Environmental DNA Sampling Strategies in Lentic and Lotic Systems

Environmental DNA is a promising new tool that has successfully been applied to detecting aquatic species, but we have much to learn about how to optimally incorporate it into monitoring programs. As with any sampling tool, the reliability of occupancy estimates based on eDNA is dependent on understanding the factors that affect detection probabilities. To investigate these relationships, we used eDNA detections and environmental covariates in an occupancy modeling framework to identify site characteristics that most influenced the likelihood of detecting fish and amphibians in streams and ponds.  We then designed sampling strategies that incorporated those factors to maximize detection probabilities.  We found that pond size had the greatest influence on detection probabilities for Chiricahua leopard frogs, while pond water temperature was the most important factor for American bullfrogs. Detection probabilities for bull trout were influenced by sampling location within the stream channel, with greater probabilities in depositional areas of the stream with slower current velocities. This information allowed us to improve species-specific sampling strategies by increasing the spatial distribution of sampling sites or adjusting the number of sample replicates.  Our results suggest that optimal eDNA sampling strategies may need to be tailored to specific aquatic systems or target species.