Cryptic Tools for Cryptic Species: Using Innovative eDNA Sampling to Find the Secretive Sharp-tailed Snake

By Laura Matthias and Carrina Maslovat

Ecological reserves protect unique species or ecosystems, and do not allow intensive recreation, making them appropriate places for education and research projects. On the south-facing Garry oak slopes of the Mount Tuam Ecological Reserve, a team of scientists have been using environmental DNA (eDNA) to develop a protocol to find the secretive, endangered Sharp-tailed snake.

eDNA is genetic material that organisms leave in the environment from things like skin, feces or mucus. eDNA sampling is a fairly new tool that has been used mainly to detect rare aquatic species from water samples. Our team is using a new approach to research its potential for detecting terrestrial species.

The Sharp-tailed Snake is a small (20 to 30 cm), slender, reddish-brown, non-venomous snake found in western North America. It is elusive because it spends almost all of its life underground. It lives in loose woody debris or talus slopes in rare Garry oak ecosystems, and mates and lays its eggs underneath the surface of the soil. Virtually nothing is known of their underground habitat use.

Because of its cryptic subterranean nature, finding this snake can be challenging and time-consuming. Traditionally, surveys have been done using Artificial Cover Objects (ACOs), which are small asphalt shingles. The shingle boards are placed on the ground and the snakes will move under the ACOs to warm up on sunny days. Turning over the boards is a good way to find a snake if you are persistent in checking for them, but it can take years of checking a site before even one snake is found.

In 2018, field biologists Laura Matthias and Carrina Maslovat began a project that coupled traditional survey methods (looking under ACOs placed in the field) with innovative eDNA sampling to investigate whether eDNA could be used as complementary, non-invasive survey technique in a terrestrial environment. They worked with Dr. Caren Helbing and Michael Allison at the eDNA lab at the University of Victoria to develop a tool that can detect miniscule amounts of snake DNA. They collected eDNA samples in the field by swabbing the underside of ACOs with cotton finger cots and collecting soil samples from where snakes had previously been found.

Given the small size of the snakes and how infrequently they are found near the surface, they were not sure if we would be able to detect the remnants of their DNA from these small samples. With intensive work developing protocols that avoid contamination during collection in the field coupled with careful lab extraction and analysis, they had positive results demonstrating that they could detect DNA of the Sharp-tailed Snake in the field from both the ACO swabs and the soil samples. They were even able to detect DNA from ACO swabs and soil samples in new locations where a snake had never been observed.

Using eDNA as a survey technique is a promising new tool to help find this species. Knowing where Sharp-tailed snakes are found is essential for ensuring their habitat is protected and appropriately managed. The team will apply the novel eDNA sampling tool to search for Sharp-tailed Snakes in new locations where they have not yet been found. This technology can also be used to help detect and protect other rare, hard-to-find species.

Funding for this project was generously provided by Interdepartmental Recovery Fund, Critical Habitat Interdepartmental Program, Habitat Conservation Trust Foundation, and Canadian Wildlife Service. The team is grateful for the support and generosity of Jared Hobbs who has been instrumental in advancing the field of eDNA, and for BC Parks in supporting this research to occur in the Mount Tuam Ecological Reserve.