Local or MSRT Comments: There are two unresolved issues with the bull trout projects. First, the tie to the FCRPS Bull Trout BiOp and FCRPS responsibility. Second, coordination with USCOE bull trout projects would be expected and cost savings should be identified. To be consistent with other mainstem/systemwide recommendations, the project budget was cut to the FY06 level of $350,000 plus a 5% increase for increased costs (The FY06 budget that totaled approximately $488,000 included efforts implemented by the Warm Springs Tribe at a cost of approximately $125,000. Those efforts are no longer part of this project but instead have been proposed through Proposal 200715700). The MSRT recommends that the budget for this project be reduced through deferral of equipment purchases and reduction in subcontracts to USFS and USGS. Development of a bull trout monitoring plan should be completed through CSMEP and not individual projects; therefore, costs associated with developing the monitoring plan can be eliminated because this effort should be implemented through funds that ODFW receives to participate in CSMEP.

The project sponsors provide adequate responses to the ISRP request for clarification of the design of the model development, the standardized monitoring protocol, and the need to continue to collect life-history data on bull trout in multiple subbasins. The ISRP continues to believe the sponsors need to improve the argument that this project will contribute to the development of recovery actions/plans for bull trout. The responses do not indicate that this proposed research is closely integrated with actual management decisions. It is not clear that the management branch of the sponsoring agency is even adequately integrated into this proposal. This is a weakness in the proposal. If this project is continued the sponsors should be able to better demonstrate that the information generated is influencing management decisions.

As an ongoing project, reporting of results has been good with consistent production on Annual Reports to BPA and several peer-reviewed papers. A complete list of these reports and papers (inserted in Section E) would be helpful.

It is difficult to ascertain how critical the results of this study would be for management. There do not seem to be any managers in the various basins actively on board and involved with this proposed work (at least as presented in the proposal). The direct linkage is not well established between the proposed research and benefits of implementation on the species basinwide. The summary of relationships to other projects (section D) is not adequate to establish that the facilities, equipment, and personnel are appropriate to complete the work identified in this proposal.

For preparing a response, the ISRP provides these additional comments/questions for the sponsors to consider. What is the bottom line on bull trout/brook trout interactions? Do we need to evaluate hybridization on a case-by-case basis or can generalizations be extended to unstudied regions? What do ecological interactions tell us about habitat protection issues? Similarly for migration patterns, from these previous investigations how should subsequent investigations be conducted? What are the new questions? Is it necessary to investigate migration of juveniles from the natal headwater areas to adult holding areas in lower tributaries or the mainstem Columbia in every subbasin? Is it possible to establish generalizations that can then be used to develop water quality and diversion performance standards in other subbasins? What do we need to learn to move from investigation of life-history variation to implementation of restoration actions?

The background section lacks focus. The text references streams (e.g., Mill Creek in the Walla Walla subbasin) without placing them in context. Some terms are used improperly (e.g., on page 4, anthropomorphic should be anthropogenic). The linkages between subbasin-specific tasks and objectives are sometimes missing. For example, movements and connectivity in the Hood River and Walla Walla (work elements 1 and 2) are not linked conceptually with work element 3 to develop standard protocols for monitoring bull trout. It is not at all clear how this project will serve to provide "guidance for reintroduction assessments” (page 6).

The listed objectives are really tasks to complete the work elements. Objectives in terms of goals to achieve protection and restoration of bull trout are needed.

Several questions for each of the three primary tasks need to be clarified. Objective 1: how is ambient water temperature determined? How are survival rates determined - specifically how is tag loss/non-detection and/or migration out of the area incorporated into the survival estimates?

How will bull trout be monitored (tracked) in Bonneville Reservoir. Task 2.1.2. Who operates the Middle Fork screw trap? Is this project going to operate a trap to catch 20 fish per year? If not, are fish trapped and captured by another project holding bull trout until they are tagged? Who does the tagging?

For objective 3, the linkage between the stages on page 18 and the tasks (work elements) needs to be established; it is not clear from the text. No tasks are associated with stages 1 and 2 or 4 and 5. The reference “Rosenberger and Dunham 2005” is not in the citations. What is going to be done with Work Element 3.4 - Landscape Modeling? It is not clear. It is not clear how the patch characteristics are going to be measured and then evaluated and finally incorporated into a landscape model.

The addition of several maps would greatly improve the clarity of the proposal, especially the section regarding the migration patterns of bull trout in the Hood River watershed.