We judge the overall implementation of the project to be adequate, but the Yes (Qualified) rating does not represent ISRP endorsement of the interpretations of data and results.

Qualification 1: The ISRP believes that natural-origin abundance trends in Johnson Creek as a response to a supplementation treatment must be interpreted by reference to an unsupplemented reference location. The Sesech River is proposed by the proponent. These analyses need to be included in future proposals and any Three-Step review for expanded production.

Qualification 2: The proposed expansion of the Johnson Creek project and facilities needs to be reviewed through the Council’s Three-Step process. Additionally, the expansion of the fish releases will require review and consultation with NOAA Fisheries for the Hatchery and Genetic Management Plan (HGMP).

Summary: The ISRP appreciated the proponent's constructive approach to the response. The proponents gave a clear and articulate response that continues to advance a positive dialog regarding the Johnson Creek project. Probably the most important issue, the proposed expansion, was deferred to the Three-Step process, and that seems most appropriate. Other ISRP concerns that were well addressed include the egg-to-smolt differential survival for wild versus hatchery fish and possible mini-jacking.

With respect to the pending Three-Step review, the ISRP believes that consideration of expansion needs to explicitly treat both demographic and genetic elements of conservation. The proponent is principally arguing for expansion based on retention of genetic diversity. Any formal plan needs to demonstrate how expansion can achieve the intended goals for genetic diversity, and for abundance and productivity. Expansion has the potential to decrease natural adult abundance by removing adults for hatchery production, and the potential to increase density dependent effects on juvenile survival and life-history/behavior by addition of juveniles beyond the stream’s carrying capacity.

The explanation of the updated replacement rates for natural and hatchery adults is not entirely satisfactory. It is clear that the updated numbers reflect an expanded geographic scale. It is less clear how the current numbers are estimated. It appears to the ISRP that this must be due to hatchery-origin adults returning in larger numbers than reported previously, and spawning below the capture weir. The types of data (weir, redd counts, carcass surveys) that are used to arrive at the updated evaluation and the actual numbers, expansion, and derivation are not transparent.

