Searching for Indigo Snake DNA


An indigo snake track leading into a small tortoise burrow. – Ben Stegenga

A fundamental goal of wildlife conservation is to identify where animals occur on the landscape. Good data describing species occurrence can be used to guide habitat protection efforts, identify areas where habitat management can be implemented, and monitor the status of imperiled species. However, many species (particularly reptiles and amphibians) are notoriously difficult to locate, even in places where populations are known to occur. Low detectability can be influenced by many factors. Many species spend large portions of time underground or in refugia and simply cannot be observed with standard survey techniques. Rare species also frequently occur at low densities, both at local and landscape scales, making it difficult to catch individuals at occupied sites and to locate previously unknown populations. A host of other behavioral and ecological factors can influence the detectability of wildlife, and few survey techniques are immune to the challenges of low detectability. The inability to detect animals even when they are present is a critical challenge in wildlife research and significant efforts have been made to improve our ability to locate difficult to detect species.

Indigo snakes are a classic example of a species where low detectability challenges our ability to make informed conservation decisions. Individuals have large home ranges and move widely across the landscape during most of the year, occurring at low densities that make targeted surveys ineffective. In the northern portion of their range, indigo snakes can be surveyed relatively reliably during the winter months when they are forced to spend time on sandhills with Gopher Tortoise burrows. However, even at the best survey sites, detection probability is rarely above 50% (i.e., half of surveys will turn up nothing even though snakes are there). At sites with small populations or poor habitat quality, detection probability can be much lower. Similarly, as you move south in the indigo snake range, indigo snakes become increasingly difficult to find, even during the winter months. Effectively monitoring indigo snake populations in most of Florida is exceedingly difficult.

An indigo snake observed on a survey in southern Georgia. – Ben Stegenga

With this in mind, we recently started a new project to examine whether Environmental DNA (eDNA) could offer a new technique to assist in surveys for indigo snakes. Surveying for wildlife populations using eDNA approaches has become increasingly common in recent years (e.g., Rees et al. 2014). As animals move through their environments, DNA is constantly left behind in the form of skin cells, saliva, waste products, or other excretions. This DNA can then be extracted from water or soil samples and used to identify species presence. These techniques have been most commonly applied in aquatic environments where the DNA can diffuse from point sources to the entire water body. Many amphibian studies have used eDNA to locate breeding sites (McKee et al. 2015). Recent efforts have applied eDNA approaches to terrestrial environments. For example, researchers have found that eDNA found in soil samples can be used as an effective sampling approach for the imperiled Louisiana Pinesnake (Pituophis ruthveni) (Katz et al. 2020). While not perfect, advances in genetic techniques have expanded the possibilities for eDNA-based monitoring projects.

The current indigo snake project will follow a similar path to the studies with Louisiana Pinesnakes. The project is being funded by the Department of Defense (DoD) and is a collaboration with DoD, PARC, Ft. Stewart, the National Genomics Center, the Orianne Center for Indigo Conservation (OCIC), the U.S. Fish and Wildlife Service, and the University of Illinois. It is a proof of concept aimed at identifying the utility of using eDNA sampling techniques to locate indigo snakes in the wild. The project has two parts: an experimental trial using captive indigo snakes at the OCIC and a test of sampling methods in wild indigo snake populations. We will also compare the costs and time commitments of eDNA sampling approaches with visual encounter and camera trap survey designs that are already being used to monitor indigo snakes.

A captive indigo snake in an experimental enclosure at the OCIC. – Michelle Hoffman

The initial phase of this project focuses on testing and refining the eDNA sampling methodology using captive snakes at the OCIC. During late summer and fall, captive snakes were placed in outdoor enclosures for varying lengths of time. Sand samples were then collected at several time intervals after the snake was removed from the enclosure. This sampling design will allow us to estimate the effects of exposure time of the animal on detectability of the eDNA in the environment. Preliminary results indicate that indigo snake eDNA can be detected from sand exposed to indigo snakes but that the DNA rapidly degrades over time. We are now moving into the field portion of the project and will be collecting samples from three sites during the winter indigo season. During the field portion of this project, we will examine whether eDNA is more likely to be detected from inside tortoise burrows, which are sheltered from the sun and warm temperatures. We expect to pick up a lot of sand over the next several months!

Having indigo snakes in captivity at the breeding colony allows research projects to leverage those snakes to answer questions that would otherwise require additional manipulations of wild individuals. – Michelle Hoffman

Overall, this is an exciting project that could have significant benefits for indigo snake conservation in the future. Identifying techniques to improve the detection of indigo snakes would allow for better habitat protections and more consistent monitoring of snakes, especially in the southern portion of their range. We are looking forward to collecting eDNA samples during the upcoming indigo snake sampling season. Stay tuned for future updates on this project!



Literature Cited

Katz, A.D., L.R. Harper, E.C. Sternhagen, S.E. Pearce, C.A. Melder, J.H. Sperry, and M.A. Davis. 2020. Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni). Environmental DNA 3:409–425.

McKee, A.M., D.L. Calhoun, W.J. Barichivich, S.F. Spear, C.S. Goldberg, and T.C. Glenn. 2015. Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands. Journal of Fish and Wildlife Management 6:498–510.

Rees, H.C., B.C. Maddison, D.J. Middleditch, J.R.M. Patmore, and K.C. Gough. 2014. REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology. Journal of Applied Ecology 51:1450–1459.