Environmental DNA (eDNA) sampling in streams is the collection of DNA released by a target species into the water. Scientists at the U.S. Forest Service’s National Genomics Center for Wildlife and Fish Conservation have pioneered developments in this field—including the first reliable eDNA assay for salmonid fish species, the first that distinguishes bull trout from other species of char (Wilcox et al. 2013, 2014), and the first that distinguishes among subspecies of cutthroat trout (Wilcox et al. 2015a). Detection of stream fish with eDNA is remarkably sensitive—100% detection efficiency of target species has been achieved despite order-of-magnitude changes in stream discharge (Jane et al. 2015). Field experiments indicate that detection probability of a single trout in 100 m of stream exceeds 85%, an efficiency several-fold better than one-pass electrofishing (Wilcox et al. 2016). We have also developed an easy-to-learn, field-proven eDNA sampling protocol that requires only 15 minutes of effort by a single person to collect a sample (Carim et al. 2016). Collected samples are portable, readily stored while in the field, and can be processed in the lab in as little as 3 days. The ease of use has led this protocol to be adopted by biologists from partner agencies in every western state.
Bull trout have been a focus of these eDNA surveys. The initial studies have been directed at precisely delineating the distribution of bull trout within select watersheds, as well as confirming their absence from potential habitats and discovering previously unknown populations (McKelvey et al. 2016). In 2015, we paired predictions of bull trout habitat occupancy from the Climate Shield model with an optimized eDNA protocol to survey all juvenile bull trout habitats throughout two 8-digit HUC river basins in Montana and Idaho, and to begin these surveys in 10 additional 8-digit HUC basins. In 2016–2018, we will extend this sampling to the entire range of bull trout in the U.S.