The ISRP reviewed this project favorably during the 2018 Research Project Status Review, and the project continues to make good progress toward achieving its objectives.

M&E matrix - support. As habitat projects and monitoring projects are not presented as part of an integrated proposal or plan, the need for a crosswalk to identify the linkages between implementation and monitoring is extremely important for basins or geographic areas. The ISRP is requesting a response from the Upper Columbia River Programmatic Habitat Project (201000100) to summarize the linkages between implementation and monitoring projects in the Wenatchee, Entiat, Methow, and Okanogan subbasins. During the response loop (September 24 to November 22, 2021), we ask this project to assist them in creating the summary and provide information to them about what is being monitored by this project and where and when the monitoring occurs. A map or maps of locations of monitoring actions would be helpful in this regard.

Q1: Clearly defined objectives and outcomes

Five objectives are listed in the proposal. The first three objectives are updated from the previous (2018) review period: (1) Continue to estimate relative reproductive success (RRS) for Wenatchee River spring Chinook for additional brood years through brood year 2018 (2023 age-5 returns); (2) Continue to evaluate environmental and phenotypic factors influencing RRS, including sex, age, size, run timing, holding and spawning location; and (3) Continue to evaluate second and third generation broodstock effects by evaluating the RRS of hatchery and natural fish with varying numbers of hatchery and natural grandparents. Objective 4 has been added to allow further investigation of new findings and opportunities based on genomic techniques: (4) Characterize genomic diversity in samples of hatchery and wild fish to evaluate differences in effective population size and test for genomic regions associated with fitness differences between individuals. Objective 5 has been added to ensure support for publication of results in this final phase of the project: (5) Make results available to managers in the form of annual reports and peer reviewed publications.

These objectives are clearly stated, achievable and highly relevant to the Council’s Program. Strictly speaking, they could be improved by specifying hypotheses and quantifying expected outcomes. (Objectives 4 and 5 are particularly vague in this respect.) That said, the project’s record of scientific discovery, primary publication and influence has been extraordinary, and the ISRP is satisfied with the focus and design of work being proposed in this final phase. Timelines are specified in the supporting text.

Q2: Methods

The proposal includes a brief but informative overview of the methods, but the details are documented in peer-reviewed publications. Standard procedures are being used to trap, sample, and enumerate downstream juveniles and returning adults. DNA samples are analyzed to determine genotypes at 96 SNP loci, which are used to identify the pedigree of parents (i.e., degree of hatchery influence) and to enumerate their progeny at both the smolt and adult stages. Reproductive success (i.e., the number of progeny per spawner) is determined for each parent and linked to co-variables associated with environmental conditions and biological traits.

Statistical analysis and general linear modeling are used to compare RRS in hatchery and natural environments among lineages with different degrees of hatchery influence (Objectives 1 and 3) and to determine causes of differences in reproductive success by analyzing the influence of co-variables (Objectives 2 and 4). Appropriate methods are being used to measure and analyze biological attributes (e.g., adult size and age at maturity, maturation timing, hatchery influence on pedigree, genomic background) and behavioral traits (e.g., spawning location, redd geomorphology, straying rates within and outside of the Wenatchee subbasin).

Q3: Provisions for M&E

The current proposal is to complete the monitoring and evaluation of RRS in Wenatchee spring Chinook during the final five years of this project (2023-2028). It emphasizes evaluation and publication of scientific findings and advice for management of conservation hatcheries.

This project is aligned with three other BPA projects: 198909600 (Genetic Monitoring and Evaluation Program for Salmon and Steelhead); 199305600 (Advance Hatchery Reform Research) and 201003300 (Study Reproductive Success of Hatchery and Natural Origin Steelhead in the Methow). The proponents work closely to coordinate their approaches, methodology, analyses, and management recommendations. The proponents also collaborate with WDFW and NMFS scientists in developing life-cycle models for Upper Columbia Chinook salmon; participate in periodic Columbia Basin hatchery forums sponsored by the Council, NMFS and CRITFC; and have collaborated with proponents of other Columbia River Basin hatchery projects to publish a review paper that synthesizes results from multiple projects (Christie et al. 2014).

