Persistence of Reptile DNA in a Terrestrial Substrate: A Case Study Using the Eastern Indigo Snake

Abstract

Environmental DNA (eDNA) analysis of terrestrial substrates, such as soil and sand, is a rapid and potentially cost-effective way to monitor rare wildlife species. A promising use-case in the southeastern United States is provided by the eastern indigo snake (Drymarchon couperi), for which accurate monitoring has been challenging due to large home ranges and low-density populations. However, knowledge gaps regarding eDNA deposition and persistence in this system currently limit our ability to apply eDNA sampling effectively at the landscape scale. To overcome some of these gaps, we used an optimized soil and sand eDNA extraction protocol and species-specific qPCR assay to conduct a full factorial experiment of eastern indigo snake DNA detection in sand as a function of the duration of snake presence and time since snake removal. We then used these data and a generalized linear mixed model to predict detection probability. Of the 224 total experimental samples, 68 (30.4%) tested positive for eastern indigo snake eDNA. Our model predicted that, with long periods in the enclosure and sampling soon after snake removal, eastern indigo snake eDNA is detectable 68.7% of the time. Eastern indigo snake DNA was detectable in as little as 100 s of snake presence in the enclosure (Pr = 21.1%) and for as long as 10 days after snake presence (Pr = 27.7%). These results suggest that DNA sampling in terrestrial systems may be an effective tool for increasing the temporal window of rare snake detection and a useful complement to existing sampling methods for eastern indigo snakes.