Fall-run Chinook Model - Enhancement and Completion of Model Development

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Background on the Secretarial Determination (SD) Process: The Klamath Hydropower Settlement Agreement (KHSA) calls for the Secretary of Interior, in consultation with other federal agencies, to make a determination by March 31, 2012, as to whether the Federal Government supports dam removal and the concepts embodied in the Klamath Basin Restoration Agreement. During this period, the federal government (in consultation with its non-federal partners) is gathering new information and analyzing existing data and reports to inform this decision. This project will provide the necessary information for this purpose. VI. BACKGROUND:This is a single source award, which had been posted on grants.gov as a notice of intent. The applicable SF424 have been received from the recipient. R2 Resource Consultants, Inc has extensive experience with the Klamath River and related fish issues. R2 Resource Consultants, Inc is currently developing a Klamath River fall-run Chinook model. This grant addresses the recently identified tasks not in the original scope of work (funded by NMFS). R2 Resource Consultants has completed a number of high profile technical documents and has a successful track record with the FWS, and the National Marine Fisheries Service on issues related to the Klamath River. This project is to enhance the development of a Klamath River fall-run Chinook salmon production model capable of providing annual forecasts of stage specific abundances under two management alternatives on the Klamath River: 1) the removal of four mainstem dams (Iron Gate, Copco I, Copco II, and JC Boyle) + the Klamath Basin Restoration Agreement; or 2) the status quo (no action). The model explicitly incorporates uncertainty into the forecasts through Monte Carlo simulations of model coefficients. Several alterations to the approach were implemented as a result of stakeholder involvement and an improvement in understanding the factors affecting fall run Chinook in the Klamath River. In particular, the fish production model incorporated SALMOD to provide coefficients for the downstream mortality component of the model, and it incorporated a disease scalar to reflect juvenile mortality due to parasite infection. Finally, the level of stakeholder involvement was under-estimated. The following is the scope of work for this project:Presentations and reportsDue to the need to keep the stakeholder groups informed on the progress of the fish production model, 3 additional meetings will be required with the stakeholders. In addition, there will be another 2 technical meetings that would require travel before the model is completed.SALMOD & DiseaseThe use of SALMOD for determining the downstream migrant mortality and mainstem spawning was not scoped in the original proposal. Using SALMOD for this portion of the life-cycle has advantages due to the existing physical framework for incorporating flow and temperature into estimates of migrant mortality (i.e., SIAM). SALMOD has a specific set of requirements; namely the abundance of juveniles, in specific size classes, at weekly intervals, and in specific locations must be supplied to SALMOD. Furthermore, the Klamath SALMOD model needs to be calibrated or validated to ensure that SALMOD will provide predictions that are consistent with observed trends in survival. These SALMOD related tasks were not originally incorporated into the scope. The model will be validated by comparing the model to juvenile abundance estimates obtained from screw traps on the mainstem Klamath River. The model coefficients will be varied in order to determine which SALMOD model coefficient sets provide the minimum error between SALMOD predictions of juvenile abundance and observed abundance. The timing of emergence, the calculations for growing fall run Chinook from emergence to Keno Dam as a function of temperature, and the proportion of the run arriving at Keno Dam in weekly intervals will be incorporated into the model. Finally, the last component of this task will be to include the disease scalar in the upper basin model to reflect the possibility of juvenile mortality due to the virulent strain of C. shasta becoming established in the upper Klamath basin.Analysis status-quo scenarioThis task would use the screw trap data from three mainstem screw traps, estimated spawner abundances in the lower mainstem tributaries, run reconstruction information from NMFS, and CWT analyses provided by Hankin and Logan (2010) to quantify the factors affecting variability in the survival of fall run Chinook from Iron Gate Dam into the ocean using a simple quantitative framework. Furthermore, once the factors are quantified, the task will provide an estimate of the effects of continued operation of the dam under status quo operations on the existing fall run populations.DELIVERABLE:The written deliverable will be a technical report including the assumptions incorporated into the fish production model, mathematical equations used to define reproduction, growth, and mortality for all phases of the fish production model besides the SALMOD component, and definition of model coefficients described based on how they were derived (e.g., from statistical fitting to data, literature review, or expert opinion – with reference to the expert). Given the effort and costs associated with developing a manuscript for peer-review, we have assumed that this would not be covered under the current modification. The electronic deliverable will be all model code, executable files (e.g., SALMOD executable) used to run the model, other supporting material in electronic formats (e.g., electronic data files), and the technical report in pdf.REPORTING SCHEDULE: Model and supporting documentation for Expert Panel use and first level of Peer Review by August 9, 2010.PERFORMANCE PERIOD: Upon Signature through June 30, 2011.

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