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 groups 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.



This project contributed towards understanding of how spring Chinook salmon fry utilize habitat following restoration activities. Over the course of the project, carcass samples from 2023 were successfully paired with fry captured during the 2024 emergence period using genetic parentage analysis. Sampling was conducted at 26 stratified sites across 27 stream miles, capturing data on fry dispersal distance, habitat use, and floodplain inundation. Preliminary results provide insight into how restored floodplain areas are being utilized by fry and how factors like redd location, stream flow, and restoration status influence juvenile survival.



This research effort, carried out collaboratively by CTWS, ODFW, CRITFC, and NFJDWC, directly supports evaluation of restoration effectiveness within the Middle Fork John Day Intensively Monitored Watershed. Findings will help restoration practitioners refine future project designs to maximize juvenile habitat accessibility and productivity. By linking habitat use to survival outcomes and reproductive success, the project enhances the ability to adapt restoration strategies in response to changing flow regimes and cl

The CTWSRO Fisheries Habitat Programs 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.