Response requested comment:

1.      Provide a synthesis of the overall approach and methodology used to achieve project objectives. Please include additional information on how the fall Chinook surveys are conducted. How often do they occur, how are redd locations identified and marked, are genetic samples being collected, are egg retention counts being made, are otoliths being collected for possible microchemistry analyses, and what type of length data are collected (e.g., FL, MEHP)? Provide variance measures of the spawning population estimates, as previously requested by the ISRP.

2.      Describe lessons learned and adaptive management resulting from past and ongoing research and monitoring. It is possible that the project consistently reviews its operations and methods on a regular basis to determine if anything might be improved. If this is the case, this procedure should be described in future reports. On the other hand, if a formal or quasi-formal adaptive management process is not yet in place, the proponents should establish one. This will provide them opportunities to discuss and possibly implement changes to existing procedures.

3.      Describe the extent to which FCRPS operators use information from this project to alter hydropower operations, as emphasized in the overall project goals. The ultimate goal of this project is to collect data that can be used to reduce potential impacts of hydropower operations on salmon spawning below the dams. The effectiveness of this effort should be reported in the proposal and annual reports. As part of this analysis, the proponents should describe and discuss the extent to which salmon redds were dewatered, if at all.

Comment:

1. Objectives, Significance to Regional Programs, and Technical Background

The purpose of this ongoing research and monitoring project is two-fold: (1) to assess the extent of spawning by ESA-listed fall Chinook salmon in the mainstem Columbia River so that the Federal Columbia River Power System (FCRPS) can be managed to protect and enhance these populations, and (2) to collect riverbed temperature data so that the emergence timing of ESA-listed chum salmon can be estimated. This allows managers to know when chum salmon emergence is complete and FCRPS operations can shift from protecting incubating chum salmon to supporting spring spill operations to aid other species.

Real-time water temperature and water surface elevation data supplied by the project, for example, are used by managers to prevent redd dewatering and estimate when chum salmon fry emergence has ended. Additionally, field surveys are used to count fall Chinook adults, carcasses, and redds, as well as collect biological information (scales, gender, length, fin clips, CWT retrieval etc.) from carcasses. This information is passed on weekly to another project for use in run-reconstruction, abundance forecasting, and VSP monitoring. The project seems to be well-integrated with other regional programs that use these data, and it addresses BiOp RPA Action 17.

2. Results and Adaptive Management

The project has routinely supplied environmental data to hydrosystem managers. This information has been used by managers to regulate hydrosystem flows to protect ESA-listed chum salmon spawning immediately below Bonneville Dam. Additionally, biological information on ESA-listed fall Chinook has consistently been sent to personnel supported by project 2010-036-00 who use it to track the status and trends of fall Chinook spawning below Bonneville Dam. Data from the project are helping to address questions in the Mainstem Habitat, Hydrosystem Flow, and Passage Operations, Population Structure and Diversity, and Climate Change categories of the Council's 2017 Research Plan. It is also directly linked to the Council's Fish and Wildlife Program which calls for sustaining abundant, productive, and diverse communities of fish and wildlife. Although the project reportedly collects and shares these data, the proposal and annual reports do not describe the extent to which this information was used to shift FCRPS operations as stated in its goals, nor do they discuss the extent to which salmon redds were dewatered.

Although an example of external adaptive management is described, no direct examples are provided on how the project has used adaptive management internally to modify or improve its objectives or methods. The proposal states that data supplied by the project are used by hydrosystem managers to adaptively manage flows to protect chum and Chinook using spawning and incubation habitats below Bonneville Dam. This is an important use of project's data for external adaptive management, but it does not address how or if the project has an internal process to refine its own operations. Clearly some changes in methods have occurred. The development of the real-time data system that is being used to convey hourly temperature and water height data would be one example how the project has changed. There are likely others as well.

In general, the results produced by the project are largely applicable to the project and its end users. However, the development and use of its "real time" data system to gather and send hourly water temperature and water height information could be a valuable tool for others examining the possible effects of dam operations on fish and wildlife populations.

Project reports have been produced on a timely basis, data has been provided to end users on a regular basis, and peer-reviewed publications on some of the project's results have been published.

