NW Fishletter #309, October 19, 2012
  1. Juvenile Chinook Survival Second Highest In Recent Years
  2. Study Says Hatchery Fish Are Boosting Idaho Chinook Run
  3. Snake's Fall Jack Count Signals Another Bonanza Likely In 2013
  4. Council Staff Recommends Changes For Data-Management Projects
  5. First Brief Filed In Litigation Over NPCC's 6th Power Plan
  6. El Niño Possibility Dims As Tropical Pacific Grows Cooler

[1] Juvenile Chinook Survival Second Highest In Recent Years

Federal scientists from the NOAA Fisheries Science Center in Seattle have released their preliminary results from this year's salmon migration through the Columbia/Snake hydro corridor, noting that nearly 60 percent of juvenile spring chinook survived from the Snake River trap (near Lewiston, Idaho) to below Bonneville Dam.

The Oct. 12 memo said this year's migration showed the second highest survival of PIT-tagged hatchery and wild fish since 1999. Only 2006 was better, when survival from the trap to the Bonneville tailrace was just over 61 percent.

Juvenile survival was significantly higher that last year's 49 percent, despite 2011's higher spring flows and 4th all-time best water year since 1960. The memo also noted that compared to long-term averages, survival in 2012 was 5.5 percent higher between Lower Granite and McNary dams and 10.3 percent higher between McNary and Bonneville dams. The 2012 water supply for the Columbia Basin ended up 5th highest since 1960.

Juvenile steelhead survival was estimated at nearly 60 percent, third highest since 1999, and close to last year's 59 percent. Only 2008 and 2009 were better.

"The pattern through time of flow volume in the Snake River in 2012 was unique among the last eight migration seasons," said the memo, "in that the highest peak in flow occurred in late April rather than in May, and in fact, the flow throughout May was no higher than in April."

The overall average of daily average flow volume in 2012 was higher than the long-term average, the memo reported, "but no other year's flow pattern had those characteristics." Snake flows stayed around 100 kcfs for the first three weeks in April and peaked quickly at 178 kcfs on April 27, dropping back in the 100-kcfs range by the end of the following week.

Mean spill volume at lower Snake dams was close to the 2006-2011 average for the first few weeks in April, then jumped when flows spiked. Spill in the first three weeks in April 2012 as a percentage of flow was below average compared to recent years, but hit nearly 50 percent when flows rose later in the month. In May, spill declined to near-to-below average.

Upper Columbia hatchery spring chinook exhibited an 84-percent survival rate from the McNary Dam tailrace to below Bonneville Dam, nearly 20 percent higher than last year.

Upper Columbia hatchery steelhead showed 100-percent survival from McNary to Bonneville Dam, compared to last year's 65 percent. But survival from release to McNary, was way down, only about 28 percent , compared to last year's 44 percent. The difference could be caused by higher predation from birds colonizing Potholes Reservoir this year, but the memo did not mention anything about it.

Snake River sockeye showed a 47-percent survival rate from Lower Granite to Bonneville this year, compared to more than 54 percent in 2010, a much lower flow year. Survival estimates to Bonneville in 2011 were not available because of low PIT-tag detections caused by debris and pulled screens during high flows last year.

Upper Columbia sockeye showed much higher survival than last year, with a preliminary estimate of more than 79 percent making it from Rock Island Dam to Bonneville. In 2011, the survival rate was barely above 50 percent.

The memo also reported that during May and June, changes to turbine operations at Bonneville Dam to reduce descaling of juvenile sockeye "drastically reduced" PIT-tag detection probabilities and made for "very low precision" of survival estimates, and impossible for some weekly groups.

Another result of the odd flow pattern was the lowest percentage level of fish barged from Snake dams in the past 20 years. Preliminary estimates found only 23 percent of wild spring chinook being transported this spring, along with about 25 percent of hatchery spring chinook. For wild steelhead, it was estimated that about 28 percent were barged, along with 27 percent of hatchery-origin steelies.

