This project has a good track record and is managed by qualified scientists. It will contribute useful information for managing adaptively within the John Day subbasin. 1. Technical Justification, Program Significance and Consistency, and Project Relationships The technical justification and scientific background was reasonably thorough. There appear to be two major topic areas in this work. First, there is evidence that straying of hatchery Chinook salmon and steelhead into the John Day River system is adding to the difficulty of determining the status and trends of naturally produced fish in this (primarily) wild fish production subbasin, and there is the possibility that interbreeding of wild and hatchery fish may be contributing to a loss of fitness among naturally spawning and rearing stocks. This project proposes to extend the existing genetic monitoring program to further assess the significance of straying of Chinook and steelhead from hatcheries in other subbasins into the John Day River's natural production areas. Second, the project proposes to expand the aquatic and riparian habitat status and trend monitoring efforts. This is of interest because of the strong emphasis on habitat restoration in the John Day subbasin. The project is consistent with a number of RPAs in the BiOp and with other programmatic emphasis areas in the region. The approach is clearly spelled out, and the ISRP appreciates that the project proponents have responded directly to our suggestions from previous reviews and incorporated them into this plan. The proposal references specific recommendations from the RPA workshop and identifies the RPAs in the BiOp that the work will address. Additional linkages are given to the John Day subbasin plan and to the Council's Fish & Wildlife Program. The 2008 FCRPS BiOp identified the Upper John Day as a priority subbasin for recovery of the Mid-Columbia steelhead DPS. The John Day River is an important reference subbasin for comparisons to other anadromous stocks in more highly impacted subbasins of the Columbia River. Further, the John Day is unique among Columbia River subbasins because its Chinook and steelhead populations have had little influence from hatchery introductions. The project, initiated in 1998, is one of the more extensive monitoring and evaluation programs in the Columbia River Basin. The proposed work is consistent with the monitoring needs identified by the Columbia River Basin Fish and Wildlife Program, the BiOp, and the Oregon Plan for Salmon and Watersheds. The project also directly addresses several important needs specified in the John Day Subbasin Plan. 2. Project History and Results The project’s history is thoroughly described, including tables summarizing results of the previous nine years of work in this project. The maps were very helpful, although most of the material referred to existing redd count, adult holding areas, and genetic sampling. It would also have been useful to have included maps or tables describing the locations of significant habitat restoration projects (perhaps by category, if available) and sites where there are records of juvenile salmonid presence-absence or abundance, because these are included in this project's objectives. The project has generated much information on smolt production and adult escapement. The discussion of results could have been improved if the proponents would have discussed how the results to date have influenced management decisions. For example, what useful information was derived from the stock-recruitment relationship? 3. Objectives, Work Elements, and Methods The objectives and work elements are generally complete and appropriate. Several questions did arise in reviewing this section: 1) Obj. 1 Are 4000 PIT tags enough to estimate SAR given the relatively few adults that will be produced from this number of smolts? 2) Obj. 1 Is a 100% detection of PIT tagged adults at the FCRPS PIT tag facilities a reasonable assumption? 3) Obj. 2 How does one obtain cost-free flight time for redd surveys? 4) Obj. 4 If habitat assessments are conducted only on channels 5th order and smaller, will some areas potentially used by Chinook for spawning or rearing be excluded? 5) Obj. 4 Ignoring fast-water habitat when snorkeling could lead to some error in estimating abundance if a substantial proportion of the populations using fat-water habitat. This is not likely to be a problem for Chinook but could be for steelhead. Could several fast-water habitats in each sample area be electro-fished to address this problem? The two elements for which Fast-Track review were requested (Chinook portion of Obj. 2 and Obj. 6) were very complete. Three of the five work objectives apply to ongoing efforts by the project's proponents, and two objectives (habitat status and trends, juvenile salmonid monitoring) have been called for by the ISRP but not yet funded. The objective of operating the rotary screw traps from October 1 to May 31 is admirable, but mechanical problems, weather-related issues, and other unforeseen problems will inevitably occur. It would be