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Independent Science Panel Reviews Upper Columbia River Spring Chinook Recovery Efforts
Posted on Friday, February 16, 2018 (PST)

After a decade of habitat improvements spurred by a 2007 NOAA Fisheries recovery plan, upper Columbia River spring chinook salmon still remain a population at a high risk of extinction and a panel of scientists wanted to know why.


The oversight panel for the Independent Scientific Advisory Board, made up of representatives from the Northwest Power and Conservation Council, the Columbia River Inter-Tribal Fish Commission and NOAA Fisheries, asked the ISAB last year in April to review the recovery and research efforts in the upper Columbia basin and to address four questions that the oversight panel thought might help the ISAB arrive at answers.


The ISAB added several more questions, including a comparison to recovery efforts in the Snake River basin, a comparison of spring chinook to fall chinook in the upper Columbia and an assessment of whether pinniped predation is a significant source of mortality, and delivered the 246 page comprehensive answer to the questions Feb. 9.


“There have been many questions about the rates of recovery of spring chinook in the upper Columbia River,” Dr. Stan Gregory, Oregon State University ecologist and an ISAB member told the Northwest Power and Conservation Council at their meeting in Portland Feb. 13. “We are still well below the recovery goal in each of the three sub-basins (Entiat, Wenatchee and Methow rivers) and the Methow is even at a lower rate of recovery.”


The full report, “Review of Spring Chinook Salmon in the Upper Columbia River,” is at


A NOAA Fisheries five year status review completed in 2016 found that upper Columbia River spring chinook are at high risk of extinction, even after a recovery plan was put into place in 2007.


Because of this extinction risk, the Fish and Wildlife Committee of the Northwest Power and Conservation Council at its Portland meeting Feb. 14, 2017, agreed to ask the ISAB to review the status and the efforts to recover the upper Columbia River spring chinook evolutionary significant unit, which was listed as endangered under the federal Endangered Species Act March 24, 1999.


The comparison to the Snake River basin was interesting, Gregory said, listing similarities and differences. The Snake River has 26 sub-basins, the upper Columbia just three, he said. Habitat quality is about the same, smolt to adult returns are about the same and the harvest rate on the fish is about the same.


And yet abundance of wild upper Columbia spring chinook stands at about 1,475 and falling over time, while the average abundance in the Snake River is 11,347 wild spring chinook and is rising.


Survival for upper Columbia juveniles to Bonneville Dam (1999 – 2016) is 45 percent, while survival for Snake River juveniles is 33 percent.


“Upper Columbia spring Chinook ESU may be exposed to greater risks than the Snake River spring/summer Chinook ESU because they have fewer populations and lower abundance,” the ISAB concluded. “Our concern is consistent with the findings of NOAA Fisheries when the Upper Columbia ESU was originally listed as endangered and the Snake River ESU as threatened, listings that were not changed in the most recent reviews. The ISAB recommends continued comparison of Chinook recovery in both ESUs with rigorous RME programs to determine which restoration actions are most effective.”


“The number of natural origin summer chinook (in the upper Columbia River basin) are almost 10-fold over spring chinook,” Dr. Steve Schroder of the ISAB told the Council.


Spring chinook arrive at the mouth of the Columbia River earlier than summer chinook. Along with a transit time difference (spring chinook are slower moving in higher flows) and the threat of pinnipeds in the spring there is “more risk of being eaten by a pinniped for fish that arrive early,” he said.


Half of the spring chinook run arrives in the river by May 13, while half of the summer run is in the river by July 4. Travel time from mouth to tributaries in March is 30 to 40 days, while transit time in mid-June is just 5 to 10 days, Schroder said.


Travel time from McNary Dam to Rock Island Dam (a distance of 293 river kilometers or 182 miles) for spring chinook is 9 days and survival is 74 percent, while for summer chinook travel time in this reach is 5 days and survival is 81 percent.


Spring chinook hold in upper river refuges and pre-spawn mortality is 46 percent. Summer chinook remain in main river pools and pre-spawn mortality is 15 percent.


pHOS, the percentage of hatchery fish on the spawning grounds, for spring fish is at a high of 45 percent in the Wenatchee and 57 percent in the Methow, but low for summer fish with pHOS of 14 percent in the Wenatchee and 33 percent in the Methow.


Added to all this is that spring fish live longer in their natal streams and so are constrained by those streams’ limitations. Also, most spring juveniles migrate out of the tributaries and down the mainstem Columbia prior to the beginning of spill at mainstem dams.


“The fish don’t have many options but to go through the powerhouse at PUD dams,” Gregory added.


The ISAB said it recommends continued investigations of the relative performance of summer and spring chinook. Management actions should be developed to lessen constraints on spring chinook abundance as information becomes available.


Harvest of spring chinook has risen over the last several decades and is currently about 10 percent, including commercial and tribal gillnetting and recreational angling, Schroeder said.


Pinniped predation is up, peaking in 2012 to 2015, and is a potentially significant source of mortality for upper Columbia spring chinook, maybe even more of an impact than harvest, Gregory said. Still, much needs to be done to quantify the impacts.


The ISAB report recommends “(1) expanding monitoring to assess interactions between pinnipeds and listed species, (2) maintaining predatory pinniped management actions at Bonneville Dam, (3) completing life-cycle/extinction risk modeling, and (4) expanding research on survival and run timing for adult salmonids in the Columbia River estuary and lower Columbia River.


The ISAB found evidence of density dependence (more spawners but not more offspring), especially in the Entiat River, although the Methow did not show strong evidence of density dependence, Gregory said.


“That tells you that something is limiting, but it doesn’t tell you what,” he added.