The memo said fish collection began on May 2 at Lower Granite, but the large spike in flows in late April meant that most juvenile spring chinook (67 percent) and steelhead (59 percent) had passed the project before barging even began. High spill levels, along with surface bypass collectors kept numbers of fish entering bypass systems low compared to other passage routes. But during May, about 60 percent of the smolts that passed Lower Granite ended up being barged from there or a collector dam downstream. -Bill Rudolph

[2] Study Says Hatchery Fish Are Boosting Idaho Chinook Run

Results of a study by several Northwest fish biologists, published in the peer-reviewed journal Molecular Ecology, show that hatchery fish have helped to boost overall fish runs when they were allowed to spawn with a wild summer chinook population in Idaho's Johnson Creek, a tributary of the South Fork of the Salmon River.

The BPA-funded study--part of a supplementation effort under way since 1998--has been making headlines because its findings run counter to earlier results derived from intense scrutiny of steelhead returns in Oregon's Hood River. Researchers from Oregon State University found that overall fish fitness declined significantly when hatchery-origin fish spawned with natural-origin Hood River steelhead.

The paper, titled "Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon," was written by lead author Maureen Hess, a geneticist with the Columbia River Inter-Tribal Fish Commission, and biologists from the Nez Perce Tribe. Using DNA analysis, they found that after seven brood years, fish removed from the creek's weir to serve as hatchery broodstock produced 4.69 times more returning adult offspring and 1.32 times as many returning grand-offspring than naturally spawning chinook in Johnson Creek.

The researchers said their results showed that reproductive success of successful hatchery-reared parents was not significantly different from wild parents, and that mating types (H x H, H x W, or H x -- [unknown]) weren't significantly different from mating by wild-origin parents (W x W; or W x --). "Thus, evidence does not support that Chinook salmon reared for a single generation in the hatchery had negative fitness effects on wild-origin-fish in Johnson Creek."

The study did note the hatchery produced far more jacks (precocious males that return a year early) than the wild population. Returns from brood year 2000 were more than 40-percent jacks, while the wild component contained only 13 percent. But the researchers said there was no evidence of a shift in age at return over time. They said the effects of hatchery jacks on the long-term viability of the natural population would be evaluated in the future.

The authors speculated in their "discussion" section that the significant reduced fitness of hatchery-produced males "may be attributable to the artificial mating of competitively less-fit males (e.g. less aggressive) that may not have otherwise successfully reproduced in the wild."

The authors also said the differing results compared to other studies that found reduced fitness in some supplemented populations may be due to the comparative lack of hatchery influence in Johnson Creek compared to the upper mainstem of the South Fork of the Salmon River. They also noted that the Johnson Creek enhancement used only natural-origin broodstock.

The study also said that since the focus of many previous hatchery/wild studies was on steelhead, maybe these fish "are simply more prone to reduced fitness due to hatchery rearing practices." Steelhead in hatcheries are raised to smolt size in a single year, while in natural surroundings, they generally take two years to mature to that level. The juvenile chinook spend a year in hatcheries to reach the smolt-stage as well, but it more closely reflects growth in a natural state.

The authors said even though wild-origin fish are used in the Johnson Creek project, small changes in genetic fitness from hatchery rearing could show up in future returns. They therefore plan to evaluate Johnson Creek chinook runs beyond the two generations examined in this study.

The Johnson Creek enhancement project was started by the Nez Perce Tribe in 1998, to boost a run that had dropped to five pairs of spawners in 1995. According to the tribe, adult return numbers are now consistently meeting the short-term abundance goal of 350 returning adults, with more than 1,000 adults returning in some years. -Bill Rudolph

[3] Snake's Fall Jack Count Signals Another Bonanza Likely In 2013

Judging from this year's jack count at Lower Granite Dam, next year's return of ESA-listed fall chinook to the Snake River could be even better than 2012's, which has been the second best since the lower Snake dams were built.

By Oct. 17, more than 21,000 jacks were counted at the dam. That's several thousand more than were counted last year, which signaled this year's excellent return of more than 33,000 adult fall chinook so far, both wild and hatchery-bred. The record is still held by 2010's lofty return of more than 40,000 (by Oct. 17). In 2009, about 40,000 jacks were counted as well.