While the information provided by this project are undoubtedly useful, there are some short-comings that need more discussion in the annual reports and proposal. For example, annual reports should describe the extent to which salmon redds were dewatered, if at all in response to water elevation fluctuations. To what extent were data from this project used to shift FCRPS operations as a means to protect salmon redds, as stated in its goals? To what extent has the project addressed previous ISRP qualifications, including the development of confidence intervals for spawning Chinook salmon? Specific information on lessons learned and adaptive management are needed.

3. Methods: Project Relationships, Work Types, and Deliverables

Methods seem appropriate but are not described in sufficient detail (or linked adequately via ~10 protocols) in the proposal. Methods for monitoring water temperature and elevation at chum spawning sites are described in detail in previous annual reports. Methods for estimating fall Chinook abundance below McNary, John Day and The Dalles dams were well documented in the Annual Report for 2001-2006, but no comparable documentation has been provided for surveys below Bonneville Dam. A qualification of the ISRP (2010-44b) review was to provide more detail on methods. For example, how often are boat and foot surveys conducted, how are redd locations identified and marked, are genetic samples being collected, are egg retention counts being made, are otoliths being collected for possible microchemistry analyses, and what type of length data are collected (e.g., FL, MEHP)?

No formal description is provided on how the project monitors whether it is meeting its objectives. However, the expected hourly delivery of environmental information and weekly submission of biological data to end users likely serves this purpose. Because of the immediate need for some of the project's data, any interruptions in data flow would be quickly recognized and corrected if possible. Nevertheless, the proposal and annual report should discuss these issues.

Qualifications:

The ISRP recommends that the proponents describe their responses to the ISRP's comments and suggestions below in their upcoming annual report covering FY 2019 accomplishments.

1.      The proponents should perform the power analyses they suggest in their proposal to help guide their sampling efforts and to provide measures of precision for all estimates.

2.      The project should begin to build a "brood table" for natural origin salmonids and show these values in annual reports, e.g., total adult recruitment produced by natural spawners. This information is needed for the evaluation of abundance and productivity, two key VSP parameters.

3.      Describe any efforts being made to link fish identification from the CWT- and PIT-tagging programs with comparable data obtained by Parentage-Based Tagging.

Comment:

This proposal clearly explains why the project was initiated, how it relates to the overall coded-wire-tag (CWT) program, and why it remains a critical monitoring effort in the Columbia Basin. However, the Adaptive Management section contains statements that reductions in funding hampered WDFW's ability to achieve sample rates targets for some fisheries in 2013-2017, and that "if additional funding is not identified, it will be necessary to prioritize fisheries and reduce or eliminate sampling of some fisheries. ... It may be possible to shift sampling effort among fisheries occurring simultaneously to come closer to sample rate targets, but this is often not possible as fisheries may occur on different days or large distances apart. Fishery sampling of the treaty Indian fishery (Zone 6) was especially challenging in recent years due to increased landings of dressed (i.e., gutted) fish and lack of access to sample some tribal fish buyers. The issues encountered by samplers in Zone 6 may result in a biased sample of the CWTs, PIT tags and individual fish weights even if sample rates met the targets due to the need to sample different stocks in proportion to the catch composition. These potential sources of bias in Zone 6 create issues for estimating harvest by stock and in general decrease precision in management by WDFW and co-managers in the Columbia River basin. WDFW is currently attempting to restructure sampling in Zone 6 to account for these potential sources of error, but difficulties may continue." These concerns parallel concerns expressed in the PSMFC proposal involving CWT (1982-031-00). These funding issues and associated implications require further discussion and evaluationby the Basin's fisheries managers, the Council, and BPA. To be effective, these discussions should occur now, prior to the Basin's fall fisheries.

1. Objectives, Significance to Regional Programs, and Technical Background

The goals and objectives of the monitoring project are well defined and justified, including (1) estimate the number of PIT tags in Columbia River fisheries, (2) estimate CWT Chinook and coho salmon contributions to escapement count in Washington's lower Columbia tributaries as a means to support VSP status, (3) Chinook salmon escapement monitoring for the Toutle River, Upper Gorge, and Upper Columbia populations (including Hanford Reach), and (4) monitoring spawning escapement of coho salmon in key Washington populations below Bonneville Dam. Anticipated outcomes are expressed quantitatively as sampling rates and data standards to be achieved and maintained over the longer-term.This is a monitoring project that requires long-term continuity to evaluate fish status in relation to fisheries.

