Optimal survey designs for environmental DNA sampling

Environmental DNA (eDNA) sampling is a promising tool for monitoring cryptic species. Numerous studies have demonstrated that eDNA sampling can achieve higher detection rates than traditional monitoring techniques, such as trapping; however, the consequences of that sensitivity for survey design requirements and resulting survey costs have not been investigated. We demonstrate how site occupancy detection models and optimal survey design methods can be used to evaluate the cost-efficiency of eDNA sampling vs. traditional survey methods. We apply these approaches to two datasets—one in which eDNA sampling and trapping were conducted simultaneously (paired dataset), and another in which sampling methods were independently deployed (unpaired dataset)—to assess the cost-efficiency of eDNA sampling for detecting a freshwater mammal: the platypus Ornithorhynchus anatinus. Conditional probabilities of platypus eDNA being captured in a single water sample (paired dataset: 0.838, unpaired: 0.879), and detected in a single water sample by qPCR (paired: 0.892, unpaired: 0.858), were higher than the conditional probability of detecting a platypus with a single trapping visit (paired: 0.470, unpaired: 0.219). eDNA sampling was more cost-efficient than trapping, regardless of whether the management objective was to (1) minimize the survey budget needed to achieve a particular asymptotic variance of the occupancy estimator, or (2) minimize the survey budget needed to detect a change in occupancy over time. Site occupancy detection models coupled with optimal survey design methods provide a powerful means with which to compare the sensitivity and cost-efficiency of eDNA sampling vs. traditional sampling methods.