The field data collected and then analyzed by the Idaho Steelhead Monitoring and Evaluation Studies (ISMES) is appropriate and used in management of steelhead populations. Because the proposal lacks a comprehensive explanation of steelhead monitoring in Idaho, the specific role ISMES contributes is difficult to ascertain. The ISRP has no reason to believe the monitoring is not essential, but the need for monitoring should be made clearer in the proposal. Consequently, a response is requested that provides the following in a revised narrative: 1. A table that outlines the ESU, MPG, Independent Populations, and streams in the Snake River system and that identifies which are potential high precision and low precision sites for RME. 2. A summary explanation of what process is underway (if any) to decide which component streams are part of the intensive and extensive sampling. 3. Greater detail of explanation for the precision/sampling intervals for intensive and extensive sites. 4. A summary table of the data collected for each of the sites by the ISMES (or cooperators) since the last ISRP review. Also include trend data that summarize steelhead abundance trends over the duration of the study period. 5. Comparison of the precision and sampling intervals in the ISMES streams with that desired by the BiOp RME statistical analysis. 6. Statements for the ISRP about any events or problems since the last review that may compromise the analysis of the ISMES. 7. Statements of whether any deficiencies in the data have been identified in BiOp, TRT, or CSMEP reports, and if so, description of how these deficiencies have been considered in the basinwide strategy and subsequent project modification. 1. Technical Justification, Program Significance and Consistency, and Project Relationships The Idaho Steelhead Monitoring and Evaluation Study (ISMES) is another long-standing project that has benefited from previous ISRP reviews and interactions with the project proponents. The project has a long and developing history. It is well justified within the proposal and in the Council's Program. Relationships with other projects are extensive (Table 3 in proposal) and involve collaborations and efficiencies for data collection, data exchange, and coordination. The project appears consistent with the Fish and Wildlife Program and BiOp and ESA management needs. There is specific reference to increase B-run steelhead monitoring in RPA 50.5. The proponent states this project is the only one focused on wild steelhead in Idaho. This, however, does not address the question of whether the objectives of this study fulfill the RPA, or whether other projects also contribute. The proposal references the Columbia Basin Regional RM&E Strategy and directs reviewers to a CBFWA website and table titled Critical Contracts and Identified Gaps, to justify continuing much of the past ISMES program. It would be helpful to the ISRP to summarize in a table in the proposal the essential monitoring that is needed for Idaho steelhead, and then identify which projects and proponents are suppose to complete these tasks. Ongoing and new tasks for ISEMS should be specifically identified. This project, together with others in the Snake River would benefit from an integrated review. Many projects overlap in duties, species addressed, and personnel. The general explanation that data collected by this project are used to estimate VSP parameters for the Snake River Steelhead ESU (DPS) is well done; the VSP parameters are summarized, the hierarchy of spawning aggregates, independent populations, major population groups, and then the ESU is explained, and the general sorts of data used to estimate the parameters are referenced. Specific information on the details of the hierarchical structure of Snake River steelhead ESU is incomplete in the technical background summary. Figure 1 (page 13) that identifies weir and screw-trap locations leads to the conclusion that there are two MPGs, and the appendix leads to the conclusion that there are a number of “populations” associated with individual tributaries. However, there is no statement as to the number of MPGs, the number of populations, and how many of these have multiple spawning aggregates. The recent steelhead genetic structure investigation that apparently forms the basis for anticipating delineation of adults and juveniles at Lower Granite Dam to MPG and perhaps population is not sufficiently summarized for reviewers to understand the state of development of this monitoring strategy. It is also not clear whether the precision of past data is sufficient for BiOp and recovery/delisting management decisions. 2. Project History and Results The project history section is well done in terms of describing activities undertaken. Missing, however, are results in terms of what the project has found out about the “status and trends of wild steelhead populations” (the project purpose, as stated on page 1 of the proposal narrative). The project has evolved and become both more rigorous and comprehensive than its earlier versions. Some rudimentary (and intriguing) results were referred to on page 11 in the proposal, but not presented. Reviewers would like to see more findings presented, given the duration and ongoing nature of the project. The narrative on pages 11 and 12, together with the maps of snorkel sites, screw traps, and weirs are helpful; however, the project history and results are insufficient to inform a scientific review for ongoing efforts and to establish that standards for quality assurance/quality control for the Columbia Basin Monitoring Strategy are being met. A summary of the genetic analysis that concludes that sampling at Lower Granite Dam can be used to estimate the proportions of MPGs and some individual populations is necessary. Estimates of metrics under objectives 1 through 8 should be summarized in the proposal. There should be evidence included that the sampling protocols are rigorous enough to meet the guidelines for precision in the basinwide strategy. The project accomplishments shown in the tabular outline and in the narrative consist only of actions performed, rather than biological results. What has been found out about what the narrative states as the project's purpose—to evaluate the status and trends of wild steelhead populations in Idaho? It is said: "We will assess abundance, productivity, spatial structure, and diversity at the population and major population group scales . . . also assess abundance, productivity, and diversity for the Snake River Distinct Population