Andrew Creasey
Special to The Union

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January 20, 2014
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Studying salmon: Numbers are up, but population is fragile


Boil down the 2013 salmon year in the Yuba River: Numbers were up.

Good news, right?

Not so fast. It turns out bigger numbers don’t always equal a healthier population.

Dig deeper into those numbers and a whole world is revealed — a world where the salmon population is fragile, genetically weak, increasingly unable to adapt to fluctuations in ecosystems ravaged by climate change, where their very ability to survive is being imperiled in the time they need it most.

Or not. Maybe we can’t look that deep into the numbers. Maybe the story they tell is obscured by climactic minutiae whose effect on rivers and watersheds has not yet been fully revealed.

Welcome to the world of fish biology, where the system shaping policy is one that is still not fully understood.

“It’s a complicated system and a complicated problem,” said Kathy Hill, environmental program manager for the state Department of Fish and Wildlife. “When you talk about salmon in California, it gets into water management, invasive species and many other aspects.”

Comparing data on the Yuba River can be problematic with data sets as recent as 2010, before the switch was made to a different system for calculating margins for error. Prior to 2010, margins of errors could range into the thousands, now, they usually don’t eclipse 200, said, Duane Massa, project manager for the Pacific States Marine Fisheries Commission, with which the Yuba County Water Agency contracts to carry out its research.

“It’s not an exact science; it’s not applied physics where there are irrefutable outcomes,” Massa said. “Ecosystems are not like that. We don’t fully understand the system, so you can’t set your foot down on something you knew 10 years ago and expect that to always be the case.”

Here’s what’s known:

In 2013, preliminary data from the hi-tech Vaki Riverwatcher — an underwater camera installed in the fish ladders at Daguerre Point Dam that is triggered into action by an array of infra-red sensors — says that 14,832 Chinook salmon returned to the lower Yuba River to spawn.

In 2012, that number was 7,731.

In 2007, the Chinook salmon population collapsed. Only 2,604 Chinooks returned to spawn in the Yuba River. Statewide, the fall-run Chinook salmon run fell from 292,954 in 2006 to 97,168 in 2007.

In 2008, the Pacific Fishery Management Council closed all commercial and recreational Chinook salmon fisheries south of Cape Falcon, Ore. It was the most restrictive fisheries measure in the history of the West Coast.

Since then, spawning numbers have slowly increased.

So what do the 2013 salmon run numbers mean? Is it a good sign or a bad sign? How can more fish be a bad sign?

Massa has spent more time on the Yuba River, studying fish, than just about anyone, and he has a saying, “Ask five fish biologists a question, and you’ll get six different answers.”

This is a truism created by the myriad factors that affect the salmon’s health. Ocean conditions, currents, food source availability, predation, water flows, water temperature, water quality all play a part. Were they hooked in the ocean? Did they store enough fat to survive the trip back to the river? How far did they swim? Were they sucked into irrigation pumps?

But one answer about the number is starting to emerge, and it involves hatcheries.

Years ago, to compensate for an ecosystem fractured by dams and other water management structures, the state built four hatcheries.

But the system has greatly simplified what was once a diverse population spread across varying habitats, according to a National Oceanic and Atmospheric Administration report.

Diversity is crucial in a population because it allows it to survive periods when the ecosystem is stressed, such as a drought.

“Climate change is now exacerbating ecosystem changes — at the very time when we need our ecosystems and populations to be most resilient, we have made them less resilient by reducing the genetic and behavioral diversity of the population,” said Gary Reedy, river science director for the South Yuba River Citizen’s League.

Reedy said studies have shown that juveniles spawned by the interbreeding of wild fish and hatchery fish have a lower likelihood to survive. Not only that, the third generation from that offspring also is less fit to survive than normal fish.

“The effect of hatchery fish interbreeding is strong enough in a negative direction to have effects on consecutive generations of offspring,” Reedy said.

The Department of Fish and Wildlife has acknowledged the problem and begun to change some practices, Hill said.

In the past, the department would transfer eggs between hatcheries when one would have a down year, but that practice was stopped.

“All of those things we part of the contribution to creating homogeneity in the salmon,” Hill said. “There is a problem in past practices at the Feather River Hatchery, but we’ve made great strides.”

Massa also acknowledged the problem. Using the Vaki Riverwatcher, his team can identify a hatchery fish through a clip on its fin, and he noticed a correlation in the amount of hatchery fish coming to the Yuba River and the amount of flows and the temperature. The higher the flows or lower the temperature, the more hatchery fish would come through.

“Straying is natural,” Massa said. “The level at which we have observed straying on the Yuba is not so natural.”

