The Basinwide Supplementation Evaluation (BSE) Project provides state-of-the-art genetic tools (e.g., sophisticated pedigree analyses) to support effectiveness monitoring and evaluation of salmonid supplementation and reintroduction projects on Tribal ceded lands throughout the Columbia River Basin. Most of these individual projects are implemented with funding from the Council and BPA, but they lack technical expertise or financial capacity to perform aspects of needed RM&E. Results from the BSE Project are published and used in adaptive management decision processes that guide future analyses, recovery actions, and management decisions.

The project uses two key metrics for assessing supplementation success, the relative reproductive success (RRS) of hatchery fish compared to natural fish in nature and the demographic boost achieved by hatchery spawned and reared fish relative to natural production. In combination, these two metrics are often used to indicate the success of supplementation programs. However, to clearly assess if hatchery supplementation is working, additional information is needed. Using RRS and demographic boost analyses does not account for longer-term natural population fitness reductions that may occur because of hatchery intervention. The value of the project would be enhanced if this risk was considered and approaches to assess it were developed.

The project is also investigating methods to reduce the occurrence of precocious maturation in reared Chinook salmon males. A suite of pilot rearing studies tested the effects of various cultural strategies on precocious maturation in males. A production scale experiment using two promising methods and control fish will begin in broodyear 2022 and run through broodyear 2024.

The project addresses many key uncertainties associated with hatchery supplementation and reintroductions identified by the ISRP and ISAB in previous reviews. It has many management applications, and results from the project’s effectiveness monitoring and precocious maturation experiments will be of value and interest to many of the Basin’s fishery managers.

Q1: Clearly defined objectives and outcomes

All BSE Project studies can be categorized under one of three complementary research objectives: to monitor and evaluate (1) supplemented populations or (2) reintroduced populations of salmon and steelhead; or (3) to conduct experiments to investigate physiological processes and development of salmon and steelhead reared in a hatchery environment.

Flow diagrams are used to illustrate the experimental design or logical sequence of tasks for major studies under each research objective. Each flow diagram possesses multiple boxes that describe a sequence of tasks that will take place to reach an expected quantitative outcome. The outcomes are meant to provide fishery managers with data that can be used to evaluate whether an individual project is meeting its programmatic goals. Or in the case of Research Objective 3, whether altered fish cultural practices can achieve reductions in precocious maturation.

The steps in the flow diagrams essentially fulfill the intent of SMART objectives. They describe specific tasks, they are measurable, attainable, relevant to the problem being examined, and they establish deadlines for project completion. The intent of having SMART objectives is to facilitate adaptive management within a project. Typically, such objectives have quantitative targets. However, the BSE Project includes too many component studies under Research Objectives 1 and 2 to produce such targets for each study. Specific quantitative targets are included when appropriate for the fish culture experiments under Research Objective 3. The series of Gantt charts in section 7 provide commendable clarity and detail about expected timelines.

Q2: Methods

The extensive methods section (20 pages) provides a clear and well-referenced summary of diverse approaches and procedures being used in the proposed studies. The proponents are using state-of-the-art genetic methods to perform pedigree assessments, stock identification, and to calculate reproductive success and relative reproductive success. Some of the methods being employed were developed by the proponents. For example, the genotyping-in-thousands by sequencing approach (GT-seq) was developed by CRITFC personnel and is being used by the project to genotype thousands of individuals at hundreds of SNP markers. Resulting genotype data are then supplied to software programs that identify parent-offspring and sibling relationships. The statistical approaches being used, e.g., the use of ANOVAs to test null hypotheses and generalized linear models (GLMs) to estimate covariate effects, are appropriate. This statistical approach is predominately used to analyze data from the supplementation and reintroduction assessments occurring under Research Objectives 1 and 2.

Relative reproductive success of sockeye reintroduced to Cle Elum Lake has been inferred by comparing GSI assignments to the two donor stocks (Osoyoos and Wenatchee) in samples at successive life stages. The broodstock for the reintroduction was collected at Priest Rapid Dam from 2011-2017 and comprised, on average, 70% Osoyoos and 30% Wenatchee origin fish. In contrast, spawner carcasses collected in Cle Elum Lake in 2013-2016 averaged 72% Wenatchee and 28% Osoyoos, and returning adults sampled at Roza Dam in 2018 were 84% Wenatchee, 7% Osoyoos and 9% hybrids. Accordingly, the proponents estimate a much higher rate of replacement for Wenatchee (0.80) than Osoyoos (0.23).

