Identifying Under-Ice Overwintering Locations of Juvenile Chinook Salmon by Using Environmental DNA

Abstract The detection of fish by using environmental DNA (eDNA) analysis has been shown to be more cost-effective than traditional sampling methods are in certain situations, but this method has not been assessed under extreme winter conditions. We conducted a multiyear pilot study to test the effectiveness of eDNA for detecting fish under ice. In the spring of 2016, 2017, and 2018, we sampled for juvenile Chinook Salmon Oncorhynchus tshawytscha in the Tanana Flats (Alaska, USA) by using minnow traps and by using eDNA in the spring of 2017 and 2018. We used traps at 97 sites and analyzed eDNA that was isolated from water samples at 36 sites, using an established, species-specific quantitative polymerase chain reaction (qPCR) assay for Chinook Salmon. We detected Chinook Salmon by using eDNA at 12 of the 36 eDNA-sampled sites but did not capture any live juveniles in the minnow traps. Assuming that positive eDNA detections are reliable indicators of recent fish presence, we found that eDNA can be a more efficient and cost-effective alternative for monitoring aquatic communities under extreme winter conditions. Based on our experience, including eDNA-based screening of target sampling sites could prove to be a significant boost to the effectiveness of fish monitoring in remote and challenging habitats.