useful to state what back-up equipment and procedures are in place to deal with such events. The spawner escapement estimation procedures were thoroughly described, and the project proponents have a lot of experience in this aspect of the work effort. It was nice to see that the proposed 2010 surveys will include some randomly selected reaches to check for Chinook salmon spawning range expansions. The ISRP wonders if any research has been done to determine the error rate for identifying hatchery fish based on adipose fin clipping in the John Day or nearby subbasins. What is the probability of mis-identifying a hatchery fish with an imperfect adipose clip, or a wild fish that has lost part of its adipose fin? The location of the habitat survey sites will be determined by a GRTS (EMAP-type) randomized design. While there will be some inevitable compromises due to landowner access issues, we wonder if there is any value in intentionally locating some of the habitat survey sites at (1) the same locations as the spawning index sites or the juvenile survey reaches, or (2) within or near riparian or channel restoration projects. We agree that the GRTS approach is appropriate for assessing overall habitat status and trends within the subbasin, but additional and very useful information might be gained by co-locating the habitat survey sites with sites where fish will be censused either as spawners or juveniles. Within the list of habitat attributes, we recommend expanding the surveys of large trees (>0.5 m DBH) to all species, not just conifers. Owing to past logging practices and wildfire history there are very few conifers of this size within 30 m of the stream channel throughout much of the John Day subbasin, but there are other species (in particular, black cottonwood) that meet this size criterion. While it is true that cottonwood will not persist as long in the streams, it is currently the best candidate for LWD recruitment. To estimate escapement of Chinook and steelhead from redd counts, the proponents propose to use data on fish/redd from another subbasin. This approach seems reasonable given that weirs are not present in the John Day to enumerate the number of adults potentially spawning above the weirs. Why are there no weirs in John Day tributaries? Steelhead redds will be enumerated in five tributaries thought to support independent populations. From this information subbasin escapement will be estimated. Why not estimate redd densities and escapement for each of the five tributaries (populations) rather than just for the subbasin as a whole? This approach could provide greater resolution and information about redd and escapement levels especially if the tributaries differ significantly in quality and quantity of spawning habitat. For Objective 3, pertaining to habitat status and trend monitoring, are any of the sample sites likely to be in reaches where restoration activities have taken place? How will data analysis deal with information from both sites where habitat enhancement has been implemented and sites that have not been treated? Will there be an attempt to distinguish between the two in analyses? Water temperature and thermal refugia are not being monitored. Is availability of cool water during summer not a limiting factor in the John Day basin? For Objective 4, will juvenile sampling be concurrent with habitat sampling? Estimation of juvenile abundance will be based upon snorkel counts of juveniles in pools. Pools will be ranked according to a visibility rating. Pools ranked 0 or 1 (poor visibility, high amount of hiding cover) will not be used in data analysis if the reach also contains pools ranked 2 and/or 3 (moderate to little hiding cover, good visibility). However, if all pools within a reach are ranked < 2, then the pools will be electrofished rather than snorkeled. This could introduce bias because for some reaches pools ranked 0 or 1 (probably the best fish habitat) will be excluded from analysis while in others (electrofished reaches) they will be included and, further, the reach data may not be comparable because two different methods of estimating fish density were employed (snorkel and electrofish). Density estimates of electrofished reaches may be greater than those of snorkeled reaches both because better quality habitat is being sampled and electrofishing may be a more effective way of counting fish. Why not electrofish all reaches and eliminate the potential problem? 4. M&E The M&E program proposed by this project has been carefully planned and well conducted to this point. The proposed additions to the ongoing M&E effort (Chinook and steelhead escapement, habitat and juvenile monitoring, genetic characterizations) would round out the program and provide much needed additional information. As in the past, the ISRP supports both juvenile and habitat monitoring to identify productive rearing habitats, establish quantitative relationships between habitat quantity and quality and juvenile abundance and distribution, quantify limiting factors for juvenile survival, and guide habitat enhancement actions.