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NW Fishletter #204, October 24, 2005
 Latest Survival Study From Fish Passage Center Ignores NMFS' Concerns
With the release of its latest fish survival study, the Fish Passage Center is likely to provide more ammunition for critics who say the agency has played too much of an "advocacy" role in the region.
In the past, some utility groups and federal scientists have locked horns with FPC over its sometimes shaky statistics and unabashed support of flow and spill measures throughout the Columbia and Snake hydro system. With an attitude like that, they say, it has no business doing research.
The situation reached critical mass earlier this year when Idaho Sen. Larry Craig added language to a Congressional spending bill that jerked 2006 funding for the beleaguered agency. The language remains in the bill as it goes into conference, and supporters say there is no chance it will be stricken.
That's why some think the latest FPC study is on a fast track to finality, so that it can be used by plaintiffs in the ongoing remand of the hydro BiOp, where they go before a judge in December to argue for more changes in hydro operations.
One big issue is whether the 200,000 hatchery fish pit-tagged every year truly represent the wild stocks of concern. Since most Idaho hatchery stocks in the study show higher survival rates than wild stocks, it was an important question raised in the last incarnation of the study, released in final form in April and covering the migration years 1997-2002.
But it's not much of an issue in the latest draft of the Center's 2005 comparative survival study [CSS] released Oct. 10, which continues to echo old themes from past FPC reports. However, the latest draft fails to acknowledge questions raised by federal scientists in the past year or two.
A NOAA Fisheries memo finished in February deals specifically with some of these issues. It was produced to update scientific findings on the hydro system effects on listed fish after the 2000 BiOp was thrown out by Oregon federal judge James Redden. Known as the "effects" memo, it was part of a court-ordered collaboration between state and tribal co-managers, and federal agencies, during the remand process developed by the court.
Both the feds and FPC agree that survival data for the past 10 years doesn't show much benefit for barging wild spring chinook from the Snake River, though it does seem to pay off more for hatchery fish that are transported downstream.
The FPC report says barging produced "little or no benefit" for wild spring/summer chinook except during the drought year of 2001. However, a review of the appropriate table included in the report shows that barged fish did have better adult returns in five of the ten years included in the analysis.
The feds characterize their own results for wild fish as inconclusive, but say over the last 10 years that barging didn't seem to either help or harm the stocks compared to inriver migrants.
One big difference is that the federal analysis uses a 95-percent confidence interval, the standard for peer-reviewed scientific work, while the CSS study uses a less precise 90-percent confidence interval.
The federal memo pointed out that pit-tagged wild fish may not represent the wild run at large, and actually may underestimate overall survival rates. The feds say it's likely that smaller juvenile chinook are guided into bypass systems at dams more easily than larger smolts, who may use spillways or turbine routes to cross the dams. Since only bypassed fish are captured for pit-tagging at the dams and smaller fish generally have lower survival rates than larger ones, the feds say results based on survival rates of pit-tagged fish may bias overall return rates toward lower values. But it's a situation the CSS report doesn't even acknowledge.
Both groups agreed that barging was a huge benefit to the wild Snake springers in 2001, when flows were the second worst on record. In fact, the latest FPC report says on average, the smolt-to-adult return rate [SAR] for the transported fish was about 1.3 percent, while the SAR for inriver migrants was only about 0.14 percent.
But the CSS study doesn't mention how the FPC felt about barging in 2001 before the results came in.
According to a February 2002 FPC memo, research showed a "considerable interaction between flow and survival in the estuary," and the agency thought transportation wouldn't help. "Despite the high proportion of Snake River fish transported from the 2001 out-migration, it is unlikely that significant numbers of adults will return from this migration year because of the estuarine conditions," said the memo. "Yet, NMFS stated in their presentation that, since over 90% of fish were transported in the Snake River, it will offset poor river conditions."
The latest CSS draft also fails to recognize another fact that federal scientists have often mentioned in recent years: the high variation in survival rates to adulthood of different groups of marked chinook that may migrate just a few days apart. The feds say rapidly changing conditions in the near-ocean could play an important role in this puzzle. For instance, when sudden upwelling begins off the mouth of the Columbia, the ocean can change from a gin-clear state to a murky brown from plankton blooms, giving chinook a much better hiding place from predatory birds and fish.