Straying can be an issue when hatchery fish enter wild populations and pollute the native stock, reducing their ability to survive.

It seems that, to some, there is more to the increased 2013 salmon run than meets the eye.

“The salmon abundance that we see is supported by hatcheries and strays,” Reedy said. “We need to work hard to improve conditions in the river so juvenile fish are fit and survive to return to the river.”

Drought causing problems for Chinook salmon

There is a looming uncertainty about the 2014 salmon season, one that could render all the discussion about water flows and temperature necessary for a healthy population moot — drought.

“Our concern is extreme,” said Kathy Hill, environmental program manager for the Department of Fish and Wildlife. “It’s not just a lack of water, but things could be very warm this summer due to the lack of a cold water pool. That’s a concern too.”

Warm water temperatures can have a range of negative effects on Chinook salmon. At the worst, they can kill fish, but they can also affect migration, birthing rates, the spread of disease and the availability of food.

“The drought is severe and will have many negative impacts, including direct mortality on salmon,” said Gary Reedy, river science director for the South Yuba River Citizen’s League. “Right now, there are salmon eggs in the American River that are not getting enough water to complete incubation.”

Yuba River holds two runs

There are two Chinook salmon runs in the Yuba River.

The spring run Chinook enter the river between March and June, where they stay until they lay their eggs in September.

While they’re in the river, the salmon don’t eat, subsisting instead on fat storage that was accumulated in the ocean.

Traditionally, spring run salmon migrate much higher into the watershed than the fall run Chinook salmon. With the presence of Englebright dam, those areas on the Yuba are inaccessible.

The fall run Chinook use the lower reaches of the watershed and arrive to the river in the fall just weeks before they lay eggs.

Overall, the use almost the entire 22 miles of the lower Yuba River below Englebright Dam to spawn, although 85 percent of spawning occurs above Daguerre Point Dam, according to studies by the Pacific States Marine Fisheries Commission, which the Yuba County Water Agency contracts to carry out its research.

For spring run Chinook salmon, there is a massive, 260-foot concrete barrier in the way of their return to historic spawning grounds in the upper Yuba watershed.

It’s Englebright Dam, and it’s the source of a continued debate about the endangered species.

It was at the center of a lawsuit that the Yuba County Water Agency filed against a 2012 biological opinion by the National Marine Fisheries Services, which stated that removing the dam was the preferred approach to improving conditions for spring run salmon.

A judge ruled in YCWA’s favor, agreeing that the cost of removing the dam, and disposing of the 28 million cubic feet of contaminated sediment from hydraulic mining it holds back, was too expensive to be realistic.

But some are still calling for a solution, albeit not one involving removing the dam.

“It’s very clear that spring run salmon are at risk of extinction and the majority of their habitat is inaccessible,” said Gary Reedy. “The single most important in this is to get a commitment from the Army Corps of Engineers to continue the planning and alternatives to getting those salmon into the upper Yuba.”

Reedy said that, historically, salmon brought vital nutrients into those ecosystems, located high in the Sierra. Their carcasses supplied nutrients to a long list of mammals and insects, as well as the soil and trees.

“Removing salmon from the ecosystem has a cascading affect on the whole watershed,” Reedy said.

Geoff Rabone, program manager for the Yuba County Water Agency, agreed that spring run salmon need a way to return to the upper Yuba.

“That’s a problem we haven’t addressed effectively these days,” Rabone said. “We’re studying the problem all the time. Getting these salmon up to spawn above the dams is not an easy situation to do.”

Englebright falls under the authority of the Army Corps of Engineers. Since the YCWA operates parts of the dam in conjunction with their Narrows 2 powerhouse below it, some groups have said that it’s the agency’s responsibility to provide passage for the fish.

But Rabone said that the agency would face an enormous challenge bearing the burden alone.

“We don’t feel like the YCWA should be the last one standing and get the final bill to fix an issue that’s been developing for more than 100 years,” Rabone said.

To look at the feasibility of fish passage over Englebright, the Corps would need direction and funding from Congress, which is not easy to obtain, Rabone said.

Rabone has been to Washington D.C., and he is working on finding a non-federal partner that would match funds to do a feasibility study. It’s the first of 24 steps that need to be completed before Congress will authorize and fund the study.

“It’s a long process, but the Army is the Army, they have their procedures,” Rabone said. “If Congress told them to do fish passage, they would do it. But right now, they don’t have the money, or the orders, to go do it.”

Creasey is a reporter for the Marysville Appeal-Democrat.


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The Union Updated Jan 20, 2014 11:46PM Published Jan 22, 2014 01:08PM Copyright 2014 The Union. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.