In recent years, some jacks have been counted as adults because they were larger than the traditional 56-centimeter cutoff used by fish counters. This has created problems and fish biologists are working to revise previous years' return numbers, along with sorting out hatchery and wild fish returns, based on coded wire tags.

A 2010 WDFW memo estimated that up to 30 percent of fall chinook jacks were mistakenly counted as adults. And yearling jacks were sometimes counted as adults, as well. The memo noted that in the spring/summer chinook run reconstruction for 2005-2008, it was found that the WDFW window counts at Lower Granite were underestimating jack chinook by roughly 37 percent.

But it's clear that there are lots of fish compared to the early 1990s, when 78 fall chinook returned one year. WDFW's Glen Mendel said smolt-to-adult returns for subyearling fall chinook have climbed, thanks to good dam passage and ocean conditions. And the adult returns of yearling chinook that migrate after a year in the hatchery are four or five times higher, reaching 3 percent.

In addition, more juveniles have been heading out. The returns in some recent years are nearly 25 percent yearling fish, Mendel said, which has skewed the age composition of the original return compared to its largely subyearling origins.

Mendel noted that this summer's low flows and summer heat created a toxic blue-green algae bloom above Little Goose Dam, the next project downstream from Lower Granite, but it does not seem to have affected the fall chinook run, though the state Ecology Department has advised fishermen not to eat anything caught behind the dam.

However, don't expect the fall chinook to be delisted anytime soon, even though the wild run keeps doubling and tripling its interim recovery goals. Mendel said the 10-year geometric mean of abundance must stay above 2,500 fish. This seems doable these days, but the feds may also want 20 years of overall productivity of the wild run to be at least 1.3, the ratio of returning spawners from one generation to the next. If ocean conditions tank, that might not be doable.

But NOAA Fisheries scientist Tom Cooney, who serves on the Interior Columbia Technical Review Team that developed the original recommendations, says the criteria for delisting fall chinook are still being developed in dialog with regional NOAA staffers.

Cooney said the TRT recommended some years ago that the 20-year running average productivity factor for Snake fall chinook be around 1.5, so that the time frame would be long enough to contain the "ups and downs in the ocean." Cooney said that number may seem high, but the TRT felt it was needed for the Snake fall chinook ESU to maintain a low risk of extinction over the next 100 years.

Cooney noted that using the running average doesn't mean scientists will just start looking at productivity when the recovery plan is completed, now scheduled for 2014, but will be able to include these current years of high abundance and productivity. So, if current levels of productivity are maintained, delisting might be possible sooner.

Cooney said it's hard to speculate whether the current numbers of wild fall chinook will stay high, but he noted that 10 years ago, he would never have thought current numbers would have got this high, especially with 60 percent or more of the fish on spawning grounds of hatchery origin. He said that leads to an important question--how certain can biologists be that the run could maintain itself if supplementation was dialed back or cut off?

Biologists think the diversity of the fall chinook has been significantly compromised since 85 percent of the spawning areas of the Snake fall chinook are blocked by the Hells Canyon Complex.

Cooney said there has been some discussion of exploring options like the possibility of reintroducing the fall chinook above Hells Canyon, but he said old spawning grounds have been compromised, and water quality would have to be restored before other issues could be tackled, like figuring how to get the fish past those Hells Canyon dams. -B. R.

[4] Council Staff Recommends Changes For Data-Management Projects

A special committee tasked by the Northwest Power and Conservation Council with examining several F&W program data-management projects has suggested eliminating or reducing funding for some projects. The Program Evaluation & Reporting Committee (PERC) released its draft recommendations to the Council's F&W Committee on Oct. 3. Under review are several long-standing projects, and supporters were on hand to voice their concerns.

It's a trial run for PERC, which met twice with stakeholders earlier this summer to map out future needs.

Council staffers on PERC recommended that the Northwest Habitat Institute ($191,000 in FY 2012), which is involved in subbasin planning, be funded for only three months in FY 2013, and its data moved over to StreamNet, the huge regional database maintained by the Pacific States Marine Fish Commission. The staff also supported a 10-percent to 15-percent reduction in the StreamNet budget, in line with potential cuts now under review by BPA for FY 2013.