Segment." Project proponents should present the findings to date on these matters as part of the proposal and to help reviewers evaluate the project's progress. Additionally, proponents should describe how this data fits and has fitted with TRT analysis of population viability and estimation of VSP parameters. Proponents should explicitly describe how their past data has been used and how the additions would inform future VSP analysis. The high precision data type is not clear. The reference to a CV of 15% or less (Crawford and Rumsey 2009) has not been established as a reasonable data standard. CV (coefficient of variation) is not usually associated with precision of data, but with the variation associated with a state of nature. That is, salmon abundance across years has a CV, fall steelhead parr length has a CV. These are descriptions of the state of variation. They are not appropriate to determine confidence intervals. Crawford and Rumsey (2009) reference Carlile et al. (2008), which makes recommendations for coefficients of variation for estimates of total spawning escapement. The reference is to standard error of the estimate, not to variation in the population. More importantly, the statistical and biological basis for the recommendation in Carlile et al. (2008) has not been reviewed. The justification that the standard represents a realistic goal for planning because it corresponds to an acceptable risk (one year of one stock in six) of failing to label a stock of concern when warranted appears to be arbitrary. The observation that the standard has proven to be attainable for many escapement estimation studies does not mean that this is the appropriate data standard. Further justification for sample size targets is required. 3. Objectives, Work Elements, and Methods Project work elements have been retained from the earlier (2007-2009) project to provide continuity; however, other elements have been added to expand the project in response to mandates in the Idaho Fish Accords. The objectives and work elements are clearly stated in the proposal. The overall objective of estimating VSP parameters for Idaho Snake River steelhead is scientifically defensible. Methods are typically general, though supporting or source methods are noted (such as the modification of Thurow et al.'s 2006 snorkel survey methods for observation of marked juvenile steelhead). Other sections include detailed and specific descriptions of equipment and methods appropriate for the proposal and its objectives. Questions regarding individual objectives follow: Objective 1. Why is the minimum sample size 2,000 (page 15)? If the wild steelhead are sub-sampled to attain 2,000 fish, how can this be called a minimum sample? This seems more like a target sample. Work element B. How are results from different scales from an individual fish reconciled (page 16)? Is there any effort to use PIT tagged fish to establish the "true" age so error rates can be estimated? How would this error affect population dynamic and viability assessments and management uncertainty? Work element D. Why a sample size of 2000 smolts? Objective 2. Identify the MPG and independent populations associated with Fish Creek, Rapid River, and Big Creek (The appendix tables are inconsistent with reference to MPGs. One table has 2 MPGs and a second table has 5). Work element G. Why are hatchery adults being released into the Lochsa River? How does this influence the abundance and productivity estimates for VSP in the associated independent population, MPG, and DPS. Work element H. It is not clear how population estimates are generated using the fish obtained through hook and line fishing. Please elaborate. Work element I. Explain why wild steelhead are being enumerated using a fish hatchery ladder. Do all the steelhead in this stream enter the ladder? How are they passed upstream? How are unmarked hatchery fish assessed and differentiated from wild fish? Objective 3, work element P. It is not clear if some of the field work associated with estimates of adult escapement above weirs in other rivers is conducted by personnel from ISMES, or if ISMES only conducts analysis. Objective 4. Work element R. Please elaborate on the GRTS rotating panel used for this analysis. For snorkel surveys (and concomitant evaluation of "gross habitat characteristics") is the "desired average site length" of 100 m always long enough to adequately sample the habitat types mentioned (pool, pocket water, riffle, or run)—or at least one of them in its entirety per site, and is this important? Use of 100-m sites is apparently based on just a single reference (Thurow et al, 2006). Adequate site length may depend largely on channel width. Size and longitudinal spacing of habitat types are generally proportional to channel width. A stream 2 or 3 meters wide could be expected to include a series of several pools and riffles within a 100-meter reach (if it has pool-riffle structure), but a stream of about 20 meters wide or larger could happen to include just part of one pool or of one riffle within a 100-meter reach, thus not cover even one habitat unit. Would adjusting site length according to channel width better represent habitat conditions than arbitrarily setting 100 meters as the desired site length for all streams? Are channel widths of the study sites reported in the narrative? The proposal could be improved by listing the project's streams and their study sites, showing characteristics, such as streamflow discharge (range of flows and those usually occurring at season of sampling), channel width, channel gradient, habitat features, and channel length sampled. The proposal cites that the goals and strategies for monitoring and evaluation of the status of Snake River Chinook salmon and steelhead were identified in the fall 2009 RM&E workshop. It is not entirely clear how ISMES has been expanded or modified to meet the basinwide monitoring strategy. More information is needed for evaluation of whether the increased effort meets the RM&E goals. In particular, one goal is to "obtain high precision status and trend data for at least one population per adult life-history type per MPG (fish in, fish out monitoring). One of the open questions is the selection of populations for this monitoring. The ISMES suggests that they may be collecting this information; however, the population is not yet selected. A succinct summary of the MPGs and independent populations established by the TRT, which have high precision data, and which are associated with the ISS, needs to be included.

