eDNA Monitoring of Fish Re-Colonization after Klamath River Dam Removal

Project Objective: This project will monitor for various anadromous fish species in tributaries and the mainstem Klamath River using environmental DNA (eDNA) from water samples. This project is intended to monitor the re-colonization of the Klamath River by anadromous fish after dam removal.



Project Description: The Klamath River Renewal Project (KRRP; also known as the Lower Klamath Project) represents an effort to remove four hydroelectric dams along the Klamath River in California and Oregon. The removal of the four dams and subsequent restoration of the former reservoir footprints to a riverine condition is intended to reconnect over 640 kilometers of habitat for migratory anadromous fishes, restore native vegetation across nearly 1,000 hectares of previously drowned land, and improve water quality in the Klamath River Basin.



The KRRP objectives include restoration actions that will benefit the distribution and abundance of economically, recreationally, and culturally valuable organisms following a return to riverine conditions and an ecosystem shift towards native biodiversity across a vast landscape. These species include Chinook Salmon, Coho Salmon, Steelhead Trout, and Pacific Lamprey among many others. Environmental DNA (eDNA) has been shown to be a cost effective non-invasive, and effective tool for monitoring the distribution of aquatic species at broad geographic scales, and specifically after large-scale dam removals.



Prior to dam removal, Resource Environmental Solutions (RES) and Genidaqs (GIQ) staff collected, filtered, and preserved the genetic material within over 400 water samples from 45 mainstem and tributary monitoring locations, across 114 river kilometers in California and Oregon. These monitoring locations were selected across the Klamath River Renewal Project (KRRP; also known as the Lower Klamath Project) to include sites with a range of characteristics as well as control sites both in and out of the impacted watersheds for a Before-After-Control-Impact (BACI) monitoring design. All samples were stabilized following protocols for the long term storage and viability of both eDNA and environmental RNA (eRNA), were collected with sufficient replicates to run 200 individual analyses per site and are suitable for analyses including: detection of rare or cryptic species, distribution and relative abundance of aquatic organisms, community composition of aquatic organisms through eDNA metabarcoding, and subsequent population demography inference through eRNA analysis.



The Yurok Tribe is proposing to replicate this sampling strategy in 2025 and 2026 to monitor the re-colonization of the Klamath River and Tributaries upstream of Iron Gate Dam by anadromous fishes. Target species would include Coho Salmon, Chinook Salmon, and Steelhead Trout. We would use the pre-dam removal dataset collected by RES to ascertain changes in the genetic signatures of fish species in water samples via Environmental DNA analysis. This project would be carried out in cooperation with Resource Environmental Solutions, Genidaqs, and other KRRP partners. Priority sites may be chosen as sampling locations based on funding availability.

Project Benefit: Information gathered during this project will be used to help monitor the re-colonization of the Klamath River by anadromous fishes upstream of Iron Gate Dam. This data can be utilized to inform numerous research, monitoring, management, and policy activities and actions.