[1] Latest Survival Data Good News For Barged Fish
Spring/summer hatchery chinook barged down the Snake River in 2009 had adult return rates ranging from 40 to 300 percent better than their inriver migrating counterparts, according to recent memos from the Fish Passage Center to some regional hatchery managers.
In recent years, barging has begun later because NMFS scientists saw patterns in survival data that showed early barged fish fared worse than fish that migrated inriver.
However, by barging later in the spring, some runs will likely get little benefit, since 50 percent of some stocks may be past collector dams by May 1, about the time barging starts. And increased levels of spill, in place since a 2006 court order, have reduced the number of smolts that are collected for barging at Lower Snake dams.
The FPC's Dec. 20, 2011 memo to the manager of Idaho's Sawtooth Hatchery says inriver migrating spring chinook from that facility had a 56-percent survival rate to below Bonneville Dam. But barged fish ultimately did much better, with the ratio of returning barged fish to inrivers (undetected at any Snake collector dams) pegged at 3.07. Only about 39 percent of the Sawtooth fish were barged.
Data for the 2010 Sawtooth outmigration is incomplete (jacks only, no adult data), but the memo reported that inriver juvenile survival was about the same (55 percent), and only 32 percent were barged. So far, the barged fish are returning at better than 2 to 1.
Rapid River Hatchery chinook showed return rates for fish barged in 2009 were also more than twice that of inrivers (2.04), with a SAR (smolt-to-adult return rate) of 1.29 percent compared to the inrivers' 0.63 percent. The FPC reported that about 44 percent of the RR fish were transported in 2009.
Hatchery fish from the McCall facility barged from the Snake in 2009 also showed benefits of nearly 2 to 1 over inriver migrators (1.94 ratio) with the transport SAR of 0.71 percent compared to the inrivers' 0.37 percent. Around 40 percent of the McCall fish were barged in 2009.
Clearwater Hatchery spring chinook showed a 41-percent benefit from barging in 2009, but only 25 percent were barged. These fish, along with chinook from the Dworshak Hatchery, reach collector dams earlier than most other stocks, since the facilities where they are raised are closer to the dams.
Dworshak spring chinook showed a 27-percent benefit from being barged in 2009, when about 34 percent were transported.
Summer chinook from the Pahsimeroi Hatchery showed a 79-percent benefit from barging in 2009, but only about 8 percent were barged that year.
Spring chinook from the Catherine Creek Acclimation Pond showed a 34-percent benefit from barging in 2009, with a 1.76-percent SAR compared to the inrivers' 1.3 percent. About 56 percent of those fish were barged, according to the FPC.
The 2009 hatchery springers from the Imnaha Acclimation Pond showed an 89-percent benefit from barging that year, with a 1.33-percent SAR compared to the inriver migrating SAR of 0.70 percent.
The final FPC 2011 CSS Report [Comparative Survival Study] released Nov. 30 estimated that transport SARS for wild Snake chinook in 2009 were almost exactly the same as for inriver migrants in 2009--1.01 percent.
That same report included an estimate of SARs for wild and hatchery steelhead that migrated in 2008, which found only a 12-percent benefit for barging wild steelhead that year. That was quite a drop from 2007's barging benefit of nearly three times over inriver migrators.
The FPC also said hatchery fish showed a 23-percent benefit from barging in 2008, down from 2007's 66 percent.
The return of the run at large could be higher than reported from the PIT-tagged hatchery and wild fish, since there is some evidence that PIT-tagged, clipped and coded-wire tagged hatchery spring chinook from the Yakima River returned at a rate about 25 percent lower than fish without the PIT tags. -Bill Rudolph
[2] Estimating Fish Benefits From Habitat Actions May Take Decades
Scientists from the ISRP, the panel that weighs the scientific merit of proposals in the BPA-funded fish and wildlife program, said last week that it could take up to 20 years to figure out how much good all that habitat spending in the Columbia Basin is doing. Or maybe even longer, they said in a presentation before the Northwest Power and Conservation Council about their 2011 retrospective report.
The ISRP reminded Council members what they had originally called for when they commissioned the review, in their executive summary. "The Council will not conclude this review without being comfortable that the monitoring and evaluation protocols and analytical methods are in place to give us a reasonable chance of knowing--in 5, 10, 20 years--whether the region's huge investment in an evolving suite of habitat actions is contributing significantly to the recovery and rebuilding of fish species important to the region."