The theme of migration timing is important to federal scientists. They say it can generally explain why different stocks in Idaho, both hatchery and wild, can have such different SARs. The rule of thumb is that the later migrating stocks have higher survival rates because estuary and ocean conditions are better as spring rolls along. It's never mentioned in the CSS report, though that report does show data indicating that some Idaho hatcheries may have three times better SARs than others.
The highly variable survival rates exhibited within season is not something that the CSS study can capture, since all migrating fish from each group are lumped together.
The D Factor
The feds' incremental approach also found little to support a single number that could characterize the annual difference in survival between transported fish and inriver migrants. The CSS report touts the infamous 'D' factor, or differential delayed mortality that generally reflects that barged fish die off at higher rates than inriver fish once both groups are past the dams, a theoretical argument that has been going on for years.
The feds say an annual D value is nonsense due to the varying ocean conditions, and that in most cases, later ocean entry improves the survival of juvenile barged fish. In fact, the latest BiOp called for barging at lower Snake dams to begin a few weeks later than in the past, a change that reflected the feds' expanded view of the importance of taking ocean conditions into account.
But the CSS report doesn't parse the delayed mortality into increments that are less than a year long, and never mentions the feds' memo that noted the inconsistent results. Averaged over years and across migration seasons, the feds said that adult survival of transported wild and hatchery fish averaged two-thirds that of in-river migrants. Also, fish did better when transported from Lower Granite Dam than from Lower Monumental.
The report also found that wild springers transported from Lower Granite had similar average survivals as inriver fish. But in some years it was higher, and in other years it was lower.
Another bone of contention between the two viewpoints is the validity of upriver/downriver comparisons, an issue that came to life in the mid-1990's when regional scientists got together in the PATH process to assess uncertainties associated with salmon recovery in the Columbia Basin.
The CSS study said SARs of transported chinook from Idaho's Dworshak and Rapid River hatcheries were lower than from the downriver hatchery at Carson, just above Bonneville Dam. They say that shows barging did not mitigate the mortality associated with hydro passage from 2000 through 2002.
But this conclusion failed to account for differences return rates between stocks, a finding that can be gleaned from one of its data tables. So far, return rates from the 2003 outmigration (2-ocean fish that returned in the spring of 2005) of Idaho's McCall hatchery chinook are nearly three times that of the downriver Carson stock. The draft report failed to note that other downstream hatcheries had been dropped from reports from past years because of poor adult returns.
Instead, the CSS report focused on wild chinook returns to the John Day River, which, it claimed, were two to four-and-a-half times higher than transported wild fish from the Snake from 2000 to 2002.
In contrast, the feds' memo cites fisheries literature (Myers et al. (1997)) "that found no correlation between freshwater survival rates among salmon populations more than a few hundred kilometers apart. As just one example of differences between John Day River spring Chinook salmon stocks and the wild stocks from the Snake River basin, the former have a relatively narrow migration window, based on PIT-tag detections at Bonneville Dam, while the latter, representing the untagged population, have a very extended migration based on estimated timing of transported PIT-tagged fish to below Bonneville Dam."
The feds noted that hatchery fish from McCall, "which have demonstrated the highest SAR for hatchery fish in the Snake River, also showed a narrow migration window similar to those wild fish from the John Day River. As noted earlier, migratory timing can have a large influence on adult returns. Thus we believe it is likely that poor correlation in freshwater survival could exist between upstream and downstream stocks. Not surprisingly then, salmon populations from distinct Columbia River basin regions responded differently to large-scale climate patterns (Levin 2003), and poor correlation existed between productivity patterns of upstream and downstream Columbia River stocks (Botsford and Paulsen 2000)."
But the NMFS scientists recognized differences of opinion, and added an appendix written by the Idaho Department of Fish and Game to their memo that explained why upstream/downstream comparisons should be used to determine "latent mortality" of upstream stocks.
The latest CSS study doesn't return the favor, nor does it even recognize that a difference of opinion exists. But it may not be able to duck the truth for long, since federal scientists say they will submit comments on the draft. The FPC has issued a Nov. 10 deadline for remarks. -B. R.
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