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A technician holds a juvenile chinook salmon up to a device that will implant a metal tag in its head at the Nimbus Fish Hatchery in Rancho Cordova last year. The tag helps track the salmon population.
Some areas saw more fall-run chinook return from the ocean to the Sacramento River and its tributaries. This includes the American River, where the state's Nimbus Hatchery spawned about 40 percent more salmon in 2009.
But the run as a whole seems likely to turn out the same or slightly smaller than in 2008, which was the smallest year ever recorded.
"We are really upset," said Dick Pool, president of Pro-Troll Fishing Products, a Bay Area manufacturer of salmon fishing tackle. "Every appearance is the fall run returns this year (2009) may set a new record low."
The Central Valley fall chinook is arguably the most important salmon run on the West Coast. It makes up virtually all of the commercially harvested salmon in California and Oregon.
The run's poor condition led regulators to ban all commercial salmon fishing in both states in 2008 and 2009. Recreational fishing was banned in 2008 and severely limited in 2009.
The cause is likely two-pronged:
• Poor ocean conditions, which reduced food supplies.
• Problems in the Sacramento-San Joaquin Delta, where young salmon contend with pollution, water diversions and non-native predators on their migration to the sea. Studies have estimated only about 8 percent of young salmon released in the rivers survive to reach the ocean.
The biggest disappointment in 2009 came on Battle Creek, where the number of fish spawned at the Coleman National Hatchery was about 35 percent less than in 2008. Coleman is normally the biggest single producer of salmon in the Central Valley.
The hatchery releases young salmon in two groups each April, 10 days apart. Few of those released in late April of 2007 returned in 2009.
"Overall, it was a pretty poor return. The expectation was we were going to see more fish," said Jim Smith, project leader at the U.S. Fish and Wildlife Service, which runs the hatchery. "Unfortunately, we can't find what I would call a 'smoking gun' to tell us what caused the differentiation."
There may be more worrisome news in the numbers.
Early analysis of new tagging data suggests the fall run consists mostly of hatchery salmon, and that wild-spawners are a small share of the modern-day population, said John Williams, a consulting hydrologist in Davis who has analyzed the initial data.
This finding could result in the fall run being protected under the federal Endangered Species Act, which could halt fishing permanently and add another layer of limits on California water supplies.
The fall run is the only Central Valley salmon species not already protected by the act.
"What it looks like, really, is hatchery fish are not supplementing naturally produced fish; they are replacing them," said Williams, author of a comprehensive scientific review of Central Valley salmon.
Hatcheries were built to replace salmon production lost when dams excluded fish from historic upstream spawning areas. They succeeded for decades in producing bountiful salmon populations.
But more recent studies show that hatcheries gradually weaken a species, producing fish with less genetic diversity that are less able to fend for themselves in the wild.
State and federal fisheries managers in 2007 began tagging a portion of hatchery salmon to track their success. Each fish had its adipose fin removed and a tiny coded wire tag inserted into its nose.
When the fish is caught, the missing fin is a prompt to recover the coded tag, which records where and when it was bred.
A full review of those data won't be done until later this year. But after an early look, Williams surmises hatchery salmon now make up 90 percent of the fall run.
"At this point it's clear that if you didn't have the hatcheries, you couldn't have a fishery," he said.
Doug Obegi, an attorney at the Natural Resources Defense Council, said no one wants to see the fall run on the endangered species list.
His group successfully sued to impose stricter controls on Sacramento Basin water management to protect salmon. He said the new rules could help salmon as they begin to take effect this year. But the rules are being challenged by water users who fear cutbacks in their supplies.
"The fall run has become the backbone of the state's fishery and it would really become a disaster if it was allowed to fail and be listed under the Endangered Species Act," Obegi said. "I really hope we haven't gotten to that point yet."
There were two bright spots in the 2009 salmon run.
First, the salmon that did return seem to carry more eggs. As a result, the hatcheries appear likely to meet their production goals for young fish.
Second, the number of 2-year-old fish returning to spawn, called "jacks," was better than in 2008.
Most of the run each year consists of 3-year-old salmon. But some are 2-year-olds, which often indicates how many 3-year-olds will return the following year.
"Hopefully that's a good sign for next year," said Anna Kastner, manager of the state Department of Fish and Game Feather River Hatchery.
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