The panel said the question implied that that a "thoughtful, efficient approach" will provide an answer in 5, 10, or 20 years--and "seems to be at the heart of uncertainty currently being articulated, including in BiOp rulings, over whether or not the huge investment in habitat restoration will achieve intended outcomes." NOAA Fisheries has pegged definite survival improvements from BiOp tributary and estuary restoration actions, and the plaintiffs in the extensive litigation over the salmon plan are holding the feds' to their promises.
The ISRP said some actions, like removing Hemlock Dam from a tributary of southern Washington's Wind River, would show quick results, but other projects like instream structure modifications or reconnecting floodplain habitat, could take years before benefits are realized. And other complicated actions, like riparian forest protection and restoration, "require decades for their full benefits to be expressed."
"In fact," said the ISRP report, "most projects aimed at restoring natural watershed processes fall into the category of projects requiring many years to achieve objectives." The panel recommended long-term monitoring for a suite of projects falling into the different categories, since the time needed to estimate benefits varied widely between them.
And then, comes an even larger problem--measuring the effects on fish populations. The ISRP said that will take even more time. "A high level of variation in abundance caused by a mix of natural and anthropogenic factors requires that considerable time, sometimes on the order of decades, is needed both before and after implementing restoration projects (ital. theirs) to measure the effects of actions on target populations with a reasonable level of certainty."
They said more monitoring of "adults in" and "smolts out" is needed to track effectiveness, but they weren't keen on a standardized approach to monitoring habitat effectiveness, which they said "is not achievable or desirable." In their report, the ISRP said some approaches will become obsolete over time, and protocols should be open to new, more efficient techniques.
But many projects don't have the time or resources to develop a statistically sound evaluation of success, and very few can compare results with an unimproved reference site, which is required to accurately identify the responses to habitat actions. For this reason, they generally support the use of Intensively Monitored Watersheds (IMWs) that call for a planned, experimental approach to evaluating restoration effectiveness at watershed scales.
"The main point here, however, is that the expectation of definitive answers to the question 'Is it working?' may, in many instances, not be achievable in a 5-20 year window. The ISRP therefore suggests that additional dialogue is needed among habitat managers so that realistic timeframes can be established, and appropriate schedules agreed upon, to monitor and evaluate different types of restoration actions, and to establish a suite of control and treatment streams, appropriately monitored over reasonable time frames to evaluate success."
The ISRP's report also called for more research to look at effects of hatchery mini-jacks on adult return rates, since nearly half of some smolt releases are made up of them, young fish that never leave the freshwater habitat before they return to the hatchery.
The panel said more work is needed to look at effects of PIT-tags on fish as well, since some studies have shown reduced return rates for PIT-tagged fish relative to runs at large, sometimes as much as 25 percent lower.
The report also recommended that supplementation projects receive more scrutiny to see if they actually produce more wild fish. So far, empirical evidence is lacking to prove a conservation benefit other than preventing extinction, the ISRP said.
They said supplementation projects that put high proportions of hatchery fish from hatchery broodstock on natural spawning grounds "are likely compromising the long-term viability of the wild populations" (see following story).
Supplementation efforts also need to be better integrated with habitat restoration efforts, "because rebuilding natural populations will ultimately depend of improving habitat quality and quantity. Recruits per spawner ratios must exceed 1 on a consistent basis in naturally-spawning stocks to achieve the ultimate goal of self-sustaining wild populations. Until this happens, supplementation is only a life support system."
More work also needs to be done related to monitoring dam passage as well, said the panel, and installing PIT-tag detectors at dam spillways is a high priority. They pointed to the value of early life history studies for Snake fall chinook to determine whether or not too many hatchery fish are competing with wild fish as the stock rebuilds.
The ISRP also suggested that the region should find out which salmonid stocks are most vulnerable to all predators, which means developing large scale life-cycle models that include predation on adults by seals and sea lions, as well as by birds on juvenile migrants. -B. R.
