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

The three goals and four objectives are well linked to the problem statement. Goal 1 (“Evaluate the genetic effects of hatchery propagation on the wild steelhead in the Methow basin”) was revised to include previous Objectives 1 and 3 (now called Objectives 1A and 1B), which address genetic effects during the first and second generations, respectively. Goal 2 (“Improve understanding of the differences between hatchery and wild steelhead to inform hatchery practices”) includes previous Objective 2 (unchanged). Goal 3 (“Evaluate the reproductive viability of reconditioned wild steelhead kelts”) includes new Objective 3. The “Short Description” section of the proposal refers to the previous objectives rather than the new objectives.

Each of the four objectives is clearly specified by one or more null hypotheses that are measurable, testable, and relevant to the Council’s Program. Timelines for the objectives are clearly specified and being met. The project’s end-date has been extended to test the effectiveness of hatchery reforms and innovations to improve the relative reproductive success (RRS) of hatchery steelhead in the natural environment. The extended study will measure improvements in RRS from using local broodstock and rearing smolts to age 2 and evaluate the reproductive success of reconditioned kelts relative to wild maiden spawners.

Q2: Methods

The proposal includes a comprehensive overview of methods and the most recent Annual Report (Goodman et al. 2020) provides greater detail supported by links through MonitoringResources.org and data. Accepted methods are being used to trap, sample, and enumerate downstream juveniles and returning adults. DNA-based pedigree procedures are used to identify and enumerate parr, smolts, and adults produced by steelhead spawning naturally. A generalized linear model is used to estimate the degree to which reproductive success in male and female steelhead is affected by demographic and biological variables such as fish origin, fork length, run timing, spawner density, pHOS, and somatic lipid content.

Figure 2 shows large variation in the number of offspring in relation to lipid content. It would have been useful to include statistical results for these regressions and to explain the influence of parental type. Might lipid content reflect degree of maturation at the time of sampling such that more mature fish had already incorporated somatic lipids into gametes or metabolism? Was there a seasonal trend?

The proponents acknowledge the ISRP’s concern (expressed in ISRP 2010, 2018) that the long history of transplants and hatchery releases into the Methow River might lead to underestimation of genetic impacts of hatchery fish on wild fish in other rivers without a history of transplants. However, they note that historical effects of hatchery propagation are widespread in the Columbia Basin, so the management implications of this study are still relevant.

Q3: Provisions for M&E

Hatchery supplementation necessarily involves multiple jurisdictions and interest groups. This project is closely linked with two other BPA projects: 199305600 (Advance Hatchery Reform) and 200845800 (Upper Columbia Steelhead Kelt Reconditioning). The proponents provide a clear and succinct overview of the process and schedule for planning and coordinating activities among these groups, and for evaluating and adjusting protocols as needed.

The precision of estimates of RRS measured at the adult (i.e., final) stage would be improved if a greater proportion of adults returning to the Twisp River could be trapped and sampled. The proponents indicate in their Annual Report for 2019 that, in some years, more adults spawned below the weir than above it. Accordingly, in 2017, they began releasing hatchery progeny farther upstream, hoping that this new release site would motivate more of the returning adults to migrate past the weir where they could be sampled. The proposal does not indicate if this or other adjustments have improved the sampling rate for adults. Future proposals could be improved by including a power analysis to determine if sampling rates of adults (and juveniles) are optimal (or adequate) for detecting statistical differences in reproductive success within the proposed time frame of the study. That said, results to date provide considerable reassurance that the study can achieve its objectives.

Q4: Results – benefits to fish and wildlife

This project is meeting objectives, successfully testing hypotheses, and generating results that will benefit fish and wildlife.

Results to date span three generations (12 brood years from 2009-2018) and confirm that average reproductive success of hatchery females and hatchery males spawning naturally in the Twisp River was significantly lower than that of their wild counterparts when measured at the age-1, age-2, and smolt life stages. The similarity in survival from age-1 parr to smolt stages in progeny of Wells broodstock suggests that the fitness impacts are occurring at spawning or early in life prior to age 1. Few significant differences in RRS have been detected at the adult stage, but returns of adults are still incomplete for many brood years, and statistical power has been limited by the relatively small number of adults available for sampling. Note that the caption for Figure 1 is incorrect – female RRS is presented in the top frame, male RRS in the bottom frame.

