droplets illuminate fluorescently if DNA of the targeted species is detected, with the number of illuminated droplets corresponding to the number of DNA molecules in the sample. This information can be used to accurately estimate the likelihood of a species being present or absent in the environment, thus improving effective resource actions, making inferences about distribution and movement patterns, and developing long-term management strategies. These techniques have been successfully applied to the detection of Burmese and rock pythons from southern Florida water samples and will be used for this study.

The initial phase of the study will involve designing a sampling strategy to optimize detection probability estimation. Water samples will then be taken from areas where pythons are known to be established to test the sampling plan. Once this sampling design has been finalized, water sampling surveys will be conducted in other areas throughout south Florida to obtain baseline occurrence and detection probabilities in different habitats and areas. Statistical sampling design will be developed for detection probabilities during the initial project phase. The sampling design will be used for initial field testing, with water sampling in areas with known Burmese python occurrence. After acquiring the field samples, water will be filtered/processes prior to conducting the ddPCR analysis. In the final phase of this study, system-level surveys will be conducted to help delimit the invasive Burmese python range in southern Florida and its expansion into previously uninhabited areas. Using the appropriate sampling density, sampling design will be determined to efficiently maximize python detections within the study budget.

Hunter - Water samples taken from areas where pythons are known to be established - WARC
Water samples taken from areas where pythons are known to be established

Future Steps: Assays have been developed for four other giant constrictor species (North African rock python, Boa Constrictor, and Green and Yellow Anaconda) which could be assessed to obtain baseline data on their presence throughout the south Florida. Environmental DNA has the potential to be a powerful tool for enhancing early detection of giant constrictor snakes for rapid response as well as providing a decision-support tool for long-term management strategies. Non-invasive monitoring of aquatic habitats can assist in identifying newly-colonized areas where pythons have not been previously detected, as well as movement corridors and pathways of dispersal. This information could be used to delimit a ‘boundary’ to restrain population expansion further to the north in peninsular Florida. More precise information on the presence of harmful constrictors in critical habitats can inform spatiotemporal assessment of risk to imperiled native species (i.e., ground-dwelling birds, Florida panther), and potentially allow for targeted removal efforts prior to major ecological and economic impacts. Environmental DNA tools can also assist with short or long term monitoring to determine whether control or eradication efforts have been successful.

Related Project(s):

  • Comprehensive Everglades Restoration Project, Greater Everglades Priority Ecosystem Science Initiative