The proponents need to provide additional clarification on the following points. The points are further elaborated in the Summary and specific comments below. 1. The proponents need to demonstrate that the expansion is needed to address the perceived problem. The increase is discussed indirectly in the Problem Statement but needs to be more clearly and directly justified. The proponents need to convincingly describe the problem and what they believe are the potential causes. There appears to have been a boost in returning adult numbers in recent years associated with the Johnson Creek supplementation effort. Recent increases in adult returns beg the question of why an expansion of the program is justified. 2. A response is needed to clarify how abundance and productivity of spring/summer Chinook is to be assessed in the Johnson Creek supplementation program, and discuss the potential for coordination with the hatchery effects proposal to bring this project into full compliance with the AHSWG recommendations. The ISRP understands that the Sesech River will serve as a reference site to evaluate JCAPE, but the methodology is not presented, and results to date are not presented. 3. There appears to be a change in numbers reported that requires clarification. There is a very important difference in the data reported here, and that reported in the 2007-2009 proposal and the ISRP requests a clarification. In the 2007-2009 proposal the replacement rate for supplementation fish was lower than for natural-origin adults for 1998 and 2000 (6.99 versus 6.95 for 1998 and 4.46 v. 2.88 for 2000). In Table 4 these replacement rates are now 6.78 versus 7.06 for natural and supplementation in 1998 and 2.81 versus 3.5 for natural and supplementation females in 2000. How did these estimates change in the interval since the earlier reporting? 4. Another issue involves the (poor) survival of wild juveniles in the Upper Salmon and their habitat use. The proposal indicates eyed egg to smolt survival for the JCAPE has averaged 97.4%, which they contrast with high mortality (74.8%) from the egg to smolt stage within the Salmon River (Kiefer and Lockhart 1997). It would seem that evaluation of the causes of those patterns would perhaps pinpoint the causes of poor wild juvenile survival. The proposal’s DELV-14 is to “Determine status and trends of Chinook salmon habitat in the South Fork Salmon River Subbasin” by implementing the Environmental Monitoring and Assessment Program (EMAP) sampling framework, a statistically based and spatially explicit sampling design to quantify status and trends in stream and riparian habitats. Such monitoring is well designed but could be more valuable if in addition it was designed to test specific hypotheses regarding juvenile habitat use and survival, and contrasting patterns for wild vs. JCAPE fish. 5. Another issue pertains to possible minijacks, the abundance of which is being seen (i.e., by proposal 200203100) to be problematic in several ways in supplemented Chinook populations. Granted, calculation of female:female ratios somewhat obviates some concern, but the proposal includes no discussion of minijacking. Summary Comments: The proposal was in general well written, and the Executive Summary does a good job giving basic history, accomplishments, and logic. This proposal is for an expansion of both facilities and scale of the Johnson Creek Artificial Propagation Enhancement. Consequently, a more thorough review of the proposal is likely warranted through the Three-Step Process. In the meantime, the proponents need to respond to several items. The main thrust of the proposal is to increase smolt production of JCAPE from the current 100,000 smolts (produced by 80 NOR adults) to 300,000 smolts, which would require 240 NOR adults for broodstock. Given the preliminary result presented in the proposal it is hard to see why the increase is justified. The increase is discussed indirectly in the Problem Statement, but needs to be more clearly and directly justified. The increased production objective also drives the hatchery facility expansion. Without a more clearly justified explanation for the proposed increase in production, it isn’t possible to support the proposed expansion of the facilities. During the presentation, the ISRP asked for additional information on the justification for tripling the smolt releases and the hatchery facility expansion? Jason Vogel said the tripling is to diminish the genetic risk – that a broodstock sampling of 80 NOR fish was not adequate to represent the entire run. If this is true and modeling could help identify whether it is adequate or what sample size might be more representative, additional NOR fish could be brought into the broodstock sample without the necessity of increasing the number of smolts released (and therefore having to increase the facility size). The proponents note that the justification for the increases (broodstock, smolts, and facilities) come from M&E findings that are detailed in the JCAPE HGMP to be submitted to NOAA Fisheries. This information needs to be in the proposal and in the response to the ISRP. Other concerns include: 1. There does not appear to be a restriction on supplementation fish on the spawning grounds. At the present time the returns of hatchery-origin salmon are not so large as to create a population largely influenced by hatchery production, especially since all brood fish are natural-origin. If hatchery returns should increase substantially this balance could shift, and there does not appear to be a decision framework or experimental design to evaluate the consequences. 2. How does abundance of natural-origin adult Chinook salmon in Johnson Creek compare with Secesh River, the designated reference location? The essential measure of supplementation is the abundance of natural-origin adults (females) in a supplemented stream in comparison with a reference location, and the productivity in the supplemented population in contrast with an unsupplemented reference site. How these evaluations are going to be conducted and preliminary analyses need to be incorporated into the proposal. Full comments: Some of the comments below are highlighted above. 