NMFS Takes Late Hits Over BiOp, But Says It's On Right Track
 Big Bucks BiOp In The Offing
 NWPPC Wades Into Hatchery vs. Wild Fish Debate
 Eastern WA Irrigators, City Of Pasco Sue State DOE Over Water Permits
 Northwest Salmon Science Goes To Center Stage
 Cushman Relicense Back At FERC Over ESA Issues
 Congress OKs $40 Million For Puget Sound Watershed Restoration
 NMFS TAKES LATE HITS OVER BIOP, BUT SAYS IT'S ON RIGHT TRACK
NMFS announced last week that its final Biological Opinion for operation of the hydro system will be completed by Dec. 15, with an internal draft ready by Thanksgiving, complete with all the trimmings--revisions made after the agency has digested regional comments.
Brian Brown, NMFS hydro operations chief, said the pile of comments the agency received was larger than the BiOp itself, which runs to hundreds of pages. He also admitted the agency hasn't read them all yet. But he was sticking to his guns.
"There's nothing in the comments yet to suggest we've got it wrong," Brown said at the monthly Implementation Team meeting in Portland last week. He said state, tribal and other agency comments showed there are clear disagreements with NMFS--especially over the value of dam breaching and flow augmentation. "But our thinking on these matters is pretty well-defined...We aren't likely to change direction and reverse field."
That brought an outburst from ODF&W representative Ron Boyce, who said his agency has serious disagreements with NMFS' jeopardy analysis of the listed stocks affected by the new BiOp. "Oregon has wasted three months writing comments," said Boyce.
The BiOp also calls for an extensive offsite mitigation plan to boost ESA-listed stocks, which will be outlined as part of an implementation plan designed to cover the next five years, said Dan Daley of BPA's fish and wildlife division. The BiOp calls for a basic plan by next January. But Daley said it looks like March would be a more realistic deadline for developing a planning template that would encompass other state and federal efforts, including the Power Planning Council's fish and wildlife program.
IT policymakers expressed some concern over how the BiOp and the NWPPC's three-year "rolling review" of the Columbia Basin's ecological provinces would mesh. The plan will have to be approved by NMFS and USF&WS before it is put into effect.
"We're probably going to be out of sync with a lot of regional processes," said Daley.
Although Brown had said federal agency comments on the BiOp have not been released because of the ongoing consultation, BuRec representative Michael Newsome tipped his agency's hand when he voiced some questions about the new plan.
Since offsite mitigation would be driven by the NWPPC's efforts, along with its deference to state and tribal fish agencies through the Columbia Basin Fish and Wildlife Authority, Newsome wondered if CBFWA policy reflects the states' policies on fish and wildlife.
He also cited another huge problem with the different hatchery and habitat BiOps already out there. With "natural river" standards dictating the new hydro BiOp's performance measures, "Why should hydro be held to a natural state when no other agency is?" he asked.
One day later and several hundred miles up the river at Lewiston, Idaho, water agency authorities were explaining to the Power Planning Council why the NMFS analysis on summer flow augmentation was faulty.
Karl Dreher, head of Idaho's Department of Water Resources, took apart the NMFS analysis used to justify flow augmentation in the lower Snake for migrating fall chinook. Dreher noted that NMFS itself has not found a flow/survival relationship for spring chinook, as analyzed in the agency's White Paper on flow augmentation. Dreher added that his agency's analysis has been included in Idaho's comments on the hydro BiOp.
"Things aren't always what they appear," he told the Council. He said a close look at the data reveals most juvenile fall chinook move faster during low flows. He questioned the NMFS methodology that looked at the two species differently. He also questioned whether the agency's culling of fish for a certain size to release in the studies (75 mm) might have some effect on reduced survival of later migrating fish, when flows are down as well. "The late growers may not be as viable," Dreher said. The NMFS analysis could be confounded by the possibility of differences in "readiness to migrate" of fish in the sequential weekly release groups.
He said the NMFS analysis does not represent flow conditions for most of the surviving fish. "NMFS should not be using this to justify summer flow augmentation," he said. "Good water years show better survival for fish. But that doesn't mean you can create a good water year out of a bad water year."
The day before, NMFS' Brown said it is not clear how much more discussion with states and tribes is needed. "We have met with each state and most tribes."
Before the BiOp is finalized, NMFS may lead information sessions on major topics emphasized in the comments it has received. These include population groups, extinction risks and jeopardy standards, hydro measures, and offsite mitigation issues. -Bill Rudolph
 BIG BUCKS BIOP IN THE OFFING
The new hydro BiOp that will soon govern the future of dam operations on the Columbia River has some big ticket items imbedded in the "aggressive" hydro options spelled out in the draft. But no costs were attached--until last week, that is, when NMFS presented some rough estimates at a monthly policy meeting in Portland.