2. Results and Adaptive Management

Results from 2013-2017 are briefly presented in the proposal for (1) Chinook and coho salmon spawning in specific tributaries, including hatchery origin (HOR) and natural origin (NOR) spawners, (2) sport fisheries, (3) commercial fisheries, and (4) fall Chinook counts at Bonneville Dam. Origin (hatchery versus natural) is identified in the recreational catches (unmarked fish are released) and commercial catches, and spawning escapements. Harvest rates based on PIT-tag data are calculated despite some logistical and technological challenges to achieving a 20% sampling rate in the mainstem fisheries. The proponents have identified a plan to overcome these hurdles; measures of precision about estimates and assumptions should be provided when possible. Ultimately, data generated by this effort are used in agency reports that describe basic salmon population trends and harvests. The proponents should begin to use the population data to create "brood tables" which are key to development of stock-recruitment relationships and assessing stock productivity. Data and evaluations produced by this project are uploaded to the publicly accessible CWT database (RMIS). A comprehensive report for the 2010 season provides many details on the methods and results. The proponents have produced a series of publications on methods and data standards in addition to their annual reports.

WDFW recognizes the need to restructure sampling in Zone 6 to account for potential sources of error and bias because of increased landings of "dressed" fish and lack of access to sample some tribal fish buyers. WDFW is testing new methods of electronic data capture and transfer to databases. Stream surveys of coho salmon are being revised.

The proposal does not mention any effort directed toward linking fish identification data from the CWT- and PIT-tagging programs with data obtained by genetic (e.g., parentage-based tagging, PBT) or acoustic telemetry programs. A major recommendation from the Pacific Salmon Commission's expert panel review in 2005 (that motivated this project) was to develop a coordinated research and implementation plan, including integration of other genetic and electronic tagging tools/techniques. This integration could be particularly useful because, as noted in the proposal, exploitation rates of wild salmon in commercial fisheries stem from analysis of CWT hatchery salmon and the assumption that exploitation rates of wild salmon are the same as hatchery salmon.

3. Methods: Project Relationships, Work Types, and Deliverables

The proposal documents activities and methods in appropriate detail and makes good use of the published literature to justify assertions and support procedures. This project primarily serves a long-term monitoring and data sharing function. The proposal provides appropriate detail about the types of activities used to detect or recover CWT in samples of catches and escapements, and to estimate escapements and calculate harvest rate. There is a need to develop and describe integrated methods that can propagate uncertainty along the entire chain of computations to get final estimates with measures of uncertainty. On page 57 of the report, it states the need to "Consider a power analysis for important fishery management groups to ensure sufficient PIT tagging and sampling to meet management precision goals." This analysis should be completed immediately. We could not verify whether the statistical methods used for CWT analyses were standard or something different.

Some typos were noted in the caption to Table 1 of the 2018 report ("do NOT provide accurate pHOS estimates...") and values in Table 14 (commas misplaced or extraneous digits).

