Middle Fork John Day Effectiveness Monitoring – Chinook Fry Genetics Analysis

Declining trends in certain salmonid populations, particularly spring Chinook salmon and summer steelhead, have been documented in watersheds within Tribally ceded lands in the John Day basin. These declines are believed to be the cumulative result of a number of factors, including the blockage of key migration routes by dam construction, rising water temperatures due to climate change, and legacy effects of degradative land management practices over the last century, among other causes. As part of the greater effort to mitigate these deleterious effects and reverse the damage to local salmonid populations, the Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO) Fisheries Habitat Program has developed and implemented a comprehensive watershed restoration strategy for the ceded lands of the John Day Basin. These strategies are centered around completing in-stream and riparian habitat improvement projects to restore ecosystem function and create key environmental conditions and features (e.g., reduced sediment loads, more spawning gravels, thermal and hydraulic refugia, greater stream channel complexity) necessary to support both anadromous and resident salmonids through all of their freshwater life history stages. Habitat restoration effectiveness monitoring is a vital component of the watershed restoration strategies. Such monitoring will answer key questions identified in project-specific monitoring plans regarding projects, inform future restoration decisions, and identify adaptive management opportunities.



The Middle Fork John Day (MFJD) Intensively Monitored Watershed program was established in 2008 with the primary goal of evaluating restoration efforts for summer steelhead and spring Chinook salmon habitat. CTWS has been a key member of this collaborative since its inception and have benefitted from the group’s collective efforts in evaluating restoration success, which includes significant investigation into tribally implemented projects on multiple CTWS-owned conservation properties along the MFJD. One of the recent efforts conducted by the IMW has examined spatial patterns of chinook fry (spring sampling) and parr (summer sampling) dispersal from spawning locations by genetically linking adult carcass tissue samples to their progeny. This has allowed researchers to describe when and how juvenile chinook distribute amongst available habitat relative to their emergence location and in the context of completed restoration efforts. In addition, they could assess dispersal patterns and the relative number of progeny assigned to individual female adults, including evaluating how habitat conditions, female adult characteristics (e.g., size, age), and location of spawning relate to female reproductive productivity.



The proposed study through this award seeks to build on and expand these efforts by continuing to study fry dispersal relative to emergence location, habitat utilization, and restoration driven floodplain inundation. From this proposal, we plan to evaluate two years of fry dispersal (2024 and 2025) and additionally, to evaluate female relative productivity from at least one spawn year (2023). We will use genetic parentage analysis at the fry life stage to determine dispersal and habitat use and the smolt life stage to determine female reproductive success. We will evaluate fry dispersal patterns and habitat use across the Spring Chinook spawning universe in the Middle Fork John Day using genetic parentage analysis by pairing samples collected from adult carcasses in 2023 to fry caught in 2024 and 2025.This proposal pairs with additional funding that will allow us to conduct these studies over several years which should more accurately describe dispersal and reproductive success, but also possible annual variation. This will be a collaborative effort implemented in tandem by core members of the Middle Fork IMW including CTWS, ODFW, CRITFC, and the NF John Day Watersh

The CTWSRO Fisheries Habitat Program’s comprehensive watershed management strategy seeks to benefit target salmonid species by 1) directly generating vital spawning and rearing habitat; 2) directly mitigating deleterious environmental effects; and 3) restoring ecosystem processes and function. Monitoring salmonid productivity is paramount in assessing the performance of restoration efforts and guiding the implementation of future projects. This effort contributes to maximizing the realized benefits of restoration to target salmonids and ensures that restoration resources are used as efficiently as possible in achieving fisheries goals.