[3] Fish Fitness Will Get Another Look
Lower Columbia tribes told members of the Northwest Power and Conservation Council last week that their supplementation efforts are being singled out for more scrutiny than other Basin programs, and that it's largely due to what a panel of independent scientists thinks about them.
The Independent Scientific Review Panel [ISRP], whose role is to judge the scientific merit of actions in the basin's BPA-funded F&W program, was on hand to describe its annual retrospective report--including supplementation efforts--where hatchery-raised fish are allowed to spawn with wild fish in hopes of boosting wild runs.
The panel said supplementation efforts should be looked at on a case-by-case method, but generally there is little evidence to date that shows a benefit to overall stocks from supplementation, and there are large risks to wild stocks from present uncertainties.
ISRP member Eric Loudenslager told the Council that it will take three generations of returning fish before enough data can be gathered to come to any conclusions about its ultimate value.
Loudenslager mentioned a recent paper that looked at the steelhead program in Oregon's Hood River, and found that the first generation of hatchery fish that spawned in the wild showed no decrease in productivity, but the second generation showed a marked decrease in spawning productivity (see following story). The first generation of Wenatchee River spring chinook that were raised in a hatchery from local wild broodstock only had 50 percent of the spawning performance of wild fish, he said.
But those numbers didn't faze tribal critics. "It almost feels like we're constantly under attack for defending our programs, trying to get them funded," said Paul Lumley, executive director of the Columbia River Inter-Tribal Fish Commission. "I, frankly, am getting really tired of the intense scrutiny of the tribal programs, when I don't see that kind of scrutiny in other programs."
Lumley said he didn't see that kind of scrutiny focused on Idaho's effort to bring sockeye back to Redfish Lake, or the mass marking and mark-selective fisheries programs. He pointed to the region's steelhead programs as a case in point. "It's been going on for several decades and I've never really seen that kind of scrutiny on that program," he said. "And you see what happened there--the fish are now listed. There's no trajectory of delisting steelhead any time in the near future."
He said the basic question is: "What is the proper role of marked fish propagation in rebuilding and recovery?"
A new process to look at artificial production is slowly ramping up. It's called the Columbia River Hatchery Effects Evaluation Team (CRHEET), and its scope and work plan are expected to be ready by 2013.
Lumley said his member tribes will "probably" join the conversation, but only if it's different from previous evaluations, where individual projects were thoroughly examined. Other tribal spokesmen said there is more of a need to look at the basin-wide picture.
Rob Jones, NMFS' branch chief for fisheries, said his agency's task is to find the "sweet spot" where hatcheries can help accomplish its mission. He said the region knows a "whole lot more" than it did 15 years ago, and hatcheries are operated better now, but improvements can still be made to run them with less detriment to wild runs.
He said CRHEET will respond to technical questions that NOAA and others have about hatchery monitoring and evaluation; will help make information more accessible; and will provide advice and guidance at the technical level on how to do a better job of monitoring and evaluating hatchery effects.
About 145 million smolts are released from hatcheries above Bonneville Dam every year, but only 26 million are raised to help increase abundance of local stocks, and most of those programs are run by tribes. About two-thirds of those 26 million fish are tied to ESA-related programs. BPA funds about 19 percent of the total hatchery production above the dam. -B. R.
[4] Quick Productivity Decline For Hatchery Steelhead In Wild
Oregon State University researchers say it only takes one generation in the wild for the most productive hatchery steelhead from Oregon's Hood River to exhibit much lower productivity than hatchery steelhead which produce less than five siblings, according to a paper published in Proceedings of the National Academy of Sciences, a few weeks ago. Their article, "Genetic adaptation to captivity can occur in a single generation," reported that amounted to a whopping 71 percent less productivity.
Earlier results from Hood River studies found that hatchery-born fish with two wild parents averaged 85 percent of the reproductive success of wild counterparts.
"We expected to see some of these changes after multiple generations," said Mark Christie, lead author and an OSU post-doc, in an OSU press release. "To see these changes happen in a single generation was amazing. Evolutionary change doesn't always take thousands of years."
It's the latest finding by OSU researchers, who have been studying Hood River steelhead for many years, and it's sure to give more ammunition for foes of supplementation--the practice of using hatchery-bred fish to help boost ESA-listed and other weak fish populations in the Columbia Basin. Whole hatchery programs, like the spring chinook produced at the Cle Elum facility, are being funded as a grand experiment.