The ISAB provided a brief synopsis of their replies to the questions on the Council’s website at


1. Is the identification of limiting factors for Upper Columbia River spring chinook based on sound scientific principles and methods?

Yes, those principles are generally sound. The ISAB recommends integrating results of freshwater habitat assessments, density dependence analysis, and life-cycle modeling to identify limiting factors across the entire life cycle and geographic range of spring chinook.


2a. Are habitat recovery actions being prioritized and sequenced strategically? How should habitat projects be prioritized?

The ISAB found the Upper Columbia Salmon Recovery Board’s system for soliciting, reviewing, and designing restoration projects to be scientifically sound with regard to habitat conditions and effects of hatcheries and the hydrosystem. However, the ISAB recommends applying a transparent cost-effectiveness analysis of each project proposed.


As much as a third of the habitat in the three rivers is impaired, according to Gregory’s presentation to the Council. A graph showed that 25 percent of the Methow River habitat remains impaired. Some 36 percent of the Entiat River remains impaired and 21 percent of the Wenatchee River remains impaired. Much of those impaired areas are in towns and cities and so difficult to improve, he said.


Still, over 20 miles of habitat in the three sub-basins have been improved, nearly 100 barriers removed, more than 500 instream structures added, close to 300 miles of habitat opened, a dozen off-channel miles of stream connected, 3,500 acres of land protected, over 100 acres of floodplain connected and 135 acres of riparian areas treated.


With the additional habitat complexity, Gregory said, there are higher numbers of juveniles in early- and mid-summer and a higher total abundance of juveniles (actions didn’t just move fish around).


2b. Is there evidence that past projects have improved habitat for this ESU? What types of habitat projects should be prioritized in the future?

Evidence shows that habitat protection is a high priority, followed by removing barriers and reconnecting floodplains and side channels, the ISAB said. Increasing habitat complexity using log and boulder structures is a useful part of any strategic restoration effort but should be considered a short-term measure that does not substitute for the need to restore processes that maintain channel complexity and supply and retain large wood in rivers.


The ISAB recommended that projects that restore and sustain key fluvial and ecological processes should be considered high priority, given predictions for future climate and evidence of successful restoration. A key goal will be to provide habitats that are resilient to changing conditions and extreme events and provide connected habitats to sustain the full range of life history diversity.


2c. How well are actions in other management sectors (all Hs, i.e., habitat and hydrosystem, hatcheries, and harvest) aligned with recovery efforts?

The UCSRB has developed a useful process for prioritizing restoration projects and coordinating recovery actions, but there is no process for integrating the separate efforts of coordinating committees and working groups for the four Hs across the three sub-basins. The ISAB encourages the UCSRB and the tribal, state, federal agencies and the public utility districts operating in the Upper Columbia to develop a systematic, collective process for coordination of the actions, monitoring efforts, and decisions across numerous working groups and coordinating committees in the sub-basins.


3. Is a research, monitoring, and evaluation (RME) framework in place that can adequately address the questions in #2 above? Can this RME framework provide suitable data to test and validate hypotheses, inform management decisions, and confirm that limiting factors were correctly identified and are being addressed effectively?

Methods of the UCSRB’s Regional Technical Team, public utility districts, and regional fisheries agencies are generally appropriate and can be used to answer questions about effects of hatcheries and the hydrosystem. The RME program focuses largely on assessing hatchery practices and their effects. Currently, there is no RME Plan that encompasses all Hs and their related working groups, and thus the ISAB recommends developing an integrated RME Plan that encompasses all Hs and the Upper Columbia’s related working groups to coordinate monitoring related to all Hs across the three sub-basins.


3a. To what extent has the fitness of the Upper Columbia spring chinook ESU been negatively or positively affected by historical and current hatchery programs in this ESU? To what extent have contemporary supplementation programs provided a demographic benefit to the natural populations?

Contemporary populations of Upper Columbia River chinook salmon exhibit significantly lowered genetic diversity compared with historical stocks. Evidence indicates some hatchery programs have altered genetic diversity and fitness of Upper Columbia River chinook salmon. Current hatchery operations have not increased overall abundance or the abundance of natural-origin spring chinook, and productivity is not changing. Straying rates in some hatchery programs are quite high and could erode stock specific adaptations.


In view of the lack of response to supplementation programs in the Upper Columbia, the ISAB recommends continued improvement of their hatchery practices and RME program and additional studies to determine why spring chinook have not responded to supplementation. Additional investigations of genetic diversity and comparison of historical samples with contemporary samples of spring chinook from the Upper Columbia are also needed to better understand the extent of loss of genetic diversity and likely causes.


4. Are the life-cycle and habitat models in development for the Upper Columbia ESU useful for informing the identification, prioritization, and evaluation of restoration actions?

In general, the life-cycle models being developed will be useful to investigate the relative impacts of restoration actions because they can be scaled up to larger spatial and temporal scales. Currently, the models are useful for ranking the relative benefit of management actions at the population level but not for predicting exact numerical responses. The ISAB recommends continued development of the life-cycle models, using the life-cycle models to rank proposed restoration actions, and incorporating their results in analysis of cost effectiveness. Multiple models can be compared to better understand uncertainties and responses to limiting factors.


Also see:


--CBB, February 17, 20176, “Council Seeks Science Review Of Upper Columbia Spring Chinook Recovery; High Risk Of Extinction.”


--CBB, January 19, 2017, “Washington ‘State of Salmon’ Report: Seven ESA-Listed Populations Showing No Recovery Progress,”


-- CBB, June 2, 2016, “NOAA Status Review: None Of 28 ESA-Listed Pacific Salmon/Steelhead Stocks Warrant Status Change”


--CBB, February 27, 2015, “New Report Documents Washington State’s Salmon Recovery Efforts,”


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