They also reported a bimodal distribution of spawning time with carcasses assigning to Wenatchee peaking a month earlier than carcasses assigning to Osoyoos, consistent with the typical spawning time of the donor stocks in their respective lake systems. The ISRP notes that spawning time in sockeye and kokanee populations is typically fine-tuned to the expected thermal regime during incubation so that fry emerge at a favorable time in the spring (Brannon 1987; Wood and Foote 1990). We think the late spawning time of Osoyoos sockeye is likely adaptive in the warmer (lake-fed) winter temperature regime of Osoyoos Lake, but mis-matched to the colder winter regime at Cle Elum Lake, thus accounting for the lower reproductive success of Osoyoos spawners in Cle Elum Lake. We recommend that the proponents test this explanation by comparing temperature profiles during incubation at the Cle Elum, Osoyoos and Wenatchee spawning sites, and ideally, by confirming similar development rates (i.e., degree-days needed to complete incubation from fertilization to emergence) under standard (“common garden”) conditions for both donor stocks.

One of the reintroduction projects being evaluated is comparing the productivity and reproductive success of NOR and HOR spring Chinook spawning in Lookingglass Creek. Data from nine broodyears is currently under analysis. NOR spring Chinook strays may return to the Lookingglass weir and hatchery. It is important that the methods being used to identify these strays are described. The inadvertent incorporation of these fish in the calculation of recruits-per-spawner would create a positive bias in the project’s R/S estimates for NOR fish.

Genetic and physiological parameter data are being used to evaluate the effects of different fish rearing strategies on the incidence of precocious maturation. The methods being employed to collect physiological data are well described and appropriate. The proposal indicates that in some rearing experiments specific growth rates (SGR) of fish undergoing different treatments may be assessed. The formula used to calculate SGR contains a typo. The second weight term in the numerator should be weight at time 1 rather than weight at time 2. A recent review of SGR states that SGRs are difficult to interpret because they express additive changes in loge weight per unit of time (Crane et al. 2020). Crane et al. algebraically rearrange the standard equation so that proportional increases in weight can be obtained and indicate that multiplying this value by 100 will provide per cent increases in weight per unit of time. The proponents may wish to investigate the use of these new formulas in their Research Objective 3 experiments. The experimental designs and statistical approaches being used in the rearing experiments are well described and are scientifically valid.

References

Brannon, E.I. 1987. Mechanisms stabilizing salmonid fry emergence timing. P.120-124. In H.D. Smith, L. Margolis, and C.C. Wood [ed.] Sockeye salmon (Oncorhynchus nerka) population biology and future management. Can. Spec. Publ. Fish. Aquat. Sci. 96.

Crane, D.P., D.H. Ogle, and D.E. Shoup. 2020. Use and misuse of a common growth metric: guidance for appropriately calculating and reporting specific growth rate. Reviews in Aquaculture 12:1542-1547.

Wood, C.C., and C.J. Foote. 1990. Genetic differences in the early development and growth of sympatric sockeye and kokanee (Oncorhynchus nerka) and their hybrids. Can. J. Fish. Aquat. Sci. 47:2250-2260.

Q3: Provisions for M&E

Funding and expertise are often too limited within individual projects to conduct adequate, RM&E. The BSE Project was established to provide tools to support effectiveness monitoring of tribally managed projects that lack RM&E capacity. Metrics and insights generated by the BSE Project about the biological effects of supplementation and reintroduction programs are being used by tribal partners to evaluate if their projects are meeting their restoration goals. Thus, expected outcomes from the BSE Project become key inputs to adaptive management cycles in the partnered projects. The proponents are in regular contact with their partners, sharing findings, and working to ensure that implementation tasks (e.g., planned genetic sampling) occur as expected.

The proponents also have their own internal evaluation and adjustment process. For Research Objectives 1 and 2, project objectives are shared with tribal managers and any involved co-managers, either informally during meetings with collaborators or formally through presentations. Plans are in place to hold annual virtual meetings with collaborators and biannual genetics workshops within the fish science community. However, the ISRP urges the proponents to develop a formal adaptive management procedure to be followed during such meetings.