But the researchers were cautious about drawing any large conclusions from the study. "It remains to be seen whether results from this one study on steelhead generalize to other hatcheries or salmon species," said Michael Blouin, OSU professor of zoology.
They also noted that in 4 out of 5 run-years, hatchery broodstock had nearly twice the reproductive success of wild broodstock, "which is a pattern consistent with adaptation to captivity."
The authors speculated that a combination of traits may be responsible for the large decline in productivity, including faster growth rates for hatchery steelhead--one year in the hatchery before release, compared to wild fish which usually take two years to smolt. Other traits that may contribute to the decline in productivity include, egg size, fecundity, physiological processes associated with smoltification, along with individual behaviors like predator avoidance. Crowding in hatcheries may be another selection pressure, since in one run-year, smolts were raised in considerably low-density conditions and their release size was much larger.
"Understanding that unintentional selection in captivity can cause rapid fitness declines has important conservation and management implications. Determining which traits are under selection and whether captive breeding programs can be modified to mitigate those selection pressures will be the next big challenge for improving the science of captive breeding," said the authors. -B. R.
[5] Fish Virus Experts Testify In Vancouver
More evidence of a potentially lethal salmon virus came to light during testimony at a three-day federal government hearing held in Vancouver, B.C., in late December. But it could take some time for the region to digest other findings packed into more than 400 pages of downloadable reading.
One U.S. scientist familiar with the Cohen Commission, under whose mandate the hearing was held, said so much material has been collected by the commission that it could be studied for years. The commission has been tasked with investigating the 2009 Fraser sockeye collapse and added the December hearing after initial reports of the possibility of ISA virus in wild sockeye were reported last October.
The virus in question, ISA, or Infectious Salmon Anemia, has devastated farmed fish stocks in Chile, Norway and eastern Canada, and signs of it were allegedly found in wild B.C. sockeye in October. But the Canadian federal government's own lab could not verify the results and declared that no ISA virus had been confirmed in B.C. salmon, wild or farmed.
But on Dec. 15, Kristi Miller, a DFO scientist who works at the agency's research station in Nanaimo, B.C., said in published testimony that she has evidence parts of the ISA virus showed up in adult Fraser sockeye and pink samples she recently tested. The results show the virus was present in 1986, she said, adding, "It's been here, probably quite considerably longer than that."
Miller said that her testing of Fraser River sockeye smolts in 2007 showed a "high incidence of a flava bacterium and it's pseudochromis, or something. It is a pathogenic strain of a flava bacterium that we haven't seen in other years. And when we samples them in the marine environment, they had quite a positive high rate for the pasendrial virus that is possibly causitive of HSMI. And they had, I believe--I can't remember, the exact percentage of ISA, as well."
Miller also said that signs of the virus showed up in 25 percent of recent tests she ran on samples from an aquaculture operation on the west side of Vancouver Island.
But a Norwegian virus expert, Arne Nylund, who testified by live video feed, argued that Miller's results were suspicious, citing highly technical elements of the testing procedures that could lead to major errors.
Stephen Stephen, DFO aquatic animal health science director, testified later that his agency has begun its own tests on Miller's samples, to see if her preliminary findings can be confirmed.
Earlier, Nylund's lab had come up with a positive sign of a part of the ISA gene sequence in one of the sockeye samples that had previously tested positive at another lab in Canada--which had sparked the controversy in October.
Nylund said he had not been able to duplicate that positive test, but added that it was not unusual because of the degraded quality of the tissue.
The Canadian Food Inspection Agency was also unable to confirm the presence of the virus in any of the 48 original samples, nor in subsequent ones (see NW Fishletter 296). It noted that many samples were of poor quality and resulted in "inconclusive" testing. According to the agency's own protocols, inconclusive tests are deemed negative.
During the hearing, testimony by scientists revealed that differences in the sensitivity of their detection equipment and in the software that went along with them might explain some differences in the results from the different labs.
Participants at the hearing also discussed findings from then post-doctoral fellow Molly Kibenge's 2002 research at DFO's research lab in Nanaimo. Kibenge found evidence of ISA in smolt samples, but her results were never published because her superiors felt the samples were contaminated.
