Fall run Chinook Model Enhancement and Completion of Model Development | Apply Online

Opportunity Summary:

This Fish and Wildlife Service discretionary grant opportunity (Funding Opportunity Number FWS R8 YFWO SECDET 15) funded additional work needed to finish and strengthen a fall-run Chinook salmon production model for the Klamath River. The larger reason for the project was to support the federal "Secretarial Determination" process required under the Klamath Hydropower Settlement Agreement, where the Secretary of the Interior (with other federal agencies) needed solid technical information to decide whether the federal government would support removal of four mainstem dams (Iron Gate, Copco I, Copco II, and J.C. Boyle) and the broader concepts in the Klamath Basin Restoration Agreement. In practical terms, the model was meant to help compare expected Chinook outcomes under two alternatives: dam removal versus continuing current operations (the status quo/no action).

The award was issued as a single-source grant to R2 Resource Consultants, Inc., and it was posted on grants.gov only as a Notice of Intent, meaning it was already awarded and no other applications were considered. The amount was fixed, with an award floor and ceiling of $75,714, and there was no cost-sharing or matching requirement. The CFDA listing was 15.658 (Natural Resource Damage Assessment, Restoration and Implementation). The performance period ran from signature through June 30, 2011, and an early reporting milestone required delivery of the model and supporting documentation for an expert panel and first-level peer review by August 9, 2010.

Technically, the project focused on enhancing an existing Klamath River fall-run Chinook model that R2 was already building (with prior work funded through NMFS), because several important tasks emerged after the original scope was set. The model’s purpose was to generate annual forecasts of abundance by life stage (stage-specific abundances) and to do so in a way that explicitly represents uncertainty. To accomplish that, the model used Monte Carlo simulations that vary model coefficients so forecasts are not presented as single-point predictions but as distributions that reflect uncertainty in parameters and processes.

A major expansion in the scope involved incorporating SALMOD into the modeling framework. SALMOD is used to estimate key parts of the life cycle associated with mainstem spawning and downstream migrant mortality, leveraging an existing physical framework that links fish survival to river conditions like flow and temperature (referenced here as SIAM). Because SALMOD has specific input requirements, the project added work to produce and format needed inputs, including juvenile abundance by size class, at weekly time steps, and by location. Another added piece was calibration/validation: the Klamath SALMOD model needed to be tested to ensure its predictions match observed patterns in survival and abundance. Validation was to be done by comparing SALMOD-predicted juvenile abundances to empirical estimates from mainstem Klamath River screw traps, then iteratively varying SALMOD coefficient sets to find those that minimize prediction error relative to observed trap-based abundance estimates. The work also included explicitly modeling emergence timing, temperature-driven growth from emergence to Keno Dam, and the weekly proportion of juveniles arriving at Keno Dam, all of which are needed to produce realistic timing and size distributions for downstream movement and survival estimation.

Another enhancement addressed disease-related mortality, specifically by adding a "disease scalar" to represent juvenile losses due to parasite infection, with attention to the risk that a virulent strain of Ceratonova shasta (C. shasta) could become established in the upper Klamath Basin. In other words, the model was not only tracking hydrology and temperature effects but was also updated to account for biologically meaningful mortality that could significantly change juvenile survival outcomes, especially under different basin conditions.

The opportunity also covered additional stakeholder engagement that had been underestimated. To keep stakeholder groups informed as the model evolved, the scope added three more stakeholder meetings plus two additional technical meetings requiring travel before final model completion. This reflected the reality that the model was being used in a high-stakes policy context and needed iterative discussion, transparency, and technical review with multiple interested parties.

Finally, the project included a focused analysis of the "status quo" scenario, designed to quantify what drives variability in survival of fall-run Chinook from Iron Gate Dam to the ocean under continued dam operations. This analysis was to use multiple data sources in a simple quantitative framework: screw trap data from three mainstem sites, estimated spawner abundances in lower mainstem tributaries, NMFS run reconstruction information, and coded-wire-tag (CWT) analyses from Hankin and Logan (2010). The intended outcome was both diagnostic (identifying and quantifying key factors linked to survival variability) and evaluative (estimating the expected effects of continued dam operations on existing fall-run populations).

Deliverables were clearly defined in both written and electronic form. The written deliverable was a technical report documenting the model’s assumptions; the mathematical equations used to represent reproduction, growth, and mortality across all modeled phases other than the SALMOD component; and a detailed description of model coefficients, including how each coefficient was derived (statistical fitting, literature, or expert judgment, with attribution to the expert where relevant). A peer-reviewed manuscript was explicitly excluded from the scope due to the extra time and cost involved. The electronic deliverables included the full model code, executable files used to run the model (including the SALMOD executable), all supporting electronic materials such as data files, and the final technical report in PDF format.

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