Qualification: A synthesis of this project, as proposed by the proponents, should be completed and reviewed by the ISRP in 2011.

This is a productive and worthwhile project that has made significant contributions to understanding relationships between Chinook and coho salmon survival and ocean and plume conditions. The ISRP commends the proposed new research on abundance, distribution, timing and migration of smolts through the estuary. Another important new feature of the project is the proposed analysis of factors affecting sockeye, chum, and steelhead. However, the proposal was not clear on the extent to which data on these species were collected in previous years but not analyzed or reported. Rapid gains in knowledge could be accomplished if previous data on these species were collected, although the ISRP recognizes that these species may not be abundant in coastal research trawl samples. An important outcome of the project has been a qualitative method for forecasting salmon runs that appears to be an improvement over past methods. It is refreshing to see a project that directly addresses management concerns. The ISRP strongly concurs with the proponents that a major synthesis of this work should be completed in 2011.

Some important issues to be considered during the contracting process and in the synthesis are listed below:

1. Strategic plan. The ISRP recommends the use of synthesis results to develop a strategic plan that prioritizes project hypotheses and management objectives. The current approach is exploratory and observational, including numerous hypotheses and investigations of trails of evidence dealing with limiting factors ranging from lipids to parasites to bird predation. When arguing for an observational rather than experimental approach, the proponents state that each year/sampling season can be considered an “independent observation.” It seems unlikely that the quantitative values of physical and biological variables are independent between years, that is, there is no between-year autocorrelation. The proponents need to justify this assertion or adjust for it in their statistical analyses, as described in the synthesis objective. The strategic plan should explain in greater detail how interaction issues arising from studying four elements (bottom-up, top-down, food-web, and plume structure) at the same time will be addressed.

2. Achievable objectives. Consider whether stated objectives are achievable. For example, can the objective (discussed in proposal’s introduction) to determine decadal-scale cycles in ocean productivity be achieved? If so, when will the periodic wave length in cycles be known? If changes are periodic events without a fixed wave length or chaotic events, then how will this objective be achieved?

3. Fishing operation effects. Consider important sources of variation in research trawl and other fishing operations and fishing efficiency with respect to what is known about diel, horizontal, vertical, and seasonal distribution of juvenile salmon that might affect time-series observational data on species composition, abundance, distribution, growth, etc., of juvenile salmon in the survey area.

4. Cruise planning and coordination. The ISRP recommends that the proponents provide annual cruise plans to other related projects. The plans should include sufficient detail on how cruises in the plume, estuary, and ocean will be organized and coordinated with these other projects. For example, the current proposal lacks details on how far upstream the estuary sampling will occur. It seems the sampling will occur only in the lower reaches, and this may not be sufficient to tie in with other work, e.g., POST tagging at Sand Island, LCREP work in the marshes, etc.

5. Monitoring ocean conditions. Consider greater use of ocean monitoring data collected by other (non-BPA funded) projects for developing indices of ocean conditions, such as hydroacoustics, remote sensing, oceanographic buoys and floats, and robotic vehicles. The ISRP recommends improved coordination and collaboration with other projects and programs collecting these data.

6. Hatchery vs. wild salmon. Consider a detailed comparison of differences in condition, growth, and survival between hatchery and wild salmon of each species. The Endangered Species Act protects many salmon and steelhead ESUs in the Columbia Basin, yet this study does not address hatchery versus wild salmon issues. Hatchery salmon are released at a large size and have high lipid content, therefore hatchery fish may respond differently to environmental factors compared with wild salmon. In earlier years, many hatchery salmon were not marked and could not be readily identified. However, in recent years, including 2010, nearly all hatchery Chinook and coho salmon and steelhead, with the exception of some tribal and conservation hatchery fish, will receive an adipose fin clip. Relatively small numbers of hatchery Chinook raised in conservation hatcheries will not be marked. The ISRP recommends a detailed comparison of hatchery versus wild salmon of each species.

7. Genetic stock identification. The ISRP recommends standardization of genetic stock identification methods used by BPA-funded estuary and ocean survival projects so that results are directly comparable among projects. Different projects may currently be using different methods, but this was not clearly explained in the proposal.