A response is needed in the form of a revised narrative. It is not clear to the ISRP how INPMEP has been modified to accomplish the basinwide strategy for monitoring. Please make clear to the ISRP how INPMEP has been modified to meet the strategy formulated in the fall 09 RM&E workshop. In particular clarify how populations will be selected for high-precision (fish-in/fish/out) monitoring and summarize the populations in the MPGs that have high precision data. Explain the relevant pros and cons of transferring the snorkel survey monitoring to ISMES. The ISRP notes that CV (coefficient of variation) is not usually associated with precision of data, but with the variation associated with a state of nature. That is, salmon abundance across years has a CV, fall steelhead parr length has a CV. These are descriptions of the state of variation. They are not appropriate to determine confidence intervals. Crawford and Rumsey (2009) reference Carlile et al. (2008), which makes recommendations for coefficients of variation for estimates of total spawning escapement. The reference is to standard error of the estimate, not to variation in the population. More importantly, the statistical and biological basis for the recommendation in Carlile et al. (2008) has not been reviewed. The justification that the standard represents a realistic goal for planning because it corresponds to an acceptable risk (one year of one stock in six) of failing to label a stock of concern when warranted appears to be arbitrary. The observation that the standard has proven to be attainable for many escapement estimation studies does not mean that this is the appropriate data standard. Further justification for sample size targets is required. 1. Technical Justification, Program Significance and Consistency, and Project Relationships Until now, the project has been intended to monitor and evaluate the status and trends of wild Chinook spring/summer salmon and summer steelhead populations in Idaho. According to the proposal, the Idaho Natural Production Monitoring and Evaluation Project (INPMEP) was designed to "provide information to managers and to regional decision-making processes. The Snake River stocks of steelhead and spring/summer Chinook salmon still have significant natural reproduction and thus are the focal species for this project’s investigations. The overall project goal is to monitor the abundance, productivity, distribution, and stock-specific life history characteristics in order to assess and annually report the status of naturally-produced steelhead trout and Chinook salmon populations in Idaho." Project goals are clear and well-justified in the context of the BiOp, the pertinent subbasin plans, and other enabling agreements. A number of significant changes to the project are proposed in the current document that would modify the project's scope. Relationships with other projects are complex and are clearly presented in the proposal. 2. Project History and Results The proposal describes project history in a helpful manner. It discusses how the snorkel survey program has undergone several changes and now will be transferred to another project. A discussion of the advantages and disadvantages of the transfer would be helpful. The ISRP commends the investigators for publishing their results in the open literature. One task was not accomplished: "Sub-objective 3.2: Locate areas of high STHD fry density. This task was not completed due to logistical reasons." It would help the ISRP to understand the logistical problems. 3. Objectives, Work Elements, and Methods Changes proposed for the project include that the genetic component will be performed by the new genetic stock identification project at Lower Granite Dam (project 201002600), as recommended in an earlier ISRP review. Another proposed change is to “narrow the scope of INPMEP to focus on spring/summer Chinook and transfer steelhead monitoring elements to ISMES. Beginning in 2010, INPMEP will coordinate summarization and reporting of redd count and carcass survey data, which supports the strategy for extensive monitoring of Chinook. For extensive steelhead monitoring, the recommended option is genetic stock identification at Lower Granite Dam. However, the technique would take at least five years to develop the first productivity data point. IDFG recommends that snorkel surveys continue as another extensive monitoring technique for steelhead. We further recommend transferring this element to Idaho Steelhead Monitoring and Evaluation Studies (project 199005500)." They elaborate that because these projects also use the experimental design, INPMEP provides similar data from other watersheds that complements and extends the spatial coverage of data from these projects. Because data from snorkel surveys are most important for steelhead monitoring, investigators recommend transferring this element to Idaho Steelhead Monitoring and Evaluation Studies (project 199005500). The ISRP does not oppose this change but would like to see a more detailed discussion of the relevant pros and cons. The proposal states "By understanding the transitions between stages and associated controlling factors, we hope to achieve a mechanistic understanding of population dynamics." The ISRP would be helped by a fuller explanation. The project provides for annual VSP (abundance and productivity) monitoring and less frequent spatial structure monitoring based on spawning ground surveys and surrogates for them. Although a response is needed, the proposal employs competent methods, adequate metrics, and qualified people.

