Designing environmental DNA surveys in complex aquatic systems: Backpack sampling for rare amphibians in Sierra Nevada meadows

Abstract

Surveys for environmental DNA (eDNA) can provide an efficient and effective means of detecting aquatic organisms in various types of aquatic systems. In the summer of 2017, the efficacy of a new, integrated eDNA backpack sampler to detect two native amphibians (Rana sierrae and R. cascadae) at risk was tested in complex mountain meadows in California. Samples were collected at 65 locations in 15 meadows where the target species were known to be present or were historically present. Collection and preservation of individual samples took less than 10 min on average. Environmental DNA analysis methods detected each species at all meadows with visual detections (N = 11) except one with one frog seen away from sampling sites. Bayesian multi-scale occupancy modelling indicated that conditional detection probabilities at the sample level ranged from 0.30 (CL 0.07–0.65) at meadow heads where no frogs were observed during visual surveys to 0.93 (CL 0.77–1.00) at the meadow foot with at least one frog observed in the vicinity. Compared with visual surveys, eDNA methods more frequently detected amphibians at the sampling-location scale. The improvement in detection using eDNA methods was most pronounced for samples collected at the downstream ends of meadows where water converges, where eDNA methods detected target species at 10 of 11 occupied meadows. These results suggest that the addition of eDNA sampling to visual surveys in mountain meadows will improve survey accuracy and increase the probability of detecting rare frogs.