Effectiveness Monitoring in the Middle Fork John Day Intensively Monitored Watershed

We will evaluate female reproductive success using genetic parentage analysis in which a random sample of out-migrating smolts captured at the MFJD screw trap will be genetically assigned to female adults sampled from spawning locations. This approach is similar to Relative Reproductive Success (RRS) studies, which typically compare the average number of juveniles/spawner among crosses of natural origin and hatchery origin spawners. However, these studies typically sample adults at weirs and do not relate specific adults to specific spawning locations, whereas we would sample post-spawn adults from spawning locations and compare juveniles/female as a function of where they spawned. Please see attached project proposal for a list of questions to be answered.



Results from parr captured across the MFJD in 2021 and paired to adults sampled from spawning locations in 2020 provide an example of the analyses and metrics that can be achieved with the proposed study. However, the approach we previously implemented – sampling over 3000 parr across mainstem and tributary sites – requires substantially more sampling effort and it is difficult to obtain a random sample of the population. Since the MFJD screw trap is located downstream of the parr rearing extent, we expect it to better represent a random sample of the juvenile population.



Intensive surveying and sampling of adult chinook carcasses will occur each fall for approximately one month from mid-September through mid-October with the goal of sampling as many individual carcasses as possible. Tissue samples will be taken from all recovered carcasses, and we expect approximately 100-300 carcasses to be sampled each year depending on run size. The location of a recovered carcass will serve as a proxy for spawning location and used as the origin location for smolts subsequently paired to a given carcass.



Out-migrating smolts will be sampled during annual outmigration events occurring in the spring and fall. Oregon Department of Fish and Wildlife operates a screw trap below the chinook spawning extent in the MFJD – the operation of this trap provides an opportunity to leverage ongoing efforts to efficiently collect genetic samples from a significant portion of smolts from a given brood.



PCSRF funds administered through this award will be allocated towards wages for technicians employed by the North Fork John Day Watershed Council to assist with 2024 fall carcass sampling, for supplies and equipment necessary for carcass and smolt sampling, for costs associated with genotyping tissue samples (e.g., supplies and technician wages) and performing genetic analyses (geneticists salary). The latter – genotyping and genetic analysis – will constitute the primary expenditure for PCSRF funds and is reflected in the attached budget. All genetics work will be performed by the CRITFC Genetics Lab (Hagerman, ID). CTWS, CRITFC, and ODFW, will each provide field personnel to complete carcass and smolt sampling as in-kind contributions.



Worksite #1: Middle Fork John Day River (MFJDR) -

Propose to trap (using non-PCSRF funds) and fin clip (using PCSRF funds) ~2500-3000 spring Chinook salmon smolts at the Ritter, OR ODFW trap site between fall of 2024 and spring of 2025. Genetic samples (~1000-1500) will be taken from adult female Chinook salmon carcasses in fall 2024 and additional genetic samples (~2500-3000) will be taken from smolts between fall of 2025 and spring 2026 (using PCSRF funds). Carcass samples have previously been collected from females in 2023 (using non-PCSRF funding). Fin clips from smolts and adults will be stored for genotyping and genetic analysis (using PCSRF funds) to pair adult female carcasses encountered on spawning surveys to smolt captured at the Ritter, OR screw trap. Water temperature and hydrologic data collected by partner agencies will be leveraged for analysis of data collected via PCS

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.