8. Otolith microchemistry. The ISRP considers the value of otolith microchemistry research uncertain. The proponents need to consider specifically how this method can provide new information without extensive baseline data collection. The validity of the proposed use of genetic methods to identify stock origin of individual fish sampled for otoliths needs to be demonstrated. Use of daily otolith increments to estimate estuary and plume residence times is also uncertain. For example, project results to date have estimated that yearling Chinook salmon spend several months in the estuary/plume, which is contrary to evidence from trawl survey and tagging research. Hatchery fish are known to have high Sr/Ca ratios because of their feed. Is this another factor that will confound the proposed microchemistry work? Also the Sr/Ca transition cannot distinguish between estuary and plume habitats, an issue that was not clearly described in the proposal. A useful reference is: Elsdon, T.S. and 9 others. 2008. Otolith chemistry to describe movements and life-history parameters of fishes: hypotheses, assumptions, limitations and inferences. Oceanography and Marine Biology: An Annual Review, 2008, 46, 297-330.

9. Avian predation and alternative prey. The ISRP recommends that the effects of Caspian terns be considered in proposed research on avian predation and alternative prey (anchovy). In the estuary, Caspian tern predation is known to be related to river flows and the Pacific Decadal Oscillation. Proponents need to demonstrate collaboration with other avian predation studies.

10. Tag recovery. In addition to collection of coded-wire tags (CWT), all salmon and steelhead sampled during fishing and tagging operations should be examined for recovery of PIT tags and acoustic tags, if this is not already being done. The ISRP recommends using a handheld wand detector, V-Detector, or tunnel detector onboard the survey vessels to examine all salmon and steelhead in survey catches for CWTs, as some Columbia River hatcheries release coded-wire tagged fish that do not have an adipose fin clip.

11. Tagging effects. New proposed research involves acoustic tagging of juvenile Chinook salmon smolts in the Columbia River estuary with VEMCO and JSATS tags and tracking them as they cross several acoustic listening-lines and with mobile units in the estuary to estimate site-specific survival during outmigration. An evaluation of the effects of tagging stress on fish that are smolting is needed, as stress may be considerable and could affect behavior and survival of tagged fish. Although the proponents think survival will be high because of positive test results in 2010, up-estuary release above the receivers at Astoria and Sand Island may be an added stress to smolts that could be evaluated.

12. Collaboration. This project is collaborating with the CDFO Salmon Shelf Survival Study (#200300900) and the Pacific Ocean Survey Tracking (#200311400, POST, re-named COAST) studies. The ISRP appreciates recent improvements in coordination with these projects. Linkages between these and others studies (e.g., JSATS tagging research) in the estuary, plume, and ocean are established, but the degree of coordination needs further explanation and development. For example, the approaches by NOAA and CDFO are somewhat similar, and integration of data collection and analyses to a greater extent would strengthen results. Likewise, the proponents should consider how data from the NOAA, COAST, and JSATS tagging projects can be integrated to provide a more comprehensive analysis of factors affecting salmon survival.

13. Scientific workshop. The ISRP recommends a scientific workshop in 2011 focused on estimation of estuarine and ocean survival, forecasting of adult returns, and adaptive estuary, plume, and ocean environmental assessment for Columbia River Basin salmon and steelhead. Perhaps the proposal should include this workshop. A workshop would help to improve coordination and collaboration, standardization of methods (e.g., genetic stock identification), development of simulation and predictive models, and integration of results among Columbia River Basin estuary and ocean projects. One aspect of all projects that needs work is how to include more detail on sub-stock structure, including hatchery versus wild fish, hatchery release time, area comparisons, in-river migration and associated ocean migration, and more in the models. CDFO and NOAA seem to be taking somewhat different approaches to salmon forecasting, i.e., stoplight charts (red, yellow, and green) with a Bayesian belief network approach by CDFO versus ecosystem indicators by NOAA. Can this be reconciled?

14. Adaptive management. Consider how to better implement adaptive management to forecasted changes in ocean survival in the Columbia River system. Consider experiments designed in concert with hatchery, hydrosystem, and harvest managers to test specific hypotheses related to estuarine and early ocean survival. Proponents have indicated that management could respond to release timing and barging vs. in-river releases based on predictions from their 16 indicators and timing of upwelling, but what do managers say about the feasibility? How can managers respond to pathogen problems identified during this project? Or is this strictly an explanatory variable?

