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NENANA — A little after dawn on a cold October morning, Victor Lord loaded a flat-bottom boat with big plastic totes and set off slowly down the Tanana River.

He crossed under the railroad bridge in his village of Nenana, past the barge landings, and under the highway connecting Fairbanks to Anchorage, then opened the throttle on the 150-horse power motor.

The fall run of chum salmon had come late, but the fishing was good. On this morning, Lord had to pick up the fish from his brother’s fish wheel, stop the wheel according to regulations, then drive back to town in time to work his own.

He drove fast, and the boat kicked up waves in the tan, glacial-fed river. A golden eagle passed just overhead.

Eight miles downriver, Lord slowed the boat and steered over to the fish wheel. Its three wire-meshed baskets turned slowly — pushed by the current of the river — and hundreds of fish lay dead in a wooden corral just above the water, covered in a layer of frozen slime and ice. Lord figured it was probably one of the last days for fishing.

Commercial fishing on the Tanana River isn’t much of a money-maker these days. Lots of people did it back in the 1970s and ‘80s, but in the ‘90s, the runs crashed and people had to get other jobs, Lord said. By 2000, hardly anyone with a fish wheel permit was fishing.

Now the runs are coming back and a processor in Nenana is buying fish again, but the prices are low. (It’s unclear why the runs crashed and why they came back.)

On this day, Lord could have been making $30 an hour at his other job building a road around the village. But he wanted to fish. So Lord stood on the driftwood raft of his brother’s fish wheel and passed chum salmon one by one onto the boat for a price so low he wouldn’t say what it was.

“We’re just getting back on our feet now,” he said.

Fish as a mainstay

Few things are more Alaskan than wild salmon.

Fishing in general is a huge part of Alaska’s history and culture, and still provides jobs for nearly one in 10 Alaskans, according to one study. Salmon, pollock, whitefish, halibut, crab, and other marine species provide subsistence food for thousands of residents, sport fishing opportunities for locals and tourists, and half of all the fish harvested in U.S. waters.

But as the Earth warms and rivers and oceans change, Alaska’s fisheries are changing, too. Scientists who study fish say man-made climate change is likely affecting fish already. On the Yukon River, a large percentage of the king salmon are infected with a disease linked to warmer water temperatures. In other places, warming waters themselves have strained some fish species and caused others to move.

At this point, the connections between fish and climate change are largely speculative. Many fish have complicated life cycles — salmon are born in freshwater streams but spend most their lives in the ocean, for instance — and their abundance in any given place is a factor of many things, including management. In many cases, scientists don’t have the data they would need to understand what’s happening to a stock and why.

But scientists say that in the coming years, climate change will very likely boost some fish stocks and reduce others and could rearrange whole marine ecosystems, affecting everything from phytoplankton to walleye pollock to whales.

“[I]n the next 100 years the combination of high-magnitude events and rapid rates of change will probably exceed the ability of biota (plants and animals) and their associated ecosystems to adapt,” the Intergovernmental Panel on Climate Change wrote of freshwater ecosystems in the Arctic. Impacts will be positive and negative, the report went on, but overall, “the negative effects will very probably outweigh the positive.”

As for salmon, scientists say warming ocean waters will likely push their distribution to the north.

Gordon Kruse, a longtime fisheries biologist and professor at the University of Alaska Fairbanks’ School of Fisheries and Ocean Sciences, put it starkly in a public lecture last year. One of the slides in his PowerPoint read simply, “Goodbye Salmon, Hello Tuna?”

A parasite arrives

One of the most alarming climate-related impacts is a disease caused by the parasite Ichthyophonus hoferi.

About 20 years ago, fishermen along the Yukon River started reporting that something was off with some of the king salmon — they smelled funny, didn’t dry right, and had to be thrown out.

“We started seeing it about ’86, ’87,” said Pat Moore, who lives and fishes in Tanana, a village on the Yukon near the mouth of the Tanana River.

At first it was one or two fish, Moore said last fall. Then there would be so many you thought your way of life was gone forever.

Moore would stop fishing for a few days.

Then it would get better.

“It was kind of an emotional roller coaster,” he said.

