Cooperative Fish and Wildlife Research Units Program: California
Education, Research and Technical Assistance for Managing Our Natural Resources

California Project

Comparison of standard and eDNA methods for estimating Chinook Salmon smolt abundance in the Klamath River (CA)

October 2018 - April 2020


Participating Agencies

  • National Fish & Wildlife Foundation

The objective of this study is to compare standard and eDNA-based estimates of weekly and season totals of Chinook Salmon at the Kinsman site, Klamath River. The project will: (1) Evaluate specificity and sensitivity of existing Chinook Salmon qPCR assays and if necessary design Chinook-specific qPCR assays. (2) Generate biweekly estimates of Chinook Salmon eDNA concentration using qPCR at the Kinsman site. (3) Evaluate the Chinook Salmon eDNA plume emanating from Iron Gate Hatchery (IGH) during periods of high, medium, and low flow. At each flow level water samples will be collected at IGH and progressively downstream at 10 km intervals until the Kinsman site is reached. These data will provide insights regarding the extent to which IGH eDNA output may bias estimates of natural-orgin smolt outmigrant abundance at the Kinsman site. (4) Statistical assessment of the relationship between the weekly eDNA concentrations and Chinook Salmon smolt abundance estimated using standard methods. Our study will leverage existing smolt abundance estimates in the Klamath River at Kinsman where weekly and season Chinook Salmon estimates have been generated since the early 1990s. The data from standard monitoring will provide a foundation for comparison of the eDNA-based estimates. Use of eDNA approaches for determining smolt abundance during seaward migration has at least three distinct advantages in comparison to standard monitoring. First, eDNA approaches are non-invasive in the sense that they do not involve direct handling and/or tagging of Chinook Salmon smolts or cause delays in their downstream migration. Second, eDNA approaches are less likely to be constrained by high water flows and debris that can result in flawed sets and/or make it dangerous for staff to implement field survey methods. Third, eDNA-based methods may provide a less expensive alternative for salmon abundance monitoring than standard methods. This study will provide eDNA-based estimates of weekly smolt abundance of Chinook Salmon within the mainstem of the Klamath River, but it could also serve as a foundation and justification for applying the eDNA methods in other areas within the Klamath-Trinity Basin and across the entire Pacific northwest where similar approaches are applied for salmon. Further, if the approaches developed herein are proven effective for monitoring Chinook Salmon, they could be easily expanded for monitoring of other commercially, recreationally, and tribally important species, such as Coho Salmon, steelhead, green sturgeon, and Pacific lamprey. Also, the same water samples collected for determination of salmon abundance could also be used for disease monitoring in the mainstem Klamath River, which is currently evaluated, in part, using environmental DNA analysis (Hallett and Bartholomew 2006). If successful, our project will generate eDNA-based estimates of Chinook Salmon smolt abundance that could be used to supplement or potentially replace standard methods in the future. Our project results should be of interest to two distinct groups of scientists. First, federal, state and tribal resource management and conservation groups should receive benefits from our anticipated project results: empirical information concerning the abundance of Chinook Salmon smolts using a non-invasive tool that is potentially less expensive than standard methods. Second, molecular ecologists should be interested in our project results, especially our application of eDNA monitoring for determination of aquatic species abundance during migration.