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Restoring the Lower Snake River

Friday, November 04, 2016

lots of fishCalling it a “mature product,” the Independent Scientific Advisory Board completed its review of the latest draft of the Fish Passage Center’s Comparative Survival Study October 21.  

As it has found in each year it has produced the CSS, smolt-to-adult returns of salmon and steelhead out of the Snake River are not meeting the 2 percent to 6 percent SARs goals set by the Northwest Power and Conservation Council. However, fish out of the mid-Columbia River generally had SARs that fell within the NPCC range.  

It also found that the effectiveness of transporting fish from the Snake River downstream to below Bonneville Dam decreases as river conditions improve.   

The draft CSS – titled “Comparative Survival Study of PIT-tagged Spring/Summer/Fall Chinook, Summer Steelhead, and Sockeye” – was released for public review by the Fish Passage Center and  the  Comparative Survival Study Oversight Committee at the FPC website ( August 31. Comments were due October 15 and some of the most comprehensive and technical comments each year are those from the ISAB.   This is the ISAB’s seventh annual review. The first review in 2010 and all subsequent reviews were called for by the Council’s 2009 Fish and Wildlife Program.   

“Overall, the presentation is well organized and well refined,” the ISAB review document said. “An overarching comment is that connections with larger ecological concerns are not apparent. That is, there appear to be opportunities to involve researchers working on studies of other species, food webs, physiology, contaminants, and disease. Such combined studies might give added insights into mechanisms causing the observed temporal patterns in migration and survival.”   

The CSS draft report is laid out in eight chapters and three appendices.  

In its summary, the ISAB says the first chapter is an overview of the entire CSS report and is similar to previous years, but with recent results added. The CSS in 2016 also added two fish populations that hadn’t previously been included – Okanagan River sockeye and natural-origin summer chinook salmon from upstream of Wells Dam.   But the CSS also says that PIT-tags increased in size from the 9 to 12 millimeters of previous reports to 11 to 12 mm. That could have impacts on tagged fish, the ISAB says, and should be explored.   

“If this is a real change, the rationale for the change is needed along with a discussion of potential impacts on the fish (e.g., are larger fish now tagged to accommodate the larger tags?),” the ISAB review says.  

The first chapter also outlines three new topics:  

1) statistical relationships among total annual flow and salmon population parameters such as survival, smolt-to-adult-return rate (SAR), and other response variables in the life cycle model;

2) impact of the juvenile bypass system on delayed mortality as measured by SARs; and 3) average age of maturity across stocks and years.   

No new features were added to the second chapter about lifecycle modeling, although the CSS did evaluate alternative levels of spill and flow on smolt to adult returns and long-term abundance of spring/summer chinook through 2050. It also looked at the benefits of improving juvenile passage versus improving spawning productivity and capacity, concluding that:   

• greatest benefits to SARS occur at highest spill and lowest flow 

• relative return abundance appears to be mostly limited by capacity of the habitat to support the fish.   

The third chapter on the effects of in-river juvenile travel time, mortality rates and survival is mainly an update with the latest information. It found that there is a variation in the results among years and among cohorts, and that mortality tends to increase over the migration season and as water temperature rises, with the exception of sockeye salmon. The mortality is likely due to a combination of increasing water temperature, according to the CSS report, and to:  

1) declining smolt energy reserves or physiological condition over the migration season,

2) increasing predation rates on smolts,

3) increases in disease susceptibility or disease-related mortality, or

4) some combination of these often interrelated mechanisms.  

The ISAB suggested that testing these hypothesis could result in survival improvements, but also wondered about the sockeye salmon anomaly.   Chapter 4 of the CSS report describes overall annual SARs and includes new data.   

“Overall SARs of Snake River wild spring/summer Chinook and steelhead fell well short of the Northwest Power and Conservation Council’s 2 – 6 percent SAR objectives, while those from the mid-Columbia region generally fell within this range,” the CSS report says. “For Snake River populations, none of the passage routes (in-river or juvenile transportation) have provided SARs within the range of the NPCC objectives.”  

Among other findings, the CSS report found that “the relative effectiveness of transportation decreases as in-river conditions improve,” and that “SARs are highly correlated among wild and hatchery populations within and between regions, indicating common environmental factors are influencing survival rates from outmigration to the estuary and ocean environments.”  

“It is not surprising that the transport TIR is inversely correlated with in-river survival (Lower Granite Dam to Bonneville Dam),” the ISAB said. “This new analysis identified the value for in-river survival when the benefits of transportation appear to disappear.” TIR is the transport to in-river ratio.  

The CSS also reported on the relatively large absolute difference in SAR based on PIT-tags versus run reconstruction, the ISAB said. While there is an evaluation of PIT-tag effects on salmon survival, the results will not be ready until after summer 2017. “Potential bias in survival caused by tagging methodology (or in the run reconstruction methodology) is an important issue to resolve, and the ISAB looks forward to the results of this study.”  

Chapter 5 looks at the association of SARs to life-cycle productivity for wild spring/summer chinook and steelhead populations. Major population declines of these Snake River stocks are associated with SARs of less than 1 percent, and increased life-cycle productivity has occurred in years when SARs exceeds 2 percent, the CSS report says. The historical (pre-1970s) SAR was in the range 4 to 6 percent.  

Faced with these figures, the ISAB asked to “what extent might improvements in hydrosystem management, predator control, and estuarine habitat lead to SARs of 4 percent to 6 percent?”   

The ISAB recommended five topics for future reports:   

1.         Use more realistic and more variable future flow conditions for the study on the impact of flow/spill modifications under future climate change. Simulating only low flows or high flows for decades may not be a realistic scenario. 

2.         What is the impact of the new restricted tag sizes? Are there fish that were previously marked and are now not marked (e.g. smaller fish) due to the larger PIT tags being used? Similarly, conclusions from studies of compensatory mortality (e.g. in relation to predator control) may be affected by the choice of fish that are tagged. 

3.         A life-cycle model is the natural way to study predator control impacts, but the current version of the CSS life-cycle model appears to incorporate density dependence only at the spawner-to-smolt stage, the ISAB said. Modify the life-cycle model to allow a range of compensatory responses ranging from complete additivity (as now is the case) to plausible compensatory mortality effects related to density dependence and predator selectivity (see ISAB 2016-1).

4.         Both the CSS and NOAA provide estimates for in-river survival. How do these estimates compare to each other? 

5.         What factors have led to declining proportions of four and five-year old and increases in three-year old spring/summer chinook? Models that include ocean factors associated with salmon growth and climate change, differences in hatchery practices, or freshwater environments (tributary temps, or annual differences in migration corridor) may be of interest.   

ISAB’s 2016 review can be found at Previous reviews are at (2010), (2011), (2012), (2013), (2014), and (2015).  

The 2016 CSS report is at It was prepared by the Comparative Survival Study Oversight Committee and the Fish Passage Center ( The committee includes Jerry McCann, Brandon Chockley, Erin Cooper and Tommy Garrison, all of the Fish Passage Center; Howard Schaller and Steve Haeseker, U.S. Fish and Wildlife Service; Robert Lessard, Columbia River Inter-Tribal Fish Commission; Charlie Petrosky and Tim Copeland, Idaho Department of Fish and Game; Eric Tinus and Erick Van Dyke, Oregon Department of Fish and Wildlife; and Robin Ehlke, Washington Department of Fish and Wildlife.   

Also see:   CBB, December 29, 2015, “2015 Salmon Survival Report Updates Smolt-To-Adult Return Data For Columbia/Snake Salmon, Steelhead,” <>

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