California's king salmon are back.

Sport anglers started going after them last week, and in San Mateo this week regulators will set guidelines for commercial fishers who weathered an unprecedented three-year stretch in which California salmon were almost entirely off-limits.

But there's a catch in this season's anticipated catch.

During the collapse, researchers learned that nearly all of the state's returning adult salmon are coming from hatcheries. They are domesticated and genetically similar, a worrisome development that raises doubt about the long-term health of the prized fish and might help explain why their numbers soared in the early 2000s before collapsing in 2008.

Like having all your money in one stock, a population as genetically homogeneous as the state's salmon is prone to boom and bust cycles, researchers say.

"It's potentially very vulnerable to any little thing. Just some change in the weather, a disease," said Steve Lindley, a research ecologist at the National Marine Fisheries Service laboratory in Santa Cruz.

For years, the fall Chinook salmon run -- the backbone of the state's salmon industry -- appeared healthy and few cared where they came from.

That changed during the collapse.

And now, thanks to new automated fish-tagging systems, biologists are crunching numbers to determine definitively, for the first time, just how many returning fish are hatchery-born.


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Clack! Clack! Clack!

Inside a $1.2 million trailer at a fish hatchery owned by the East Bay's largest water district, Braden Buttars fine-tunes a high-tech array of equipment that can noisily count, sort and process more than 20,000 salmon fingerlings an hour.

Thousands of 3-inch salmon are drawn through hoses and tubes in the state-owned trailer here, where a loud, clacking machine sorts the tiny fish into different ports. The biggest ones go here, the smallest ones there -- eight ports for eight sizes.

"The whole body is held in these clamps here," said Buttars, who coordinates the state salmon hatchery tagging program. One in four fish is held in a clamp for 1.8 seconds. Automated clippers remove a fin and a wire encoded with microscopic numbering is stuck in its snout.

Today, the wire reads 06.87.56. That's Raceway A, Mokelumne River Hatchery, 2011.

The East Bay Municipal Utility District built the hatchery near Lodi to offset the loss of salmon habitat caused by the Oakland-based district's two Mokelumne River dams.

Before the state bought four of these trailers in 2007, one for each of California's major salmon hatcheries, fish tagging was done by hand for limited experiments and did not give biologists enough data to determine how many of the coastal salmon were coming from hatcheries.

Then, in 2008, UC Santa Cruz fisheries biologist Rachel Barnett-Johnson announced results of a study in which she used a new method of examining salmon ear bones to determine their origin. It was a small study, but what she found was stunning: Some 90 percent of salmon were from hatcheries.

"People were worrying about it, but Rachel's study was the first one to put a firm number to it," Lindley said. "It was a bit alarming at the time."

By the fall, the expanded, automated tagging program had produced enough data to confidently determine the origins of returning fish.

Those numbers have yet to be fully analyzed, but from what biologists have seen, they appear to be consistent with what Barnett-Johnson found, Lindley said.

Whether the figure is as high as 90 percent is yet to be determined. The number may be that high in some streams and lower in others, and it might vary year to year.

But California sport fishers, in one survey last year, reported that about 23 percent of the fish they caught had their fins clipped. Since 25 percent of the hatchery fish are clipped, that figure is close to what one would expect if all the fish came from hatcheries.

The collapse

In the early 2000s, more than 1 million fall-run salmon were caught or returned to spawn each year, according to the Pacific Fisheries Management Council, which regulates offshore fishing.

But in 2007, the number fell sharply, and the following year it collapsed to just 70,000 fish, easily a record.

In 2009, the estimate plunged again to about 41,000, further alarming both fishers and biologists.

The numbers rebounded somewhat last year, and biologists estimate about 730,000 fish will be caught or return to spawn this year.

A 2009 study led by Lindley was commissioned to determine the collapse's cause. It found many reasons, but the trigger was a cyclical condition in the ocean that produced little food off the California coast in 2005 and 2006.

The baby fish migrating out to sea starved or became easy prey, which is why so few returned to spawn as adults in 2007 and 2008.

By contrast, the fish that returned last fall swam out of San Francisco Bay in spring 2008, where they encountered the best conditions in decades.

While ocean conditions have always affected salmon numbers, the emerging realization that California's salmon are genetically similar might help explain why their response to changes has been so dramatic.