15. Sources of variation in forecasts. Consider whether ocean survival forecasts could be improved by integration of additional sources of variation in freshwater and ocean survival (e.g., ocean harvests of immatures, jacks, and adults in Alaska and Canada; bycatch in commercial groundfish fisheries; and climate and ocean conditions in offshore rearing areas)?

16. Quantitative forecasts. Qualitative methods of forecasting are helpful, but difficult for managers to apply and rely upon. That being said, proponents need to exercise caution in promoting the idea that their monitoring data will eventually lead to reliable, quantitative forecasts of ocean survival of salmon. Clearly, it is a goal of their agency to provide scientific forecasting tools to improve fishery management, but to date all quantitative ocean forecasting tools for salmon have failed, and thus expensive, long-term research vessel monitoring surveys are necessary.

17. Communicating results. Consider developing more effective approaches for communicating project results and forecasts of ocean survival of salmon directly to hatchery, hydrosystem, and harvest managers. The websites, scientific meetings, and peer-reviewed scientific publication are excellent methods for communicating with other scientists, government agencies, educational institutions, and conservation organizations, but are likely not effective tools for communicating directly with hydro, harvest, and hatchery managers.

18. Online proposal. Consider improvements to the online proposal form. Descriptions of methods in the online proposal were overly brief for some reviewers. Methods should provide sufficient stand-alone detail in the online form to enable evaluation of scientific and technical merit. The proposal could be improved if methods and metrics were explicitly stated for each objective. This is a complex proposal with six general objectives, both broad and narrow hypotheses, and “Studies” that provide metrics and methods that are intended to address multiple objectives, but the association between each specific objective and the metrics and methods that are intended to address it are unclear. For example, Study One provides methods and metrics that the proponents indicate address objectives one through six, but it is not entirely clear what methods and metrics presented in Study One address which of the six general objectives. The discussion of results in the online form would benefit from an ecosystem diagram depicting important physical and biological variables and their known or hypothesized interactions (perhaps indicated by arrows between variables). Such a diagram would provide a synopsis of the proponent’s current view of the system and how it might work, and would be beneficial in understanding the proposal. More complete details are needed on sampling methodology and analyses, along with a format that reduces the redundancies. Information on the percent of salaries for the PIs and what outside support they have would also help.