This project has the potential to benefit Columbia River Basin fish and wildlife by filling important gaps in recovery of passive integrated transponder (PIT) and coded-wire tagged (CWT) for salmonids in the Lower Columbia Region (LCR). However, the proposal narrative often referenced unpublished reports for details of viable salmonid population (VSP) monitoring methods and software to be used for different estimates. The ISRP requests a response in the form of a revised narrative to provide augmented details on methodologies outlined below. An adequate response should provide the following information: The metric numbers provided for tagging, RME designs, and analysis and interpretation of data need to be augmented with a description of the metrics. Similarly, the metric numbers provided for tagging, random sampling of CWT and PIT tags, and analysis and interpretation of data need to be augmented with a description of the metrics. The first proposed test of the tag detection rates appears problematic due to small sample size. In the second test plans to conduct the test at a hatchery or commercial sampling site have not been confirmed. Evidence of confirmation is necessary and details showing that the number of tags will be adequate should be provided. Details of how this test will be extended to examine differences between individuals/detectors should be provided. Details for the sampling design to sample CWT and PIT tags from Columbia River sport and commercial fisheries should be provided. The reference to a CV of 15% (Crawford and Rumsey, 2009) has not been established as a reasonable data standard. Crawford and Rumsey (2009) reference Carlile et al. (2008), which makes recommendations for coefficients of variation for estimates of total spawning escapement. 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 or 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 The technical justification was straightforward and adequate for expanding the tag recovery program by adding PIT tagging. The proposed project will address several deficiencies (that are clearly stated) in the current CWT program. In particular, the project will fill significant fall Chinook and coho salmon monitoring gaps in the Lower Columbia River during the Columbia River Tributary Research, Monitoring, and Evaluation (RME) process. The proponents provided very good detail on how this project will respond to the Lower Columbia River Subbasin plans (LCFRB 2004) and generally the BiOp, PSC recommendations, and other Fish and Wildlife Program elements. The proponents listed many projects (CWT and PIT) as related to and sharing data with this one. Also, this project coordinates with and shares data with the Pacific Northwest Aquatic Monitoring Project’s (PNAMP) Integrated Status and Trend Monitoring (ISTM) project (#200400200) by using the same spawning distribution models for CWT recoveries and escapement. 2. Project History and Results This is a new project that builds on three previous BPA-funded CWT recovery projects (# 198201301, #2007236800, and #2007355000). A brief history of the current CWT program (# 198201301) was provided. 3. Objectives, Work Elements, and Methods Objective 1. "Escapement Sampling for CWTs" is not a fully stated, measurable objective and not until paragraph two following this statement do we find the full objective 1, which is "In this CWT and VSP monitoring effort, we intend to recover CWTs on spawning ground surveys to estimate exploitation rates for hatchery Chinook and coho salmon and concurrently gather data for VSP metrics (productivity, abundance, diversity, and spatial structure) using methods and sampling designs to meet the NOAA monitoring guidance (Crawford and Rumsey 2009)." The proponents provided useful tables summarizing assumptions needed to calculate unbiased population estimates. The methods for this objective are described in good detail for the most part, but often we are referred to reports for details of VSP monitoring methods and software to be used for different estimates. Links to some/many of those would be useful for reviewers. The proponents state that this project will provide "better managing and maintaining of existing databases" (WDFW's CWT, age, scales and biological data, and spawning ground survey databases in Olympia), but there is not a clear description of what this entails. Objective 1 includes marking and tagging of salmon for mark-recapture studies, but no details are provided on tagging methods, numbers and species of fish tagged, or possible negative effects of tagging on fish. The metric numbers provided for tagging, RME designs, and analysis and interpretation of data need to be augmented with a description of the metrics. Objective 2. "Fisheries Sampling for PIT Tags" should expand to "Fisheries Will be Sampled and Reported for PIT Tags as well as CWTs". This effort will be shared with ODFW and both agencies will upgrade to new detectors and data loggers. Methods for this objective are also well detailed and appear to be adequate for both sport and commercial Columbia mainstem fisheries. Carcasses will be PIT tagged to assess PIT tag detection rates, but a concise summary of experimental design and methods was not provided. The proponents state that CWT and PIT tags will be randomly sampled from Columbia River sport and commercial fisheries, but no sampling design is provided. The metric numbers provided for tagging, random sampling of CWT and PIT tags, and analysis and interpretation of data need to be augmented with a description of the metrics.

Qualification: The following additional requests for information should be addressed in contracting and discussed in future proposals and annual reports. The ISRP is not asking for an immediate response.

1. Information is needed on variance measures of the spawning population estimates. How are they determined, what have they been, and are the end users satisfied with them?

2. Details are needed on specific methods and survey techniques. Over what time periods are the redd surveys conducted, and how many times per week are they carried out? Are any shoreline surveys performed in areas inaccessible to jet sleds? Where are the piezometers located, relative to redd concentrations? How often do temperature loggers record intragravel water temperatures? Is dissolved oxygen ever measured in the egg pocket?