Knowing the environmental or genetic mechanisms that reduce RRS is key to redesigning hatchery protocols. This project was the first to document the effect of somatic lipid content on RRS. It will now field test recommendations (from the Advance Hatchery Reform project) to release steelhead smolts at age 2 rather than age 1 as a strategy to reduce the prevalence of residual males and minijacks that have adverse consequences for natural populations. Analysis of RRS of second-generation natural spawners is partially complete for the Wells hatchery-origin experiment, but only just beginning for the local Twisp hatchery-origin experiment.

Future proposals and annual reports could be improved by including additional hypotheses and details to explain how the proponents plan to distinguish environmental and genetic effects on fitness. Presumably, persistent differences in RRS of Twisp hatchery-origin fish spawning naturally in the second generation after hatchery release would demonstrate genetic effects on fitness due to hatchery supplementation. In contrast, persistently lower reproductive success in the Wells hatchery line could be attributed to the non-local provenance (i.e., less well adapted traits) of that brood line. However, improvement in RRS over successive generations in the progeny of Wells hatchery-origin would provide evidence for genetic adaptation of non-local hatchery fish to the natural environment of the Twisp River.

The project has already successfully evaluated reproductive success for 11 reconditioned wild female kelts and shown that they are reproductively viable and produce more offspring than maiden-spawning wild females. The proposed adjustments to the project will allow these and other issues related to hatchery reform to be researched more thoroughly.