Bill Hevlin of the agency's hydro branch said the aggressive options package would cost around $130 million to $140 million annually over the new BiOp's first few years, "to get things done." That's about double the funding expected for next year's spending at the dams. The additional money for new BiOp spending would pay for extensive passage improvements for both juvenile and adult fish throughout the system.
As for FY '01 spending on the dams, the Corps of Engineers had asked for $85 million this year, which was pared down to $81 million by congressional appropriations committees, Hevlin reported. He pointed out that 16 percent of that is held back by Congressional purse keepers for "savings and slippage," so the region is expected to get around $68 million for next year's work.
Hevlin said that includes a major upgrade of the juvenile bypass system at Bonneville Dam's first powerhouse. About $6 million was spent this year and up to $30 million is being planned on that project alone. He reported the Corps is still deciding whether to go for a $70 million upgrade or a $200 million bypass system that would be similar to the one being tested at Lower Granite Dam on the Snake River.
Nearly 30 percent, or $25 million of the fish mitigation budget for FY '01, is designated for system-wide improvements to juvenile bypass systems, monitoring and evaluation. Another $25 million is earmarked for surface bypass development and evaluation, $14 million for adult passage improvements, $13 million to study juvenile passage behavior and survival studies, $3.6 million for dissolved gas abatement, and $4.4 million for other miscellaneous work.
"More money quicker won't help," said Hevlin, noting that once prototype structures are evaluated, biological benefits "are always different than what we anticipated." -B. R.
 NWPPC WADES INTO HATCHERY VS. WILD FISH DEBATE
The Power Planning Council has a few bones to pick with federal fish authorities over the way NMFS wants to save salmon in the Columbia Basin. Though supportive of the federal fish authorities' wish to use "existing process" to achieve the offsite mitigation proposed to help the hydro system out of a fish jeopardy ruling, the Council is concerned about issues of priority and funding. Members told NMFS that BPA funds should not be the exclusive source of ESA funding in the basin, noting that other federal agencies bear some responsibility for the loss of salmon and their habitat, including NMFS itself.
The Council also took issue with the proposed BiOp's extinction analysis of listed stocks and several tables included in the document that "could be interpreted to suggest" that any hatchery fish that spawn in the wild with listed salmon have depressed the growth rate of the wild ESA fish and will continue to do so. "If this is NMFS' conclusion, there are serious management implications that must be considered by the federal caucus, the Council and the region."
The issue of hatchery influence could have considerable impact on the future of the Basin's fish and wildlife program. Currently, about 40 percent of the F&W budget in the direct program overseen by the NWPPC goes for hatchery construction and operations.
Earlier, NMFS had responded to the Council's draft fish and wildlife plan, noting that "general weaknesses" included the need for more guidance in hatchery and habitat approaches and subbasin planning. The agency also said that ESA priority items listed in its draft BiOp should be expressly mentioned and implemented in the program. The feds also said the program must recognize the critical need for wild stock assessment, pointing out that non-indigenous species are a "neglected threat" to salmon recovery. They recommended the Council address this threat more vigorously. -B. R.
 EASTERN WA IRRIGATORS, CITY OF PASCO SUE STATE DOE OVER WATER PERMITS
Eastern Washington irrigators and the City of Pasco filed a lawsuit against the Washington Department of Ecology last week for its failure to process water rights permits from the mainstem Columbia River. The suit, filed in Benton County Superior Court, asserts that DOE's support of NMFS' "no net loss" water policy for ESA-listed fish takes away the state's power to manage its water. The plaintiffs say the NMFS policy is both illegal and without technical merit.
Applications pending before the state agency for water withdrawals number over 7,000--up from 4,800 in 1994, when the state changed its processing policy. Since then, it has not approved non-emergency permits without basin assessments or unless it decides groundwater sources are sufficient.
Darryll Olsen, spokesman for the irrigators, said DOE head Tom Fitzsimmons has requested settlement discussions. Olsen said the state can't use the NMFS policy as an excuse to keep from approving permits. -B. R.
 NORTHWEST SALMON SCIENCE GOES TO CENTER STAGE
In recent weeks, one of the nation's highest profile research weeklies, Science magazine, has produced a spate of salmon-related reports. Two of them are even based on recent "gumboot" science--actual field work.