3. A map of the principal spawning areas for Chinook and chum salmon below Bonneville Dam would be helpful, particularly if it highlighted sites where the majority of redds occur. Information on use of the Ives Island area by coho (mentioned in passing in the proposal) and lamprey would also be useful.

4. Information about movement of sediments in the spawning grounds as the river channel migrates would be helpful. Is this metric being monitored?

5. Have other potential limiting factors on chum fry emergence been considered, e.g., predation on eggs or recently emerged fry? Does boat activity in the area affect egg and alevin survival through substrate disturbance?

6. To put this project in context, it would be useful to find out why was the decision made to remove data analysis from this project and place it in two related projects? Was this done for efficiency or for another reason?

1. Purpose, Significance to Regional Programs, Technical Background, and Objectives

The proposal is reasonably clear about the importance of understanding the effect of hydrosystem operations on the reproductive success of mainstem-spawning fall Chinook and chum salmon immediately below Bonneville Dam. This field program is an important element of regional fish population monitoring.

The technical background and objectives were, in general, adequately described. A couple of issues need further explanation. First, why was the decision made to remove data analysis from this project and place it in two related projects? Was this done for efficiency or for another reason? Second, what is being done to track mainstem spawning in the Ives Island complex by species other than Chinook and chum salmon? The proposal mentions coho salmon in passing (in connection with carcass tagging), and it would be interesting to know if Pacific lamprey use the area too.

2. History: Accomplishments, Results, and Adaptive Management

The proponents have a good track of publications and reports. Results of fall Chinook population estimates for the Ives Island complex are presented for the last decade. A similar set of estimates for chum salmon would be useful, as would a summary of the temperature and water surface elevation monitoring over this period. The water elevation data would be especially helpful in demonstrating how the precursor to this project influenced hydrosystem operations by preventing redd dewatering. The mapping products provide habitat managers with managers to avoid development and damage to critical spawning habitat.

Adaptive management is not really shown by proponents – they describe how end users do modify their needs according to changes in the fish populations.

3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging)

Relationships to two other projects (Project Number 1982-013-01 titled “Coded Wire Tag Recovery Program” and Project Number 2010-036-00 titled “Expansion of Washington’s Tag Recovery Program in the Lower Columbia Region to Improve Fisheries and Viable Salmonid Population Monitoring”) are adequately described. The other projects will assume responsibility for analyses of tag recovery data collected through this project.

Throughout the proposal the implication is that hydrosystem operations causing redd dewatering limit reproductive success of fall Chinook and chum salmon spawning in the Ives Island complex, but have other potential limiting factors been considered, e.g., predation on eggs or recently emerged fry? Does boat activity in the area affect egg and alevin survival through substrate disturbance? Is there any evidence that channel movements (if they have occurred) have influenced hyporheic flow pathways, or that intragravel temperatures have changed over the monitoring period?

R&ME seems reasonable and the proponents have a good track record of data archiving.

4. Deliverables, Work Elements, Metrics, and Methods

Because this project does not include data analysis, deliverables consist of providing field data to the appropriate other projects for analysis and summary.

The work elements, metrics and methods are generally described; however, more details are needed for scientific review. A map of the principal spawning areas for Chinook and chum salmon below Bonneville Dam would be helpful, particularly if it highlighted sites where the majority of redds occur. Additional information on survey techniques is requested above under response item 2.