199005500-ISMES
Project needs coordination with other PIT tagging through PIT Plan.	PIT tagging protocols used by this program were designed to meet specific research objectives as described in the ISMES study design, which has passed several critical reviews by ISRP.  In the past we have provided PIT tag support to other RM&E programs such as CSS when approached by these programs to increase efficiency and provide more cost effective ways to use limited resources. IDFG as not been contacted by anyone to provide input or help develop a regional PIT-tag plan.  If (and when) a proceess is developed to draft a regional PIT plan,  IDFG will fully engage in its development.
What is the value of ongoing snorkle surveys?	Extensive and intensive snorkel surveys for juvenile abundance (parr density) and spatial structure were considered critical at the RM&E workshops. In addition, and in lieu of redd counts, parr densities are the only measure for steelhead spatial structure for most populations. They are also a surrogate index for steelhead adult abundance at smaller spatial scales. We record information for steelhead, Chinook, and resident fish which contributes to over 30 years of trend monitoring for these species. These snorkel surveys monitor juvenile abundance, productivity, and spatial structure, which are all required by the BiOp.

Please also see ISRP 2010 Reply - Addendum (PDF) 
https://pisces.bpa.gov/release/documents/DocumentViewer.aspx?doc=P117155

199005500-ISMES
Project needs coordination with other PIT tagging through PIT Plan.	PIT tagging protocols used by this program were designed to meet specific research objectives as described in the ISMES study design, which has passed several critical reviews by ISRP.  In the past we have provided PIT tag support to other RM&E programs such as CSS when approached by these programs to increase efficiency and provide more cost effective ways to use limited resources. IDFG as not been contacted by anyone to provide input or help develop a regional PIT-tag plan.  If (and when) a proceess is developed to draft a regional PIT plan,  IDFG will fully engage in its development.
What is the value of ongoing snorkle surveys?	Extensive and intensive snorkel surveys for juvenile abundance (parr density) and spatial structure were considered critical at the RM&E workshops. In addition, and in lieu of redd counts, parr densities are the only measure for steelhead spatial structure for most populations. They are also a surrogate index for steelhead adult abundance at smaller spatial scales. We record information for steelhead, Chinook, and resident fish which contributes to over 30 years of trend monitoring for these species. These snorkel surveys monitor juvenile abundance, productivity, and spatial structure, which are all required by the BiOp.

The project sponsor's response clarifies the objectives and value of the project and adequately addresses the ISRP's comments from the preliminary review.