1. Purpose, Significance to Regional Programs, Technical Background, and Objectives The principal linkage for this project to regional programs, based on the proposal, is to Wy-Kan-Ush-Mi Wa-Kish-Wit; the Columbia River Anadromous Fish Restoration Plan developed by the Nez Perce, Umatilla, Warm Springs, and Yakama Tribes. The proposal identifies elements of the 2008 BiOp that recognizes the actions in Johnson Creek, and considers Johnson Creek to be an important component of the South Fork Salmon spring Chinook Major Population Group. No specific reference is provided to the Council Research Plan or to the recent Anadromous Salmon Monitoring Strategy. Problem Statement/Technical Background: The explanation of where the project is taking place and the status of the spring/summer Chinook population is adequate. The technical background is incomplete. The stated purpose of the supplementation in Johnson Creek is to reduce the extinction risk (extirpation risk) for this spawning aggregate. The discussion of this topic does not quantify either the extinction (extirpation) risk, the anticipated reduction in risk owing to the project, or provide a sufficient method for evaluating any benefit. As elaborated on elsewhere in the review, and emphasized in the ISAB supplementation report (ISAB 2003-3) and ISAB and ISRP memo on supplementation monitoring (ISRP/ISAB 2005-15), the essential metrics of interest are the abundance of natural-origin adults returning to Johnson Creek and the productivity (female to female replacement rate) of natural-origin adults resulting from supplementation. While there are many interesting metrics being collected, there is not an analytical framework presented in the proposal to address these essential uncertainties. The project should have clear objectives for performance of the fish in the hatchery, performance of both hatchery and natural fish in the wild, and measures of benefit (abundance of NORs) and deleterious risk (productivity of NORs spawning in the wild). The monitoring that takes place (weir counts, redd counts, juvenile (parr, smolt)) provides valuable information on an important population of spring/summer Chinook. Objectives: Obj-1. Maintain and enhance natural production in the Johnson Creek summer Chinook population: The ISRP does not believe that productivity of the Johnson Creek spawning aggregate can be increased by hatchery smolt releases. The proponent states that they assume this objective will be attained by having supplementation and natural productivity equal. This may increase abundance, but is unlikely to increase productivity. The concern with supplementation is that the increased abundance owing to supplementation will be at the cost of natural spawning productivity. Obj-2 Maintain life-history characteristics in Johnson Creek summer Chinook salmon. The comparison needs to be between natural-origin juvenile and adults in Johnson Creek with an unsupplemented reference location, not a comparison of supplementation and natural fish within Johnson Creek. As the accomplishments demonstrate, there are a variety of life-history difference between natural and hatchery fish in Johnson Creek, and these have been demonstrated in a number of spring/summer Chinook supplementation programs (Grande Ronde, Tucannon, Imnaha). The important uncertainty is the extent to which natural fish life-histories are being altered by interbreeding with the supplementation fish, and whether there is a productivity decline as a consequence. Obj-5 Operate the hatchery program to achieve optimal production effectiveness while meeting priority management objectives for natural production. Description: The desired outcome...if hatchery smolt-to-adult return rate is equal to JCAPE criteria (0.65 and 0.87). It is not clear to the ISRP what the JCAPE criteria are. What do the 0.65 and 0.87 refer to? It would be useful to include the JCAPE criteria in the problem statement. 2. History: Accomplishments, Results, and Adaptive Management The history, accomplishments, and results are generally adequate. The proponents include a substantial summary of data collected from the project. One element that is missing is a summary of the numbers of hatchery-origin and natural-origin adults (by sex) that were passed above the weir for spawning. It may be possible to summarize this from Table 8, but a simple table would be useful. There is a very important difference in the data reported here, and that reported in the 2007-09 proposal and the ISRP requests a clarification. In the 2007-09 proposal the replacement rate for supplementation fish was lower than for natural-origin adults for 1998 and 2000 (6.99 versus 6.95 for 1998 and 4.46 vs. 2.88 for 2000). In Table 4 these replacement rates are now 6.78 versus 7.06 for natural and supplementation in 1998 and 2.81 versus 3.5 for natural- and supplementation females in 2000. How did these estimates change in the interval since the earlier reporting? The observation that hatchery spawning yields an increase in adult fish is not surprising. This common observation is the primary reason supplementation is contemplated as strategy to improve the status of ESA listed species. When this is realized in a supplementation system it is not evidence of success of supplementation. It is a necessary, but not sufficient, condition for supplementation to provide a benefit. The report in 2007 that supplementation fish had a lower replacement rate than natural-spawning female was evidence that a fundamental condition for supplementation was not being achieved. Supplementation cannot provide a benefit if the fish taken into the hatchery produce fewer adults than fish left in the stream. The corollary, that if supplementation fish produce more adult progeny than natural spawning fish, then supplementation is beneficial is not true. The measure of benefit is whether natural spawning by a mix of supplementation and natural adults produces more adult progeny than the natural adults alone would have. This is a challenging evaluation. It requires comparing the production from the supplemented system to a reference unsupplemented population. This essential evaluation does not appear in the proposal accomplishments. Perhaps the most significant finding is that hatchery broodstock do reproduce in the wild successfully, at a rate that is 7.25 times that of their natural counterparts. 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging) The principal linkage for this project to regional programs, based on the proposal, is to Wy-Kan-Ush-Mi Wa-Kish-Wit; the Columbia River Anadromous Fish Restoration Plan developed by the Nez Perce, Umatilla, Warm Springs, and Yakama Tribes. The proposal identifies elements of the 2008 BiOp that recognizes the actions in Johnson Creek, and considers Johnson Creek to be an important component of the South Fork Salmon spring Chinook Major Population Group. No specific reference is provided to the Council Research Plan or to the recent Anadromous Salmon Monitoring Strategy. 4. Deliverables, Work Elements, Metrics, and Methods The project is part of the DFRM database management program. This looks strong, but is difficult to evaluate from this prospective. Also, the plan for five-year review looks commendable. The hatchery expansion or new construction needs the Council’s Three-Step Review.