Qualification: The following additional requests for information should be addressed in contracting and discussed in future proposals and annual reports. The ISRP is not asking for an immediate response. 1. Information is needed on variance measures of the spawning population estimates. How are they determined, what have they been, and are the end users satisfied with them? 2. Details are needed on specific methods and survey techniques. Over what time periods are the redd surveys conducted, and how many times per week are they carried out? Are any shoreline surveys performed in areas inaccessible to jet sleds? Where are the piezometers located, relative to redd concentrations? How often do temperature loggers record intragravel water temperatures? Is dissolved oxygen ever measured in the egg pocket? 3. A map of the principal spawning areas for Chinook and chum salmon below Bonneville Dam would be helpful, particularly if it highlighted sites where the majority of redds occur. Information on use of the Ives Island area by coho (mentioned in passing in the proposal) and lamprey would also be useful. 4. Information about movement of sediments in the spawning grounds as the river channel migrates would be helpful. Is this metric being monitored? 5. Have other potential limiting factors on chum fry emergence been considered, e.g., predation on eggs or recently emerged fry? Does boat activity in the area affect egg and alevin survival through substrate disturbance? 6. To put this project in context, it would be useful to find out why was the decision made to remove data analysis from this project and place it in two related projects? Was this done for efficiency or for another reason? 1. Purpose, Significance to Regional Programs, Technical Background, and Objectives The proposal is reasonably clear about the importance of understanding the effect of hydrosystem operations on the reproductive success of mainstem-spawning fall Chinook and chum salmon immediately below Bonneville Dam. This field program is an important element of regional fish population monitoring. The technical background and objectives were, in general, adequately described. A couple of issues need further explanation. First, why was the decision made to remove data analysis from this project and place it in two related projects? Was this done for efficiency or for another reason? Second, what is being done to track mainstem spawning in the Ives Island complex by species other than Chinook and chum salmon? The proposal mentions coho salmon in passing (in connection with carcass tagging), and it would be interesting to know if Pacific lamprey use the area too. 2. History: Accomplishments, Results, and Adaptive Management The proponents have a good track of publications and reports. Results of fall Chinook population estimates for the Ives Island complex are presented for the last decade. A similar set of estimates for chum salmon would be useful, as would a summary of the temperature and water surface elevation monitoring over this period. The water elevation data would be especially helpful in demonstrating how the precursor to this project influenced hydrosystem operations by preventing redd dewatering. The mapping products provide habitat managers with managers to avoid development and damage to critical spawning habitat. Adaptive management is not really shown by proponents – they describe how end users do modify their needs according to changes in the fish populations. 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging) Relationships to two other projects (Project Number 1982-013-01 titled “Coded Wire Tag Recovery Program” and Project Number 2010-036-00 titled “Expansion of Washington’s Tag Recovery Program in the Lower Columbia Region to Improve Fisheries and Viable Salmonid Population Monitoring”) are adequately described. The other projects will assume responsibility for analyses of tag recovery data collected through this project. Throughout the proposal the implication is that hydrosystem operations causing redd dewatering limit reproductive success of fall Chinook and chum salmon spawning in the Ives Island complex, but have other potential limiting factors been considered, e.g., predation on eggs or recently emerged fry? Does boat activity in the area affect egg and alevin survival through substrate disturbance? Is there any evidence that channel movements (if they have occurred) have influenced hyporheic flow pathways, or that intragravel temperatures have changed over the monitoring period? R&ME seems reasonable and the proponents have a good track record of data archiving. 4. Deliverables, Work Elements, Metrics, and Methods Because this project does not include data analysis, deliverables consist of providing field data to the appropriate other projects for analysis and summary. The work elements, metrics and methods are generally described; however, more details are needed for scientific review. A map of the principal spawning areas for Chinook and chum salmon below Bonneville Dam would be helpful, particularly if it highlighted sites where the majority of redds occur. Additional information on survey techniques is requested above under response item 2.

I welcome continued discusssion with PNAMP data workgroup.  I would like to discuss the questionable and deleted RPAs with the COTR and appropriate RM&E workgroups.

Dan

 

We agree with BIOP RM&E Workgroup decision to delete RPA Association with (50.2)

This is an extremely well-prepared and well-documented proposal. The background on technical and scientific issues is thoroughly presented. The project history appears complete and identifies that management calls upon the project for information to support hydrosystem operations, and that system operation modifications are under consideration because of the products of the project. There is a clear statement of objectives with a well-established need. The rationale and significance are clearly identified. Information on chum and fall chinook spawning and adaptation to the hydrosystem is crucial to system modifications to accommodate fish. The data will undoubtedly lead to management that will provide persisting benefits.

The project is directed by experienced personnel who have an appropriate mix of expertise. The methods employed are sound, usual practices in fisheries investigations with the exception of the DIDSON sonar, which is rather new. The correct population parameters are being measured. The proposed activities are well integrated with past work and other agency projects.