The proposal does not include an overview of the process and schedule for planning activities and adjusting objectives or protocols. However, the proponents note (and their publication record attests) that they have been quick to respond to new information and to adopt new technology. For example, new questions related to straying and genetic effects on age-at-maturity arose over the course of the project and were investigated successfully. We commend the proponents for their creative and continuing efforts to distinguish environmental and genetic influences on RRS, and to address potential bias by comparing RRS at different spatial scales among tributaries and for subsets of fish that are known to have survived migration to the spawning areas.

Q4: Results – benefits to fish and wildlife

The project is meeting its objectives and providing information of value to managers in the upper Columbia River and throughout the Pacific Northwest. To date, RRS has been estimated for nine brood years (2004 to 2012; work on brood years 2013-2018 is still in progress). Major findings include:

1. Hatchery Chinook spawning in the wild have, on average, less than half the reproductive success of natural fish (i.e., RRS < 50%);
2. RRS of females (average 52%) is reduced primarily by higher pre-spawning mortality and spawning lower in tributaries in areas of reduced habitat quality;
3. RRS of males (average 29%) is reduced primarily by spawning location and changes in age structure;
4. To date, RRS of hatchery Chinook with two generations of hatchery breeding is not lower than RRS of hatchery Chinook with only a single generation of hatchery breeding, which suggests that RRS is reduced primarily by environmental factors, not genetic factors;
5. The natural-origin progeny of hatchery Chinook salmon “stray” (i.e., disperse) from parental spawning sites to other spawning sites within the Wenatchee River at higher rates than natural-origin progeny of natural Chinook.

The key finding that hatchery rearing and release practices affect subsequent spawning success of released fish will help to refine future hatchery procedures. Advice from the project has also been used to develop escapement goals for hatchery Chinook in tributary streams within the Wenatchee subbasin.

Annual reporting is adequate, and the record of primary publications and conference presentations is excellent. Important analyses and reporting of final results will be completed in 2022 to 2028.

This project is a study of the relative reproductive success of naturally spawning hatchery and natural spring Chinook salmon in the Wenatchee River above Tumwater Dam. The study was initiated in 2003 in response to the 2000 BiOp RPA 182.

The project is called for in the 2008 BiOp, is consistent to the Fish and Wildlife Program research and monitoring plans, and the Wenatchee subbasin plan. The reporting of results and adaptive management implications was succinct and thorough in a much-needed ongoing project of significance to the Columbia Basin on issues of supplementation and hatchery straying. The study design is appropriate and appears to be logistically feasible (that is, they can catch the adults and juveniles to obtain genotypic data for executing the parentage analysis).

This investigation concludes that hatchery spring Chinook salmon in this watershed have substantially reduced reproductive success relative to natural-origin individuals. Reproductive success increases as fish move upstream in the watershed. Most hatchery fish spawn lower in the watershed, near where they are released. It is not entirely clear whether the reduced success of hatchery-origin adults is a consequence of their hatchery background or their choice of spawning location.

The proponents have answered the fundamental question that they originally set out to address. The initial findings raise mechanistic questions, which are amendable to further exploration. The proponents plan to run this investigation for two complete generations, through 2018 with last brood in 2013, to expand on the initial findings and gain insight into mechanistic explanations of the observations.

1. Purpose, Significance to Regional Programs, Technical Background, and Objectives

The significance to regional programs, technical background and problem description, and objectives are all well described and appropriate for the investigation.

2. History: Accomplishments, Results, and Adaptive Management

Financial Performance and History - adequate response

Deliverable Performance - Based on Pisces reports, the project has delivered fine responses.

Major Accomplishments - The project has achieved the objective of evaluating the RRS of hatchery versus natural spring Chinook in the Wenatchee River subbasin. The hatchery fish have about 50% of the fitness of natural fish. Initial investigation of potential explanatory variables suggest spawning location, age, size, and spawning date influence the difference in performance between hatchery and natural parents.

Adaptive Management - The findings have contributed to the development of hatchery fish exclusion at Tumwater Dam, a revised HGMP reflecting limits on the genotype of fish passed upstream to spawn, and ongoing efforts to develop Parental Based Tagging (PBT) to reduce or eliminate the need for broodstock collection weirs in tributaries.