The third piece, and arguably the most important, was published just last week and describes the life-cycle model developed by NMFS scientists over the past couple of years, an effort that grew out of an attempt to analyze biological effects of breaching dams on the lower Snake. As NMFS scientists grappled with difficulties and uncertainties from PATH, the previous modeling effort developed by various state, tribal and federal agency scientists, their new analysis began. Though it lacks the ability to model various hydro passage routes in its analysis, results from the new NMFS matrix model have been cited in the proposed hydro BiOp to strengthen a federal decision that puts dam breaching on the back burner for five years--a finding that has plenty of critics claiming the analysis is too optimistic.
"Recovery and Management Options for Spring/Summer Chinook Salmon in the Columbia River Basin," in the Nov. 3 issue of Science, authored by NMFS scientists Peter Kareiva, Michelle McClure, and Michelle Marvier (now teaching at Santa Clara University), describes the matrix model applied to long-term population data and concludes that dam passage improvements, including fish barging, have improved juvenile survival from 10 percent to 40-50 percent in recent years.
"If such improvements had not been made," say the authors, "the rates of decline would likely have been 50 to 60 percent annually, and spring/summer chinook salmon might well have already disappeared from the Snake River. Hence, past management actions have reduced in-river mortality but have not reversed population declines."
They also conclude that even if all juvenile and adult fish survived the dams, index stocks would continue to decline. But modest reductions in first-year or estuarine mortality would reverse declining numbers, the authors indicate.
The article also says there are uncertainties associated with measuring potential effects of the lower Snake dams on juveniles--specifically, indirect mortality--because of difficulties in establishing "control" populations. Their model suggests that if indirect mortality is 9 percent or more, dam breaching could reverse declining stocks of spring chinook.
"Given the current uncertainty," the authors conclude, "policymakers may have to view the decisions they make as large experiments, the outcomes of which cannot be predicted, but from which we can learn a great deal pertaining to endangered salmonids worldwide."
The Gold Standard
"This is the gold standard for research," said NMFS scientist Mike Schiewe, director of the agency's Fish Ecology division in Seattle. "With policymakers calling for the 'best, available science,' this is it," Schiewe said, because of the rigorous peer review that articles undergo before publication.
But he was also quick to point out that large uncertainties still remain in the salmon recovery equation, notably over the lack of real data, the delayed mortality issue, and the potential negative effects on wild stocks from hatchery strays.
Schiewe said the new analysis moves the debate away from the "hydro-centric" focus of the earlier PATH analysis. He said PATH gave little credit to possible effects of hatchery fish and habitat. The PATH results found that dam breaching would recover spring chinook, but leaving the dams in place would also eventually recover the fish.
"In fact," Schiewe said, "since PATH used the Ricker Curve and its assumptions about density dependence, the analysis actually said it was impossible for those stocks to go extinct. You'd think such a result would have raised some questions."
Coincidentally, the Nov. 3 issue of Science also contained a letter from the four scientists who reviewed the 1998 PATH results. Though billed as an external peer review by PATH facilitators, the exercise was not an academic peer review in the normal sense because the reviewers were not anonymous and they were paid for their work. They took issue with the way PATH was characterized in a news article by Charles Mann and Mark Plummer, published in Science last September, that summarized the state of science and salmon recovery.
The four said there is little chance of increasing early survival rates before fish reach the dams. "The only measure with any chance of success is to eliminate mortality of the smolts in the reservoirs and mortality downstream of the last dam, which may be related to the presence of dams and/or transportation effects."
Mann and Plummer responded by quoting the reviewers' own remarks expressing uncertainties about the PATH model's inputs and optimistic recovery estimates from dam removal options.
NMFS scientists, meanwhile, have more papers in the works. The CRI folks have an article just about ready for publication in the Proceedings of the National Academy of Sciences on their use of a modified Dennis Extinction Model to develop "lambda," the percentage generational increase in stocks needed for recovery.
They also will soon have a paper in Ecological Applications on the 12 ESUs, "evolutionarily significant units," of ESA-listed salmon in the Columbia Basin. And the group is working on yet another paper on density dependence, since the NMFS/CRI matrix model's analysis of weak stocks does not assume population density has any effect. Other NMFS scientists in Seattle have other papers in the works as well.