Her preliminary results from nearly ten years ago came to light last month after the CFIA announced its negative findings for other samples--originally sent for testing by anti-fish farm activists--to her husband Fred Kibenge, who runs a lab on Prince Edward Island. He found signs of the virus in two of 48 samples of wild B.C. sockeye smolts from Rivers Inlet in northern B.C. (see NW Fishletter 297).
Molly Kibenge's 2002 results included 100-percent positive ISA tests for Cultus Lake sockeye (a lower Fraser River stock) that she could not replicate. Her results, reported in a 2004 draft paper, found that 28 percent of juvenile chinook samples and 17 percent of the juvenile pink salmon (from Vancouver Island and southeast Alaska) showed signs of ISA. All samples from spawning sockeye (Cultus Lake in the lower Fraser watershed) and one cultured Atlantic salmon showed signs, and other parts of genomic sequences for the virus were found in some chinook--more than 100 different salmon in all. No signs of the virus were found in chum or coho samples.
According to the draft paper, "these results lead us to conclude that an asymptomatic form of ISA occurs among some species of wild Pacific salmon in the north Pacific."
However, in Dec. 16 testimony at the commission hearing, DFO scientist Simon Jones said some of Molly Kibenge's samples had been sent to her husband's lab for testing as well, ten positives and ten negatives. The PEI lab found several of her positives tested positive for them, but other positive results turned out negative.
Jones said after that, about 90 of Molly Kibenge's samples were sent to the CFIA lab, but the federal government lab could not reproduce any of the positives.
Fred Kibenge testified on Dec. 16 that some of his positive tests could not be false positives, and argued that his testing technique at the time was adequate.
But DFO expert Nellie Gagne, who works at the agency's lab in Monckton, New Brunswick, where Molly Kibenge's samples were tested, said the sequence that matched the then post-doc's samples "has nothing to do with fish. The match is random mouse, human, and I have seen that with FA3/RA3 primers we were using at the time. We dropped using them."
Fred Kibenge testified that he also saw matches in another segment of the gene sequence. "What people miss here," he said, "is that this study was not only doing ISA, it was actually testing for three different viruses. The other two viruses, all the results were negative. But ISA was being done by the same person. So the negative results were quickly accepted. The positive results were considered contamination."
Kibenge said he didn't believe the contamination to be virus-specific.
Molly Kibenge's boss at the time of her post-doc work in Nanaimo, DFO scientist Simon Jones, told the commission on Dec. 19 that he had received an email from her shortly after she had run her assays, "and when she obtained sequence from the intervening segment of DNA between the primer binding sites, that there was a list of top hits that included zebra fish, human, and possibly some other, but certainly not ISA virus. That was not in her list of top hits."
Norwegian scientist Nylund told the hearing that there were lots of indications that the ISA virus was present in Pacific salmon, but still "no hard evidence."
DFO scientist Miller said she clearly believed there "is a virus here, and it is very similar to ISA virus in Europe."
Nellie Gagne, also with the DFO, said the European and North American strains of the ISA virus probably came from a common ancestry that separated physically, and geographically, at least a hundred years ago. She said the viruses have been in nature for thousands of years and have evolved with their hosts.
"I don't know where we are at this point," Gagne said at the hearing, "because we don't have enough information, but it could really be that we're looking at another ISA that has been there for a long time."
She said if it is ISA, it doesn't match the picture they have of the virus as it exists in Atlantic salmon aquaculture, "because we're talking of all below normal level that we detect in carriers, at this stage. We're talking of an unsusceptible species. Atlantic salmon are the susceptible species of the disease. Right now, what we see, there's none reported in Atlantic salmon."
Meanwhile, both the United States and Canada are developing monitoring programs to test fish this year to see if the virus is present in wild, hatchery and farmed fish, even though wild fish do not seem to be bothered by it. The worry among scientists is that it could mutate into a strain dangerous to wild fish, and fish farms are places where mutations could occur quickly. -B. R.
[6] Water Supply Forecast Below Average, But Building
The newly streamlined and updated-daily April-September water supply forecast for the Columbia Basin at The Dalles was running 86 percent of average by Jan. 5, according to NOAA's River Forecast Center, and 90 percent by Jan. 18. Before the region got a good dumping of precipitation shortly after Christmas, the forecast was only 75 percent of average.
