Determining accurate species distribution is crucial to conservation and management strategies for imperiled species, but challenging for small populations that are approaching extinction or being reestablished. We evaluated the efficacy of environmental DNA (eDNA) analysis for improving detection and thus known distribution of Chinook salmon in the Methow and Okanogan Sub-basins of the UpperColumbia River, Washington, USA. We developed an assay to target a 90 base pair sequence of Chinook DNA and used quantitative polymerase chain reaction (qPCR) to quantify the amount of Chinook eDNA in 1-L water samples collected at 48 sites in the sub-basins. We collected samples once during high flows in June and again during low flows in August 2012. Results from eDNA surveys were compared to the current known distribution of Chinook. Using eDNA methods, the probability of detecting Chinook given that they were present was 0.83. Detection probability was lower (p = 0.69) in June during high flows and at the beginning of spring-Chinook migration than during base flows in August (p = 0.98). Based on our triplicate sampling, we had a false-negative rate of 0.07, suggesting that fewer replicates could be collected at a site while maintaining reasonable detection. Of sites that tested positive during both sampling events, there was a higher mean concentration of eDNA in August than in June, probably because of reduced discharge, more fish, or both. As expected, eDNA concentration increased from upstream to downstream, but only in one tributary and this pattern varied considerably among streams suggesting that other factors influence the spatial pattern of eDNA concentrations. For example, highest eDNA concentrations were found at sites with water temperatures centered around the optimal rearing temperature for Chinook and decreased rapidly around the approximate lethal temperature for the species. These results demonstrate the potential effectiveness of eDNA detection methods for determining landscape-level distribution of anadramous salmonids in large river systems.