The mass production in hatcheries, combined with the crossbreeding that occurs as fish get lost on their way to spawn, has led to a gene pool in which salmon in one stream are indistinguishable from salmon in another.

When the fish are all genetically similar, they are more likely to all respond the same to changes in the environment.

Other factors are also at play. Net pens used to acclimate fish were temporarily unavailable. Regulators miscalculated the number of fish they expected in 2007 and allowed more fishing than they should have.

Baby salmon also face the daunting task of migrating through a highly altered Delta, where pollution and flows altered by channelization and pumping are so severe that hatcheries now truck their fish to the western Delta and San Pablo Bay.

The fish don't migrate downstream anymore. They migrate down highways, which may be why adult Chinook salmon in California tend to stray from the rivers of their birth as they swim through unfamiliar waters to spawn.

Environmentalists and fishing industry representatives suggest the uptick in salmon off the coast this year may be the result of restrictions on Delta pumping in 2009 that, they contend, could have increased the survival of salmon that swim, rather than ride in trucks, out to sea.

The prevalence of hatchery fish does not surprise Bill Smith, California Department of Fish and Game's hatchery manager at the Mokelumne River Hatchery.

In fact, he said, it may be evidence that the hatcheries, which were built to offset the loss of habitat caused by dams, are working as planned.

"The reason that 90 percent of the fish are hatchery fish is 90 percent of the habitat that wild fish utilized has been inundated by dams," Smith said.

"You get rid of all this natural spawning habitat, then if you ask why the wild population is so low, it's ridiculous. It's self-explanatory."

Indeed, scientists say the heavy reliance on hatcheries is the direct result of badly degraded conditions inland, from historic spawning grounds through the San Francisco Bay-Delta estuary.

The dominance of hatchery-raised Chinook raises an uncomfortable question: If fall-run salmon, which just a few years ago appeared robust, are actually on life support, should they be declared an endangered species? And if so, what would be the consequences?

"Nobody likes to talk about that," said Peter Moyle, fisheries biologist at UC Davis. Based on his research, Moyle said he believes that the wild fall runs are mostly destroyed, and that fishery managers would be wise to admit it.

"It's likely that most of the fish we think of as wild Chinook are at most two generations removed from a hatchery fish," said Moyle, who has estimated that dams have blocked access to 70 percent of salmon spawning habitat.

Moyle said the state would do better to concentrate its resources on preserving what's left of endangered winter- and spring-run Chinook populations.

"Once you've made the decision that fall-run is a hatchery fish, to support the fishery, then you start having more options in what you can do with it," Moyle said.

Like a war

Out in the docks at Half Moon Bay's Pillar Point Harbor, salmon fishermen feel like they've been through a war, said Jim Anderson, a second-generation commercial fisher and captain of the Allaine.

In the late 1970s, commercial and sport fishing for salmon generated more than $100 million. By the early 2000s, the industry was still generating $30 million to $50 million a year, according to the Pacific Fishery Management Council.

But in 2008 and 2009, the industry was nearly worthless.

Many of Anderson's friends have been living off their credit cards and are deeply in debt. They have deferred boat maintenance. Some simply gave up and sold their fishing licenses.

It's not just fishers who were affected.

"We're finding at some of the ports the ice machines aren't working anymore. The businesses have been bought out. It's getting harder to find gear stores where you can purchase the equipment and stuff that you need," Anderson said.

Financial bailouts for fishers and businesses affected by the salmon crisis saved many from bankruptcy, he said.

Though fishermen are grateful to be fishing again this year, by historical standards it is likely to be a mediocre season, said Zeke Grader, president of the Pacific Coast Federation of Fishermen's Associations.

"There's still a lot of work to be done," Grader said. "We've lost thousands of jobs."

And Anderson said the economy -- and the price of fuel in particular -- hardly makes an outing worthwhile unless California coastal waters are so filled with Chinook that fishers don't have to go out and scout for them.

"Everyone's kind of sitting around and waiting for someone else to go find the fish, and as soon as somebody finds something, everybody's going to bolt out of the harbor and go after him," Anderson said.

Fishermen, like the public, want a sustainable Chinook fishery, he said. From Anderson's perspective, that means enough hatchery-raised fish to overcome whatever conditions might befall them in the ocean or Central Valley streams.

"By the time they've left the hatchery, gone through the gauntlet to get back in the ocean, and then returned to the hatchery, that is as wild a fish and as natural a fish as you're ever going to need to have," he said.