With La Niña firmly in place, but an unusually dry December in the book, precip for the Columbia Basin above The Dalles was running only 17 percent of average by Christmas. January has been better--47 percent of average, with the Oct.- Jan. time frame running 81 percent.
A series of storms hit the region after the holiday, boosting snowpack in the Cascades to nearly normal levels by Jan. 2, but the lower Columbia Basin was still running 65 percent of normal. By Jan. 18, the lower basin was up to 73 percent, while the north Cascades was 98 percent of average snowpack.
Watersheds in Idaho were running from 87 percent of average in the north, to 60 percent around the Salmon River
By Jan 5, the water supply forecast at Grand Coulee was estimated at 89 percent of average, and 79 percent of average at Lower Granite Dam on the Snake River. Two weeks later, both Grand Coulee and Lower Granite were up to 92 percent of average for the April- Sept. period.
NOAA's Climate Prediction Center said Jan. 5 that it expects the La Niña conditions to persist into the early spring and dissipate between March and May.
"During January-March 2012, there is an increased chance of above-average temperatures across the south-central and southeastern U.S., and below-average temperatures over the western and the northwest-central U.S.," said the latest update. "Also, above-average precipitation is favored across most of the northern tier of states and in the Ohio and Tennessee Valleys, and drier-than-average conditions are more likely across the southern tier of the U.S." -B. R.
[7] Dukes To Chair NWPCC In 2012; Whiting Voted Vice Chair
The Northwest Power and Conservation Council last week elected Oregon member Joan Dukes to chair the four-state body for the coming year.
Dukes has served on the Council since 2004 and was vice chair last year. She said she is looking forward to her new position.
"The rapid increase in wind power, the future of fish hatcheries, predation on adult and juvenile fish in the Columbia River, and improving our ability to monitor and evaluate the success of fish and wildlife projects, which cost the region's electricity ratepayers more than $200 million per year--these all are issues that are on the Council's plate in 2012. It will be an interesting year," Dukes said in a statement.
Before Dukes was appointed to the Council by then-Oregon Governor Ted Kulongoski, she was a longtime member of the Oregon State Senate.
Montana member Rhonda Whiting was elected vice chair for 2012. She has also served on the Council since 2004. Before that, she served as VP for communications and intergovernmental affairs for Salish and Kootenai Technologies, the largest information technology company in Montana. -B. R.
[8] Big Spring Chinook, Sockeye Runs In The Columbia Predicted For 2012
Columbia Basin harvest managers are expecting 314,000 spring chinook to show up in the Columbia in 2012, after the second largest jack count on record materialized last spring.
If the prediction comes true, the 2012 return would be the fourth largest since 1938, according to ODFW, and close to 2010's big run. Last year, about 221,000 returned to the mouth of the river, more than 20,000 fish above the pre-season forecast.
The technical advisory committee for the U.S. v. Oregon process said close to 33,000 are expected to be headed for the Upper Columbia, nearly twice last year's numbers. About 2,800 should be wild, it said in its Dec. 12 memo.
The Snake should see around 168,000 spring/summer chinook, according to TAC, with 39,000 wild ones. In 2011, about 127,500 spring/summer chinook returned to the Snake, including about 31,600 wild fish.
The upper Columbia should also expect 91,000 summer chinook. That would beat this year's return by more than 10,000 fish.
The managers had more good news to report on the sockeye front. They are predicting a 462,000-fish return, with 431,300 expected to be headed to the Okanogan River, 28,800 to the Wenatchee and 1,900 to the Snake River.
The harvest managers said most 2012 fall chinook stocks should perform similar to last year's actual return--around 600,000 total. TAC had predicted a 766,000-fish return in 2011. They said all stocks appeared to have come in below predictions, especially Lower River Hatchery, Bonneville Pool Hatchery and mid-Columbia brights.
Fall jack returns were average or similar to 2010 returns, they reported, except for upriver brights, which appear to be above average, and are expected to have another strong return. However, they also expect fewer Bonneville hatchery tules than this year.
TAC also noted that 2011's coho run totaled almost 271,000 fish, while the jack return was only 13,000, way off the 10-year average of 28,000. -B. R.
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