Sockeye and the Little Ice Age
Another recent paper in Science (Oct. 27) chronicles research that shows how pronounced changes in salmon populations in Alaska appear to be related to climatic change. Bruce Finney of the University of Alaska and other researchers (Irene Gregory-Eaves, Jon Sweetman, Marianne Douglas and John Smol) studied sediments in lakes on Kodiak Island and other western Alaska sites that have been home to spawning sockeye for hundreds of years. They tracked sockeye abundance by measuring sediment layers for amounts of nitrogen-15, an isotope that is picked up by fish feeding on zooplankton in the ocean. Higher levels of the isotope reflect higher levels of nutrient loading by the fish in their two to three years at sea.
The researchers were able to track populations back 300 years and found that large changes in sockeye numbers occurred before the onset of commercial fishing, with a prominent decline in the early 1800s that coincided with the coldest sea and air temperatures in the last 250 years. But they found the relation seemed to break down after 1850, when temperatures went down and sockeye numbers went up, suggesting that boosted nutrient levels from carcasses in the lakes played a role in fish productivity. The research also suggests the collapse of the Karluk sockeye fishery on Kodiak Island in the early 1900s was related to overharvest and a consequent reduction in carcass-driven nutrients.
Examination of the sediments showed that fish populations rebounded quickly in the 1800s, "when the natural nutrient feedback loop was operating. In contrast, the disruption of this nutrient cycle during the commercial fishing period appears to have had a strong negative impact on lake productivity, thereby preventing a similar recovery in the 20th century."
When they looked at nursery lakes in the Bristol Bay region, however, the scientists found that the carcass-derived nutrients seemed to have less effect on productivity. Their conclusion: "This further highlights the need to assess the implications of both climatic change and altered nutrient cycles in determining management strategies for Pacific salmon stocks."
And Then There Were Two...Populations
Research on sockeye in Seattle's own backyard indicates the population has developed into two groups in the space of only 60 years--about 13 generations. The study was reported in the Oct. 20 edition of Science.
Looking at populations in the Cedar River and Lake Washington, scientists found that it didn't take long for the two groups to no longer be able to spawn together successfully. The main population spawns in the river, and a much smaller group has bred in the lake since the late 1950s, a few miles from the mouth of the river.
Led by ex-University of Washington graduate student Andrew Hendry (now at the University of Massachusetts), the researchers found that deep-bodied male sockeye would be more successful mating off the beach than in the river, where they could be stranded in shallow water, eaten by predators, or have more trouble maneuvering in fast water than smaller fish. Large-bodied female fish seemed to prefer river spawning, where their size allowed them to dig deeper redds than smaller females, thereby affording their eggs more protection from flooding. Genetic analysis showed that river-hatched fish that tried to spawn at the beach had little success.
An essay in the same issue by University of Edinburgh professor Nick Barton pointed out that the sockeye study, along with another report on fruit flies, "provides strong evidence for the rapid evolution of reproductive isolation." But Barton wondered why more species aren't seen if evolution moves this fast. "It may well be that new species (that is, reproductively isolated populations) do form often," Barton writes, "but that only rarely do they evolve sufficiently to be recognized as separate species by biologists or such that they find a distinct ecological niche."
 CUSHMAN RELICENSE BACK AT FERC OVER ESA ISSUES
The Federal Energy Regulatory Commission got what some might term a pre-Halloween trick last week, when the DC Circuit Court of Appeals issued an order Oct. 30 remanding the relicense of Tacoma Power's 124-MW Cushman hydro project back to the commission. "Given the practical concerns of judicial administration and efficiency, it does not make sense for the court to review the licensing order at this juncture," the Appeals Court ruled. At issue are ESA-related concerns that FERC failed to address in its July 1998 Cushman relicense, which will be the topic of a forthcoming Biological Opinion from NMFS.
The groundwork for this latest twist in the now 26-year-old Cushman saga--previously labeled "the relicensing case from hell" by no less than FERC chairman James Hoecker--was laid when NMFS proposed listing two more salmon species as threatened under the ESA, just a few months before the commission finally issued its relicensing order for the project. At the time, FERC rejected the notion that it had to open an ESA consultation, noting that the listings had not yet taken effect and that, in any case, the license would allow it to make changes--if necessary--after informal consultations with NMFS.
FERC took no action on the ESA issue until this June--almost two years later, and nine months after NMFS finalized the salmon listings in March 1999. The commission sent NMFS a June 9 letter, requesting formal consultations, from which it subsequently backpedaled, calling its request "in error." But in August, NMFS wrote back, articulating its intent to proceed with formal consultations, developing a biological opinion addressing the ESA-listed salmon and operations of the Cushman project under the now-stayed relicense.