For the response loop, the project sponsor submitted a letter from BPA that listed BPA's existing ESA implementation commitments and an estimation of new work anticipated to be a priority in addressing limiting factors for ESA-listed fish. The Johnson Creek Artificial Propagation Enhancement Project is listed in a table attached to the letter. The BPA letter does not address the scientific issues raised by the ISRP in its review. The ISRP recommendation of "Fundable in part" from the preliminary review stands.

The Johnson Creek Artificial Propagation Enhancement Project is Fundable in Part for one year (FY07) with subsequent annual funding contingent upon reporting of monitoring results and evidence of adaptive management decisions justified by the results. Sponsors also need to analyze and report on extinction risk. The annual report should be reviewed by an independent team.

The ISRP's preliminary review comments (June 1, 2006) were:

This is a long and complex proposal that richly documents its history including numerous iterative reviews by the ISRP. Significant exchanges have occurred between the project sponsors and the ISRP since the late 1990s and the removal of Johnson Creek from the ISS control stream status.

The goal of the Johnson Creek Artificial Propagation Enhancement project is to reduce the demographic risk of extirpation of the ESA listed Johnson Creek summer Chinook salmon and begin its recovery through supplementation while maintaining genetic diversity of the artificially propagated summer Chinook salmon population and the natural population. The sponsors hope to increase adult returns through increased juvenile survival and improved homing in order to preserve and recover the Johnson Creek salmon population. The ISRP has long been critical of this project for a variety of technical reasons. Most of these have been addressed through the above described iterative review exchanges.

A decision was made to initiate a supplementation program in Johnson Creek to increase the population size as it appeared to be at increasing demographic risk during the 1990s. Decision-makers must have concluded that removing Johnson Creek from the ISS study design would not compromise the objectives of the ISS. The current proposal redirects the Johnson Creek work to become an additional stand-alone assessment of supplementation. What is the reason for another stand-alone assessment?

The sponsors have provided an excellent summary of the results of their project to date. The proposal is well done. Proponents should be commended for reporting and making these data available. The next step is to make adaptive management decisions on the appropriateness and scale of further supplementation. This discussion is absent from the proposal.

The important data that the sponsors provide calls into question whether the supplementation program is providing any demographic benefit or whether it may be creating a demographic loss (page 24, Table 10). For both the 1998 and 2000 brood years, the female-to-female replacement rate was lower for supplementation than for natural spawning (6.99 vs. 6.95 for 1998, and 4.46 vs. 2.88 for 2000). In both these cases, more fish would have returned had the collected females been permitted to spawn in the wild than by bringing them into the hatchery.

With results to date, the ISRP does not currently see justification for supplementing Johnson Creek. Moreover, this project could result in harm to the wild population based on the data reported. What are the limits to broodstock mining? Continuing the project with adequate monitoring may only be valuable in better understanding the problems with supplementation.

The proponents provide appropriate evidence that the summer Chinook population in Johnson Creek has decreased over the past 50 years. The purpose of supplementing the population is to reduce a risk of extirpation of the population. What is needed to more fully justify the action is a quantitative assessment of the likelihood of extirpation within specific timeframes. This should be followed by a presentation of the level of demographic support from supplementation that would be required to reduce this risk; i.e., how much supplementation at specified performance levels would lead to a 10, 20, 30, 40% etc. reduction in the risk of extirpation? This provides a context for comparing the project to alternatives. If for example, the population has a 50% chance of extirpation in the next 25 years, will we only reduce that chance to 40% under the expected performance of the supplementation program? Finally, this type of analysis would logically lead to clear performance thresholds by which to judge the artificial production portion of the program.

While it is clear (p. 29) that natural origin adults are used for broodstock, it is not clear whether adults of hatchery origin are also used for brood stock purposes. This should be clarified. Supplementation in its strictest sense (RASP) would rely solely on natural origin adults.

This project has changed from what it was first intended to be. It is now viewed as a stand-alone assessment of supplementation rather than as a part of the ISS assessment program. It appears that several issues that were contentious in the recent past have been resolved. Benefits of the program are unknown at this point, but objectives seem vague in terms of reducing the risk of extirpation - by how much, in what timeframe. They also are vague with respect to adaptive management loops to modify, expand, or terminate the supplementation.

The monitoring indicates they are adding contrasts between supplemented and unsupplemented reference streams, but no detail for this contrast is provided. It is still unclear just how supplemented and unsupplemented "reference" streams will be compared. The reliance on contrasts of supplementation with natural fish within Johnson Creek are informative but not sufficient to evaluate demographic or fitness benefits or losses from supplementation. Evaluation for the project is dependent on suitable data from reference streams, but available streams are not free from stray fish from adjacent supplementation programs.

The sponsors have made information from the project available for independent review.

The identification and magnitude of adverse outcomes for non-focal species is unknown.