3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging)

Adequate responses are given for project relationships, emerging limiting factors, and tailored tagging questions.

There are no emerging limiting factors that would reduce the likelihood of success of the investigation.

4. Deliverables, Work Elements, Metrics, and Methods

The objectives of the investigation are appropriate for the topic – RRS of hatchery salmon and evaluation of supplementation. The deliverables, work elements, metrics, and methods are all acceptable. The proponents have a commendable track record of publication in peer-reviewed literature and have solved logistic and technical issues that have arisen during the course of the project.

This project is a study of the relative reproductive success of naturally spawning hatchery and natural spring Chinook salmon in the Wenatchee River above Tumwater Dam. The study was initiated in 2003 in response to the 2000 BiOp RPA 182. The project is called for in the 2008 BiOp, is consistent to the Fish and Wildlife Program research and monitoring plans, and the Wenatchee subbasin plan. The reporting of results and adaptive management implications was succinct and thorough in a much-needed ongoing project of significance to the Columbia Basin on issues of supplementation and hatchery straying. The study design is appropriate and appears to be logistically feasible (that is, they can catch the adults and juveniles to obtain genotypic data for executing the parentage analysis). This investigation concludes that hatchery spring Chinook salmon in this watershed have substantially reduced reproductive success relative to natural-origin individuals. Reproductive success increases as fish move upstream in the watershed. Most hatchery fish spawn lower in the watershed, near where they are released. It is not entirely clear whether the reduced success of hatchery-origin adults is a consequence of their hatchery background or their choice of spawning location. The proponents have answered the fundamental question that they originally set out to address. The initial findings raise mechanistic questions, which are amendable to further exploration. The proponents plan to run this investigation for two complete generations, through 2018 with last brood in 2013, to expand on the initial findings and gain insight into mechanistic explanations of the observations. 1. Purpose, Significance to Regional Programs, Technical Background, and Objectives The significance to regional programs, technical background and problem description, and objectives are all well described and appropriate for the investigation. 2. History: Accomplishments, Results, and Adaptive Management Financial Performance and History - adequate response Deliverable Performance - Based on Pisces reports, the project has delivered fine responses. Major Accomplishments - The project has achieved the objective of evaluating the RRS of hatchery versus natural spring Chinook in the Wenatchee River subbasin. The hatchery fish have about 50% of the fitness of natural fish. Initial investigation of potential explanatory variables suggest spawning location, age, size, and spawning date influence the difference in performance between hatchery and natural parents. Adaptive Management - The findings have contributed to the development of hatchery fish exclusion at Tumwater Dam, a revised HGMP reflecting limits on the genotype of fish passed upstream to spawn, and ongoing efforts to develop Parental Based Tagging (PBT) to reduce or eliminate the need for broodstock collection weirs in tributaries. 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging) Adequate responses are given for project relationships, emerging limiting factors, and tailored tagging questions. There are no emerging limiting factors that would reduce the likelihood of success of the investigation. 4. Deliverables, Work Elements, Metrics, and Methods The objectives of the investigation are appropriate for the topic – RRS of hatchery salmon and evaluation of supplementation. The deliverables, work elements, metrics, and methods are all acceptable. The proponents have a commendable track record of publication in peer-reviewed literature and have solved logistic and technical issues that have arisen during the course of the project.

This is a well-written proposal that was a pleasure to review. This kind of project is high priority and critical to conduct prior to larger scale implementation of supplementation projects. This project continues quantitative evaluation of the relative reproductive success of naturally spawning hatchery- and natural- origin spring Chinook salmon in the Wenatchee River watershed.

The statement on the need for this project, "All major reviews of hatchery programs have hatchery risks, including the relative reproductive success of hatchery fish, as a critical uncertainty for salmon recovery" says it all. The need for this work was also identified clearly in the subbasin plan.

The project objectives fit, except objective 2 on causes for differences, which could be considered more of an academic question, but still of great interest. Methods are appropriate and described in considerable detail. The proposal shows evidence of collaboration with related experiments in the basin and with other researchers.

The proposal includes a good summary of progress to date (2 years) and interesting unveiling of problems in sampling (hatchery progeny assignment) and proposed solutions (modeling and sampling) and study refinements (adaptive management of the experiment and the management actions already evident).