Abstract
Researchers have recently begun using environmental DNA (eDNA) sampling and analyses, a minimally invasive, sensitive, and cost-effective alternative to traditional sampling methods, to detect aquatic species. The purpose of this study is to use eDNA sampling and quantitative polymerase chain reaction (qPCR) analyses to determine the distribution and timing of juvenile Chinook salmon (Oncorhyncus tshawytscha) emigration in Auburn Ravine, Doty Ravine, and Raccoon Creek, three creeks located within the Placer County Conservation Program (PCCP) Reserve Acquisition Area in western Placer County, California. Since the 1950s the abundance of Chinook salmon in California’s Central Valley has decreased by more than 25%. Due to the decline of the species, Chinook salmon are a California species of special concern and a Covered Species under the PCCP that requires local protection, monitoring, and management. eDNA sampling was conducted weekly at four locations in each creek over an 8-week study period during March and April of 2020. eDNA was then extracted from each sample and analyzed using quantitative polymerase chain reaction (qPCR) to determine the spatial and temporal distribution of juvenile Chinook salmon eDNA in the three creeks. Additionally, warming water temperatures and spring precipitation events were expected to potentially trigger emigration, so these variables were characterized throughout the study period. A mixed effects model was then performed to determine if sampling site, date, precipitation, and/or water temperatures have a significant effect on eDNA concentrations where positive detections occurred. A post-hoc test was also performed to determine which sampling sites differed in their eDNA concentrations. Overall, eDNA was not detected at all in Doty Ravine, but it was detected in Raccoon Creek and in Auburn Ravine in all 8 weeks of samples. eDNA was detected at all 4 sampling locations in Raccoon Creek and at the 3 sampling locations furthest downstream in Auburn Ravine. The results from the mixed effects model showed that sampling site and water temperature had a significant effect on eDNA concentration throughout the study period. However, date and precipitation did not have a significant effect. Furthermore, the post-hoc analysis revealed that Auburn Ravine had significantly higher eDNA concentrations than Raccoon Creek. Based on the current published literature, this research is the first time that eDNA sampling and qPCR analyses have been used to determine the emigration timing of juvenile Chinook salmon. This work contributes baseline data that can be used for long-term monitoring efforts essential for the recovery of the species in western Placer County.