Qualification: A synthesis of this project, as proposed by the proponents, should be completed and reviewed by the ISRP in 2011. This is a productive and worthwhile project that has made significant contributions to understanding relationships between Chinook and coho salmon survival and ocean and plume conditions. The ISRP commends the proposed new research on abundance, distribution, timing and migration of smolts through the estuary. Another important new feature of the project is the proposed analysis of factors affecting sockeye, chum, and steelhead. However, the proposal was not clear on the extent to which data on these species were collected in previous years but not analyzed or reported. Rapid gains in knowledge could be accomplished if previous data on these species were collected, although the ISRP recognizes that these species may not be abundant in coastal research trawl samples. An important outcome of the project has been a qualitative method for forecasting salmon runs that appears to be an improvement over past methods. It is refreshing to see a project that directly addresses management concerns. The ISRP strongly concurs with the proponents that a major synthesis of this work should be completed in 2011. Some important issues to be considered during the contracting process and in the synthesis are listed below: 1. Strategic plan. The ISRP recommends the use of synthesis results to develop a strategic plan that prioritizes project hypotheses and management objectives. The current approach is exploratory and observational, including numerous hypotheses and investigations of trails of evidence dealing with limiting factors ranging from lipids to parasites to bird predation. When arguing for an observational rather than experimental approach, the proponents state that each year/sampling season can be considered an “independent observation.” It seems unlikely that the quantitative values of physical and biological variables are independent between years, that is, there is no between-year autocorrelation. The proponents need to justify this assertion or adjust for it in their statistical analyses, as described in the synthesis objective. The strategic plan should explain in greater detail how interaction issues arising from studying four elements (bottom-up, top-down, food-web, and plume structure) at the same time will be addressed. 2. Achievable objectives. Consider whether stated objectives are achievable. For example, can the objective (discussed in proposal’s introduction) to determine decadal-scale cycles in ocean productivity be achieved? If so, when will the periodic wave length in cycles be known? If changes are periodic events without a fixed wave length or chaotic events, then how will this objective be achieved? 3. Fishing operation effects. Consider important sources of variation in research trawl and other fishing operations and fishing efficiency with respect to what is known about diel, horizontal, vertical, and seasonal distribution of juvenile salmon that might affect time-series observational data on species composition, abundance, distribution, growth, etc., of juvenile salmon in the survey area. 4. Cruise planning and coordination. The ISRP recommends that the proponents provide annual cruise plans to other related projects. The plans should include sufficient detail on how cruises in the plume, estuary, and ocean will be organized and coordinated with these other projects. For example, the current proposal lacks details on how far upstream the estuary sampling will occur. It seems the sampling will occur only in the lower reaches, and this may not be sufficient to tie in with other work, e.g., POST tagging at Sand Island, LCREP work in the marshes, etc. 5. Monitoring ocean conditions. Consider greater use of ocean monitoring data collected by other (non-BPA funded) projects for developing indices of ocean conditions, such as hydroacoustics, remote sensing, oceanographic buoys and floats, and robotic vehicles. The ISRP recommends improved coordination and collaboration with other projects and programs collecting these data. 6. Hatchery vs. wild salmon. Consider a detailed comparison of differences in condition, growth, and survival between hatchery and wild salmon of each species. The Endangered Species Act protects many salmon and steelhead ESUs in the Columbia Basin, yet this study does not address hatchery versus wild salmon issues. Hatchery salmon are released at a large size and have high lipid content, therefore hatchery fish may respond differently to environmental factors compared with wild salmon. In earlier years, many hatchery salmon were not marked and could not be readily identified. However, in recent years, including 2010, nearly all hatchery Chinook and coho salmon and steelhead, with the exception of some tribal and conservation hatchery fish, will receive an adipose fin clip. Relatively small numbers of hatchery Chinook raised in conservation hatcheries will not be marked. The ISRP recommends a detailed comparison of hatchery versus wild salmon of each species. 7. Genetic stock identification. The ISRP recommends standardization of genetic stock identification methods used by BPA-funded estuary and ocean survival projects so that results are directly comparable among projects. Different projects may currently be using different methods, but this was not clearly explained in the proposal. 8. Otolith microchemistry. The ISRP considers the value of otolith microchemistry research uncertain. The proponents need to consider specifically how this method can provide new information without extensive baseline data collection. The validity of the proposed use of genetic methods to identify stock origin of individual fish sampled for otoliths needs to be demonstrated. Use of daily otolith increments to estimate estuary and plume residence times is also uncertain. For example, project results to date have estimated that yearling Chinook salmon spend several months in the estuary/plume, which is contrary to evidence from trawl survey and tagging research. Hatchery fish are known to have high Sr/Ca ratios because of their feed. Is this another factor that will confound the proposed microchemistry work? Also the Sr/Ca transition cannot distinguish between estuary and plume habitats, an issue that was not clearly described in the proposal. A useful reference is: Elsdon, T.S. and 9 others. 2008. Otolith chemistry to describe movements and life-history parameters of fishes: hypotheses, assumptions, limitations and inferences. Oceanography and Marine Biology: An Annual Review, 2008, 46, 297-330. 9. Avian predation and alternative prey. The ISRP recommends that the effects of Caspian terns be considered in proposed research on avian predation and alternative prey (anchovy). In the estuary, Caspian tern predation is known to be related to river flows and the Pacific Decadal Oscillation. Proponents need to demonstrate collaboration with other avian predation studies. 