The staff called for convening the wildlife crediting forum to discuss whether the Habitat Evaluation Procedures team, which conducts vegetation surveys for wildlife managers, will still be needed in the future. It's managed by the Columbia Basin Fish and Wildlife Authority.

The staff also recommended a 10-percent to 15-percent reduction in the budget for the Pacific Northwest Aquatic Monitoring Partnership, a coordinating body that works to develop standardized data collection. In addition, council staffers recommended ending funding for the annual Status of the Resources Report managed by CBFWA, but to maintain personnel for at least a year to provide technical services for reporting needs for the F&W program. It also recommended that the work of the Fish Screening Oversight Committee be maintained in the future.

The recommendations, which did not include any idea as to how much money could be saved, will be discussed at the F&W Committee's meeting later this week in Whitefish, Mont.. Council staffers said they do not recommend specific budgets, "but rather the work or work projects." If the recommendations are approved, they will be sent to the full Council for a vote at its November meeting.

PERC's work has already garnered criticism from some stakeholders. On the day before the meeting, Northwest Habitat Institute Director Thomas O'Neill sent a letter to F&W Committee members, complaining about the process that announced the potential termination of the NHI project "in a document that is globally distributed." He also explained at length why the NHI funding should be maintained. O'Neill said his project maintains and serves over 5,000 files developed and made accessible for subbasin plans. He said 59 subbasins have used or cited this data.On Oct. 10, the Council's F&W Committee [http://www.nwcouncil.org/news/2012/10/6.pdf] reported on the PERC recommendations to the full Council, which is scheduled to vote on them at its November meeting. It was estimated that the region could save about $500,000 if the recommendations are approved. -B. R.

[5] First Brief Filed In Litigation Over NPCC's 6th Power Plan

An Idaho conservation group says the Northwest Power and Conservation Council's newest Power Plan (2009) shortchanges fish and wildlife mitigation, and has gone to the 9th U.S. Circuit Court of Appeals to try and prove it.

In a Sept. 21 brief filed by Earthjustice, which is representing petitioner Idaho-based Northwest Resource Information Center (NRIC), the group argues that the Council has not given "due consideration" to protection, mitigation, and enhancement of anadromous fish in the Sixth Power Plan, "despite the plain language of the Power Act."

The NRIC brief says the Council's power plan gave no independent consideration to whether other fish and wildlife measures were necessary or "how the plan's conclusions and forecasts of power generation, conservation or efficiency would meet the Power Act's requirements to protect, mitigate and enhance ... anadromous fish.

"Instead," it continued, "even after finding that the Northwest could readily and economically meet or exceed its future power needs largely through conservation, efficiency and renewable energy development, the Council gave no further consideration to how those conclusions could facilitate achieving the fish restoration requirement of the Act by, for example, reducing reliance on hydropower and embracing additional renewable power generation, conservation, and efficiency to include additional fish protection measures necessary to meet the fish restoration objective of the Act."

Terry Flores, executive director of Northwest RiverPartners, a respondent-intervenor, said her group is taking this lawsuit seriously and is actively engaged.

"These are not new issues," said Flores, pointing out that some conservation and fishing groups have long advocated that the region should embrace more renewable energy generation to make up for power that would be lost if the region embraced the groups' agenda of higher flows, even more spill, and removal of the lower Snake dams.

The petitioner's brief says the Council erred by not describing or applying a methodology for evaluating environmental costs and benefits of power resources or measures, but instead added an appendix to the plan whose methodology failed to account for the costs of utilizing power resources "that fail to protect anadromous fish and fails to account for the benefits of measures that meet the Act's fish restoration goal, in violation of the Power Act."

The petitioner also said the Council included a methodology in the plan "based on irrelevant calculations of forgone hydropower generation" that overstated the costs of fish protection measures.

"The Council arbitrarily included that methodology in the Sixth Plan," the brief said, "despite its earlier recognition that calculations of forgone power were irrelevant and confusing, without explaining why it abandoned more valid methods ... and without considering the chilling effect that inaccurate and inflated cost estimates would have on measures necessary to achieve the fish protection goal of the Act."