Q4: Results - benefits to fish and wildlife

The Progress to Date section of the proposal provides an extensive (34-page) overview of the research questions being addressed; objectives, approaches, and quantitative results for the diverse suite of component studies; plans for future work, and implications of the results so far obtained. These accounts showcase how useful outcomes from the BSE Project are to individual tribally managed projects. The methods used and results obtained also have broad value to fishery managers dealing with similar questions in the Columbia River Basin and beyond.

In our review of research projects in 2018 (ISRP 2018-8), we noted that NOAA researchers had identified an underappreciated problem of precocious maturation of males in many of the Basin’s Chinook hatcheries. In some hatcheries, over 50% of the males may mature as two-year old minijacks. Such fish may distort smolt-to-adult recruit (SAR) values, potentially compete with wild conspecifics for resources, induce numerical predator responses, and cryptically inflate pHOS values in natural spawning populations. Ongoing work and planned experiments by the proponents are examining how fish cultural methods can be implemented to substantially reduce the occurrence of precocious parr in cultured Chinook. Pilot studies performed by the proponents suggest that periods of starvation and photoperiod manipulations can significantly reduce precocious maturation. Future work to refine each of these approaches is scheduled and a production-scale study is planned to evaluate their effectiveness under normal hatchery operations. Results from these studies will be of value across the Basin and elsewhere.

Objective 1. Use Dual-Frequency Identification Sonar (DIDSON) to estimate natural escapement of spring Chinook salmon above Castile Falls, Klickitat River – RESPONSE REQUESTED Objective 2. Complete development of mark-recapture likelihood model which incorporates tag loss – MEETS SCIENTIFIC REVIEW CRITERIA (QUALIFIED) Objective 3. Perform relative reproductive success study of NO versus HO salmon in population associated with an ongoing supplementation project – MEETS SCIENTIFIC REVIEW CRITERIA (QUALIFIED) Objective 4. Perform relative reproductive success studies of NO versus HO salmon in four to five reintroduced salmon populations [Phase I] – MEETS SCIENTIFIC REVIEW CRITERIA (QUALIFIED)

In the RM&E section “Where will you post or publish the data your project generates?” I mistakenly checked the “NOT ELECTRONICALLY AVAILABLE” box – it should have been left blank (as were the other optional check-boxes).  Activities within this Project involve collection of two types of data.  The first involves acquisition of continuous hourly DIDSON sonar recordings at the upstream outlet of the Castile Falls Fishway in the Klickitat River, and subsequent reading of the files to note instances of upstream migration.  These counts of adult spring Chinook are used to produce an annual escapement estimate into the upper basin.  The second type of data is genotype information acquired for individual fish tissue samples analyzed for a suite of DNA (microsatellite) loci.  These samples are provided annually to CRITFC by various tribal and state agencies for adult and juvenile fish associated with a series of salmon supplementation or reintroduction/supplementation hatchery programs.  The genotype information is then used to identify parentage, followed by analyses to estimate relative reproductive success of hatchery versus natural origin fish.  Neither of these data set types concord with the options provided in this section of Taurus.  Therefore, I indicated immediately below under “Other”, the URL and Title for the web site at which our agency’s technical reports are posted.  As particular studies within the scope of the project are completed, technical reports are produced and posted to this web site.

Indeed, two reports for the Klickitat spring Chinook escapement studies (for 2009 and 2010) are already posted.  The raw data for the fish passage counts is provided in an Appendix to each report, and a compilation of the sonar video file clips of the associated fish passage events is also posted to the web site.  Copies of these reports were, of course, provided to the Yakama Nation collaborators/co-authors, and the reports are also posted as Attachments to the Project’s site within PISCES, with View Permission indicated as “Public (anyone can access via web)”; unfortunately, PISCES will not accept the video file.

Unlike the annual DIDSON escapement studies, the relative reproductive success studies are multi-year efforts, and summary reports will be produced only every few years.  The reports will be produced with co-authorship by representatives from the collaborating agencies, and posted in PISCES and in the CRITFC technical reports sites.  The first of these, concerning the reintroduced spring Chinook in the Hood River, will be produced later in 2011.  Results from these studies will also be summarized in written manuscripts for publication in scientific journals, as well as in oral slide presentations and posters for presentation at scientific meetings – copies of which will be included as attachments in PISCES.  The raw data sets of genotype information will be made available to the participating tribal and state agencies as well as the subsequent parentage and statistical analyses.  This information will also be made available to other interested persons upon request.