The study of relative reproductive success of hatchery and natural steelhead in the Twisp River proposed is needed. The ISRP believes investigation of natural production by spawning hatchery steelhead in the tributaries above Wells Dam is essential for understanding the status and viability of the natural population. The proposal included three primary objectives: 1. in a first generation compare the relative production from hatchery and natural fish spawning in the Twisp River, a tributary to the Methow River; 2. evaluate potential biological attributes of the fish and environmental attributes of the spawning site and time that might account for differences in the performance of hatchery and natural steelhead; and 3. in a second generation compare the success of natural spawning adults that had zero, one, or two hatchery-origin parents in the previous generation. The ISRP raises questions about the field and analytical methods in section 3 below. A response is requested in the form of a revised proposal narrative that elaborates on the analysis anticipated for each objective. This investigation also becomes a test of the AHA model. AHA should be run on this population (if not done already by the HSRG) and this project used to test the assumptions in AHA. The ISRP is interested in how the environment—tributary habitat capacity, interannual variation—might affect the outcome. Could different environmental conditions be added to the study? This would add a dimension to objective 2 - correlation analysis. 1. Technical Justification, Program Significance and Consistency, and Project Relationships The proponent proposes to examine Relative Reproductive Success (RRS) for Twisp River (Methow River subbasin) summer steelhead. The steelhead run is part of the upper Columbia River basin Evolutionarily Significant Unit (ESU) and is listed for Endangered Species Act (ESA) protections. This project is similar to ongoing RRS investigations in the Hood River, Oregon, that have provided evidence that multi-generation hatchery stocks of steelhead are less productive when spawning naturally than non-captive fish, that a single generation in the hatchery results in depressed performance in the wild, and that hatchery effects on natural production persist in wild-born individuals with hatchery-born parents. The objectives, rationale, and approach are clearly presented and suggest a project that will provide another data set for comparing hatchery and natural steelhead reproductive performance that will complement the Hood River investigations. Until initial evaluations of progeny production from natural and hatchery steelhead are completed it will not be known whether the Twisp River “case” is biologically similar to the Hood River “case.” In the Hood River many of the interesting results that have been published are based on comparing recently established hatchery stocks with natural fish. The hatchery stocks have been established from the local natural stock. In the Methow subbasin, the hatchery fish are a long-established (1969) composite stock with broodfish collected at Wells Dam and progeny historically scatter-planted throughout the Methow and Okanogan subbasins. Recently the juveniles released from the hatchery program have been hatchery x wild crosses. The proposal does not present information on the relationship of the natural and hatchery steelhead, but it is possible that the natural fish are descendents of wild-born hatchery fish. This possibility is important to consider when interpreting the results of the investigation. For example, hatchery- and natural-origin coho salmon in Minter Creek, Washington have indistinguishable reproductive performance in the natural stream, and this is attributed to 60 years of hatchery production with the majority of natural spawning by hatchery-origin adults (Ford et al. 2006). It is noteworthy that in the Minter Creek coho situation the production of smolts has decreased from levels in the 1940s and run- and spawn-timing are earlier. Analysis suggests that optimum run-time is later than the present timing (Ford et al. 2006). The important point is that likelihood of substantial past crossing of wild and hatchery fish will complicate using a difference in relative reproductive success between the hatchery- and natural-origin steelhead as a valid basis for drawing biological conclusions and useful management implications. Indeed, if the high proportion of hatchery-origin steelhead present in the past were reproductively successful at reasonable rates, smolt yields would have been much higher. Even with these caveats, the investigation is important and will contribute to our understanding of the population status of upper Columbia River steelhead. 2. Project History and Results This is a new project. Proponents indicate that methods to collect tissue samples, genotype fish, and operate the Twisp weir and juvenile trap have been tested. 3. Objectives, Work Elements, and Methods The general outline of the proposed investigation employs established protocols for parentage assignment and assessment of relative reproductive performance of different categories of individuals. Most, or all, of the potential parents will be captured and genotyped; juveniles will be sampled, genotyped, and assigned to parents. The number of progeny produced by different categories of parents will be compared to establish their relative reproductive performance. The ISRP has several concerns about individual methods that need to be addressed before initiating the investigations. Reliance on rotary smolt traps for smolt capture may not provide sufficient sample size to confidently determine the relative reproductive success of wild versus hatchery recruitment to the smolt stage—the key response variable. A full smolt enumeration and sub-sample routine should be explored and employed if feasible. Sample size requirements to detect differences in reproductive performance should be established a priori. This should consider the power and minimum effect size that is likely to be detectable. For objective 1 and 3 the proponent outlines a comparison of production from parent pairs (4 for objective 1 and 16 for objective 3). In most investigations of RRS the contrast is among 4 categories – hatchery males and females and natural males and females. Additionally, the Hood River investigators have completed and published an evaluation of “carryover effects” identical to that proposed in objective 3 (Araki et al. 2009). This study was not listed in the literature citations. The ISRP urges that a compatible study design be employed in the Twisp, so this study can serve as a replication/comparison. The ISRP believes the proponents need to revisit the analysis design and ensure it is using contrasts compatible with other Pacific salmon and steelhead RRS investigations. It is not clear to the ISRP that the assumptions for testing random mating will be met. This should be addressed in a response. For objective 2 - determine the degree to which differences in fitness between hatchery and natural steelhead can be explained by measurable biological or life-history traits that differ between hatchery and natural fish the analytical approach to evaluating selection appears appropriate (using the methods from Lande and Arnold 1983), but the interpretation of whether the differences between hatchery and natural fish are genetic (from domestication selection) or from environmental effects of hatchery rearing is not clear. On page 8 the proponents conclude they will be able to determine not only if hatchery steelhead have lower relative reproductive success than natural steelhead, but also why. It is not evident that the design of the investigation can lead to interpretations of causation. In particular, on page 21 final paragraph the proponents state “If there are differences in relative reproductive success between hatchery- and natural-origin spawners, it is possible that these differences are more a function of biological factors that are correlated with the origin of the spawners rather than any direct hatchery effect.” It is not clear to the ISRP what is intended by this distinction – which is the genetic effect, which is the environmental effect? And how will the design not confound these effects? This should be addressed in a response. For objective 3, if the natural-origin steelhead in the Twisp are functionally the wild-born descendents of Wells hatchery steelhead, and the two components (hatchery and wild) are at genetic equilibrium because of past interbreeding, then one generation of wild parents may not yield an important production distinction between categories (wild with hatchery parents versus wild with wild parents). Both categories could have low productivity. The ISRP is under the impression that a longer term investigation of re-adaptation is underway with coho salmon at Minter Creek. The status of that investigation and approach should be confirmed. It would be worthwhile to have a longer term investigation of the re-adaptation of steelhead. This component should be added to the plan. Araki, H., B. Cooper and M. Blouin 2009. Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild (Biology Letters doi:10.1098/rsbl.2009.0315) Ford, MJ, H. Fuss, B. Boelts, E. LaHood, J. Hard, J. Miller. 2006. Changes in run timing and natural smolt production in a naturally spawning coho salmon (Oncorhynchus kisutch) stream after 60 years of intensive hatchery supplementation. Canadian Journal of Fisheries and Aquatic Sciences 63:2343-2355.