The petitioners said the Council's "due consideration" of anadromous fish needs in the power planning process "has contracted to such an extent that in the Sixth Power Plan, the Council fails to give any consideration whatsoever to this criterion."

The brief pointed out that the phrase "due consideration" is not defined in the Act, but it argued that, given the context of the Act and the legislative history, "it makes clear that the Council must independently consider--and give significant weight to--the needs of anadromous fish in its scheme for implementing conservation measures and developing resources in the plan."

The petitioner argued that the "due consideration" duty is a big part of the "two-step feedback loop Congress established between fish and wildlife and the power plan.

"Just as the Council must consider the impacts of fish measures on the reliability of the power system when developing the program, the Council is also required in the plan to consider whether it is meeting the anadromous fish restoration goals of the Act."

In a lengthy footnote, the brief says the council's fish and wildlife program, "when it simply relies on a BiOp that that has been overturned by a federal court, cannot be characterized as sufficient to 'protect, mitigate and enhance' salmon and steelhead affected by the FCRPS [Federal Columbia River Power System]."

The NRIC called on the 9th Circuit to declare the latest power plan a failure and issue a tailored remand to correct the "legal errors" within 180 days of the court's decision.

It asked the court to direct the Power Council to consider specific goals to achieve adequate fish protection, especially for Snake River salmon and steelhead stocks, "including, but not limited to provision of flows of adequate quantity and quality to provide safe migration conditions and any changes to the power system required to make these changes.

It also asked the court to direct the Council to recognize that fish and wildlife measures cannot be rejected "solely" because of power losses and economic costs, "and document how such measures can be implemented with additional conservation or more resources without interfering with maintaining a reliable and economical adequate power supply."

RiverPartners' director Flores says the litigation will be dealing with an important question--whether the ESA trumps the Power Act. Power Council attorneys are scheduled to file the government's first brief around Thanksgiving, and RiverPartners' brief will be filed about a month later, along with fellow intervenors the Public Power Council and BPA.

The Northwest Resource Information Center originally filed the lawsuit July 6, 2010, in the 9th Circuit Court, claiming in its original petition that the latest power plan illegally inflated the cost of salmon mitigation and ignored the benefits of increased fish runs. -B. R.

[6] El Niño Possibility Dims As Tropical Pacific Grows Cooler

The tropical Pacific is continuing to cool, the Australian Bureau of Meteorology reported Oct. 9, in its latest ENSO update, continuing "its retreat from El Niño thresholds for the second consecutive fortnight." The Bureau said ocean temperatures stayed within neutral ranges, neither El Niño nor La Niña.

"Climate models surveyed by the Bureau of Meteorology have increased their chances of sea surface temperatures in the tropical Pacific Ocean remaining at neutral levels, though still warmer than average, for the remainder of 2012," said the Aussies.

The Bureau reported that sea-surface temperature anomalies in the central and eastern tropical Pacific had cooled further over the past two weeks. "While the distribution of warm anomalies remains similar to last fortnight, the pattern is breaking down and no longer shows the organized tongue of warm anomalies along the central equatorial Pacific characteristic of an El Niño."

NOAA's Climate Prediction Center said Oct. 15 that borderline ENSO neutral/ weak El Niño conditions are expected to continue in the Northern hemisphere this winter, "possibly strengthening over the next few months."

In an Oct. 18 statement, NOAA described its current uncertainty. "This is one of the most challenging outlooks we've produced in recent years because El Niño decided not to show up as expected," said Mike Halpert, deputy director of NOAA's Climate Prediction Center. "In fact, it stalled out last month, leaving neutral conditions in place in the tropical Pacific."

The agency's winter forecast (December-February) says the odds still favor:

Meanwhile, the negative PDO conditions in the Northwest are getting stronger, according to the latest PDO index update from University of Washington atmospheric science researcher Nate Mantua. The PDO index for September was -2.21, compared to -1.91 for August, which means that overall cooler, moist conditions are likely to persist. The index has been in negative territory since June 2010, but hasn't been this strongly negative since last November. -B. R.

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