10. Tag recovery. In addition to collection of coded-wire tags (CWT), all salmon and steelhead sampled during fishing and tagging operations should be examined for recovery of PIT tags and acoustic tags, if this is not already being done. The ISRP recommends using a handheld wand detector, V-Detector, or tunnel detector onboard the survey vessels to examine all salmon and steelhead in survey catches for CWTs, as some Columbia River hatcheries release coded-wire tagged fish that do not have an adipose fin clip. 11. Tagging effects. New proposed research involves acoustic tagging of juvenile Chinook salmon smolts in the Columbia River estuary with VEMCO and JSATS tags and tracking them as they cross several acoustic listening-lines and with mobile units in the estuary to estimate site-specific survival during outmigration. An evaluation of the effects of tagging stress on fish that are smolting is needed, as stress may be considerable and could affect behavior and survival of tagged fish. Although the proponents think survival will be high because of positive test results in 2010, up-estuary release above the receivers at Astoria and Sand Island may be an added stress to smolts that could be evaluated. 12. Collaboration. This project is collaborating with the CDFO Salmon Shelf Survival Study (#200300900) and the Pacific Ocean Survey Tracking (#200311400, POST, re-named COAST) studies. The ISRP appreciates recent improvements in coordination with these projects. Linkages between these and others studies (e.g., JSATS tagging research) in the estuary, plume, and ocean are established, but the degree of coordination needs further explanation and development. For example, the approaches by NOAA and CDFO are somewhat similar, and integration of data collection and analyses to a greater extent would strengthen results. Likewise, the proponents should consider how data from the NOAA, COAST, and JSATS tagging projects can be integrated to provide a more comprehensive analysis of factors affecting salmon survival. 13. Scientific workshop. The ISRP recommends a scientific workshop in 2011 focused on estimation of estuarine and ocean survival, forecasting of adult returns, and adaptive estuary, plume, and ocean environmental assessment for Columbia River Basin salmon and steelhead. Perhaps the proposal should include this workshop. A workshop would help to improve coordination and collaboration, standardization of methods (e.g., genetic stock identification), development of simulation and predictive models, and integration of results among Columbia River Basin estuary and ocean projects. One aspect of all projects that needs work is how to include more detail on sub-stock structure, including hatchery versus wild fish, hatchery release time, area comparisons, in-river migration and associated ocean migration, and more in the models. CDFO and NOAA seem to be taking somewhat different approaches to salmon forecasting, i.e., stoplight charts (red, yellow, and green) with a Bayesian belief network approach by CDFO versus ecosystem indicators by NOAA. Can this be reconciled? 14. Adaptive management. Consider how to better implement adaptive management to forecasted changes in ocean survival in the Columbia River system. Consider experiments designed in concert with hatchery, hydrosystem, and harvest managers to test specific hypotheses related to estuarine and early ocean survival. Proponents have indicated that management could respond to release timing and barging vs. in-river releases based on predictions from their 16 indicators and timing of upwelling, but what do managers say about the feasibility? How can managers respond to pathogen problems identified during this project? Or is this strictly an explanatory variable? 15. Sources of variation in forecasts. Consider whether ocean survival forecasts could be improved by integration of additional sources of variation in freshwater and ocean survival (e.g., ocean harvests of immatures, jacks, and adults in Alaska and Canada; bycatch in commercial groundfish fisheries; and climate and ocean conditions in offshore rearing areas)? 16. Quantitative forecasts. Qualitative methods of forecasting are helpful, but difficult for managers to apply and rely upon. That being said, proponents need to exercise caution in promoting the idea that their monitoring data will eventually lead to reliable, quantitative forecasts of ocean survival of salmon. Clearly, it is a goal of their agency to provide scientific forecasting tools to improve fishery management, but to date all quantitative ocean forecasting tools for salmon have failed, and thus expensive, long-term research vessel monitoring surveys are necessary. 17. Communicating results. Consider developing more effective approaches for communicating project results and forecasts of ocean survival of salmon directly to hatchery, hydrosystem, and harvest managers. The websites, scientific meetings, and peer-reviewed scientific publication are excellent methods for communicating with other scientists, government agencies, educational institutions, and conservation organizations, but are likely not effective tools for communicating directly with hydro, harvest, and hatchery managers. 18. Online proposal. Consider improvements to the online proposal form. Descriptions of methods in the online proposal were overly brief for some reviewers. Methods should provide sufficient stand-alone detail in the online form to enable evaluation of scientific and technical merit. The proposal could be improved if methods and metrics were explicitly stated for each objective. This is a complex proposal with six general objectives, both broad and narrow hypotheses, and “Studies” that provide metrics and methods that are intended to address multiple objectives, but the association between each specific objective and the metrics and methods that are intended to address it are unclear. For example, Study One provides methods and metrics that the proponents indicate address objectives one through six, but it is not entirely clear what methods and metrics presented in Study One address which of the six general objectives. The discussion of results in the online form would benefit from an ecosystem diagram depicting important physical and biological variables and their known or hypothesized interactions (perhaps indicated by arrows between variables). Such a diagram would provide a synopsis of the proponent’s current view of the system and how it might work, and would be beneficial in understanding the proposal. More complete details are needed on sampling methodology and analyses, along with a format that reduces the redundancies. Information on the percent of salaries for the PIs and what outside support they have would also help.