The role the data collections and monitoring effort contributing to steelhead management was thoroughly presented. The ISRP query about smolt age and smolts/spawner as metrics of production was clarified with examples of data collected by the project. In response to the ISRP question regarding management actions taken as an example of the project, sponsors identify that steelhead supplementation was discontinued because of the project data. The ISRP recommends to the sponsors that they continue to identify uses for the data in developing management actions for steelhead, not just for the viability assessments of this species. Sponsors identify that genetic analyses will involve analyses beyond Hardy-Weinberg Equilibrium, Fst, and assignment tests, and will include evaluation of straying, effective population size, and estimation of ESA-recovery unit adult run size at Lower Granite Dam. The ISRP appreciates the clarification of differences in the approaches of Idaho Natural Production Monitoring and Evaluation Program and Idaho Steelhead Monitoring and Evaluation Studies. Finally, while the ISRP acknowledges that annual abundance estimates are not typically published in peer reviewed journals, we believe that when placed in a management context the data that is being produced by this project would be of high quality. For example, contrasting effective population size estimates with census population sizes is unreported for most species, and would be publishable.

Reporting of results in the proposal is good, but the ISRP encourages the sponsors to further explore opportunities to publish information produced by the project as further evidence of its value.

These remaining ISRP concerns with this project should be addressed in subsequent ISRP reviews. In addition, it may be time to conduct a more in-depth review of monitoring in Idaho. It is not clear who collects data how, when, and where in Idaho and how this collection feeds into NOAA TRT analyses, etc.

The sponsors responded to clarify the primary questions raised by the ISRP. The adequacy and depth of the clarification varied across the questions raised.

In response to the ISRP questions of whether the project could be scaled to provide only the data needed for regional RME needs, and how past uses of the data justify continuation, the sponsors provided a succinct and sufficient response. The ISRP recognizes that the Idaho Natural Production Monitoring and Evaluation project has been instrumental in providing critical data for assessing the status and trends of salmonids (principally spring and summer Chinook) in the Salmon River subbasin.

The response provided by the sponsors clarified how their objectives relate to recovery planning in general. It is clear that valuable data has been generated and that the project has added value to these data in the past through appropriate analyses. The ISRP appreciates the perspective concerning the project changing due to information demanded by regional decision-makers.

In response to questions on the need for additional genetic and life history data on Chinook salmon, the sponsors respond, "The details of life history and genetic structure of Chinook salmon populations in Idaho are not well-known on the scales required for population-level recovery planning and monitoring. INPMEP should be the main source of this information for groups like the ICBTRT. Many of the population delineations made by the ICBTRT were made using professional judgment and not backed by hard data."

The ISRP recognizes that microsatellite and SNP genotypes are not available for all the spring and summer Chinook in the Snake River region. At the same time NOAA Fisheries and others have been using microsatellite genotyping to evaluate a number of salmon management problems in the Snake River system. Sponsors did not show how any of this new data had altered the understanding of Chinook salmon metapopulation structure and how additional data was essential to management decisions. It is not clear if this data would do little more than reinforce the existing understanding of population structure. While more data would almost always be useful, sponsors have not identified what management decisions hinge on the data. This should be made evident before undertaking further genotyping to define Chinook salmon metapopulations. The ISRP's intent is that the management questions and the sponsors' methods and tasks to address them be made explicit. The purpose is to help ensure that the data collected is the most useful. Further explanation of the need for describing the fine-scale genetic structure of Chinook salmon in Idaho is necessary before this component of the project is justified.

The sponsors clarify that they are not involved in the investigation of hatchery effects on natural spawners and natural populations, but that data they collect on natural populations is used by projects that are conducting those investigations. This response is appreciated by the ISRP, and the importance of that effort is understood.

The sponsors' clarification of objective 1) Describe the population structure of Snake River spring/summer Chinook salmon, and 4) Evaluate life cycle survival and the freshwater productivity/production of Snake River spring/summer Chinook salmon, were unconvincing. The ISRP comment on 1 is found in the paragraph above on genetic and life-history investigations. For objective 4, the primary purpose of engaging in life cycle survival estimation is to support tributary habitat restoration effectiveness monitoring. The proposal is insufficient to evaluate whether this is the suitable vehicle to accomplish that task. The proposal does not discuss tributary habitat restoration in the subbasin and provide a connection between this project and those efforts. The sponsors' clarification of objective 2 and 3, estimation of juvenile and adult abundance and distribution is sufficient.

Fundable in part to conduct the essential juvenile (parr and smolt) abundance data collections and the essential adult redd and age distribution information. The genetics work component is not scientifically justified in the proposal or response.