Tacoma Power on July 20 filed a motion requesting the court case be held in abeyance until the ESA issues were resolved, arguing that the license being litigated could potentially change as the result of NMFS' findings. Most parties in the slew of Cushman challenges and ancillary litigation opposed Tacoma's motion--among them FERC, the Skokomish Tribe, environmental groups, EPA, Interior, NMFS and the state of Washington.
Instead, a number of the parties, including the federal agencies and tribe, filed counter motions asking the court to remand the matter to FERC--a move both Tacoma and the commission opposed, but which the Appeals Court last week granted.
"It would be a better use of judicial resources to wait until the court has before it the full administrative record, including the biological opinion [NMFS] plans to issue in late October 2000," the DC Circuit wrote. "A remand will enable FERC to take any action it deems appropriate in response to that opinion, and any other administrative action that may be required in order to comply with the applicable statutes."
"The court has basically relinquished its jurisdiction over the whole case, unless and until FERC issues another final order and parties appeal it back up to the DC Circuit--as is perhaps inevitable," explained Tacoma attorney Mike Swiger.
"From our view, we didn't think it made sense to litigate the license's conditions if they were going to change because of the ESA requirements," he added. "We wished the court would hold on to the case, to facilitate resolution. But all in all, this might make the most sense."
In light of the remand, Swiger said, "our position is that FERC is going to have to take another look at the whole license now. It's FERC's responsibility to take all of the various factors into account and arrive at a balanced decision that's in the public interest. If the ESA requires additional conditions, the others will have to be re-evaluated to ensure there's a coherent result." Tacoma, Swiger said, will "oppose any attempt to just pile the ESA requirements on top of what's already in the license."
While the remand paves the way for FERC to potentially reopen all of the Cushman license's conditions, Swiger suggested FERC may also decide the ESA listings don't necessitate any additional measures. "It's been FERC's position thus far that the license adequately protects listed species," he pointed out.
But whether FERC is ultimately obligated to include conditions suggested by NMFS may surface as an area of conflict. In recent cases--such as Okanogan PUD's aborted attempt to relicense the Enloe dam--FERC has said it is obligated to defer to NMFS' opinion on ESA-related measures, whether it agrees with them or not.
But one difference in the Cushman case is that, with the mid-summer flurry of exchanged letters, NMFS and FERC never seemed to agree on whether a formal ESA consultation had actually been initiated. "One of the issues is going to be whether in fact the listings in Puget Sound have triggered a formal consultation, or whether NMFS is merely serving in an advisory capacity in this case," Swiger predicted.
From NMFS' perspective, the BiOp does in fact constitute formal consultation, agency attorney Brett Joseph said last week. "We received FERC's request to initiate formal consultations under Section 7 of the ESA in early June," Joseph recounted. "We then got a letter from FERC clarifying that they had made a 'not likely to adversely affect the listed species' finding. NMFS responded that it did not concur. Therefore, under the regulations...Section 7 formal consultation automatically proceeds. Through that exchange, consultations were initiated."
Joseph also acknowledged the possibility the court's remand could open up the entire constellation of issues included in the Cushman relicense order. "This could potentially open the door to consideration of other issues raised in the litigation over completeness of the record," Joseph said. "I expect FERC will use this opportunity to address those aspects of their own process that parties have alleged are incomplete."
Joseph added that the Cushman BiOp, which the Appeals court tabbed as due at the end of October, is now on track for release at the end of this month. -Angela Becker-Dippmann
 CONGRESS OKS $40 MILLION FOR PUGET SOUND WATERSHED RESTORATION
Some may call it pork, but it's all going for salmon, and passed by the US Senate just before they adjourned last Friday, it adds up to $40 million in funding restoration projects in the Puget Sound region. It was the Senate's final order of business before they left town for last minute electioneering.
Weeks ago, local agency folks were pretty sure it was coming their way. Last month, after the House passed the Water Resources Development Bill and sent it on to the Senate, Dennis Canty, funding coordinator for King County's ESA Policy Coordination Office told the tri-county executive committee that "It's another banner year for habitat for Puget Sound."
The $40 million will allow the Corps of Engineers to work with other federal, tribal, state and local agencies to identify and implement "critical" restoration projects, with the feds picking up 65 percent of the tab. Single project costs are limited to $2,500,000. The legislation defines "critical" to mean water resource projects "that will produce, consistent with existing federal programs, projects and activities, immediate and substantial environmental protection and restoration benefits."
Local agencies mentioned in the legislation include the state Salmon Recovery Funding Board, Northwest Straits Commission, Hood Canal Coordinating Council, and county watershed planning councils and salmon enhancement groups. -Bill Rudolph
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