Fish pathologists at the state’s Department of Fish and Game tested samples of the fish and concluded they were infected with a relatively widespread parasite called Ichthyophonus, which has also been found in herring, cod, and other species. The parasite wasn’t harmful to people, but the infected fish weren’t good to eat. Biologists told the fishermen to keep the infected fish separate so they wouldn’t infect other fish, and commercial buyers – the Yukon has a relatively small commercial fishery — discarded up to a fifth of the fish they bought.

In 1999, a professor and post-doctoral researcher at the University of Washington’s School of Aquatic and Fishery Sciences started sampling kings near the mouth of the Yukon River in Emmonak with funding from the Bering Sea Fishermen’s Association.

The scientists, Richard Kocan and Paul Hershberger, didn’t find much at first. Then, with funding from the U.S. Fish and Wildlife Service, they started testing the fish with a different method. They found that nearly a third of the fish were infected and just weren’t showing visible signs of the disease.

Kocan and Hershberger spent the next three years sampling thousands of fish at seven sites along the Yukon River and its tributaries. They found that a quarter to nearly a third of the king salmon entering the river between 1999 and 2002 were infected with Ichthyophonus. The same number of fish were infected near Tanana – about 700 miles up the river – as at the mouth, but the disease was more visible in the fish higher upriver.

The two scientists concluded that the disease was probably killing some of the fish. Infection rates actually dropped in a few spawning streams and very far upriver in Canada, which they took as a sign that infected fish were dying before they could spawn.

They also proposed that the disease worsened with warmer water temperatures. Fish that entered the river early in the run, when water temperatures were still low, showed fewer signs of the disease than those that entered later, when the water was warmer. More fish showed signs of the disease in 1999 and 2001, when water temperatures were high, than in 2002, when they were lower.

Kocan and Hershberger didn’t argue that warmer water was causing the disease, but they did argue that it allowed the disease to develop more in individual fish — and likely kill more of them.

The two scientists released their findings in 2003 — the findings were later published in the Journal of Aquatic Animal Health — and, according to Kocan, were subsequently barred from working in the state by the Department of Fish and Game. (“They didn’t like the results of our study, so they decided to do it themselves,” Kocan said.)

John Hilsinger, the department’s regional research biologist at the time, said he wasn’t aware of any effort to silence Kocan.

“But I do know that we had a comprehensive program going on, so I don’t know that it was really necessary to have duplicate research going on,” Hilsinger said recently.

Ichthyophonus became a touchy issue.

Kocan had essentially accused managers of not paying enough attention to it. If a sizable percentage of fish aren’t spawning successfully, he argued, the state should limit fishing and let more fish pass up the river. But cutting the number of fish available would only make it harder to meet the needs of people fishing for food and those fishing commercially. (The Yukon represents a tiny fraction of the overall commercial salmon fishery but has the largest subsistence harvest in the state.)

Steve Hayes, who manages the king salmon and summer chum runs on the Yukon for the Department of Fish and Game, said later there wasn’t enough evidence to show that fish were actually dying and argued management was already conservative enough to account for any fish that were.

And the science was still incomplete. Data only covered a few years, and neither Kocan nor the department could say for sure what was causing the disease, whether it was killing fish, or whether infected fish could still spawn.

Then there was the question of climate change.

Ted Meyers, the state’s chief fish pathologist, cautioned against linking Ichthyophonus to climate change, simply because of the lack of data.

“It’s all pretty much speculation at this point,” he said.

But Meyers said problems like Ichthyophonus could become more common as ocean temperatures warm. Some disease-causing organisms do best when water temperatures reach 50 or 55 degrees Fahrenheit, he said. That used to be high for Alaska, but now temperatures are approaching that in the summer. (Water temperatures in the lower Yukon River are now frequently above 64 degrees in June and July and can approach 70 degrees.)

Warming ocean temperatures were blamed for an outbreak in 2004 of Vibrio parahaemolyticus in farmed Alaska oysters. The outbreak sickened dozens of people.

According to Kocan, Ichthyophonus has been found in a few chum salmon and burbot in the Yukon River, king salmon in the Kuskokwim River near Bethel and Taku River near Juneau, sockeye salmon in British Columbia, and coho salmon along the Pacific coast. (Before it showed up on the Yukon, the parasite had never before been documented in salmon, he said.)

In Tanana, Moore agreed that Ichthyophonus was a serious threat, but not that climate change was driving it, or even that the water near Tanana was getting warmer.

“I don’t really see it,” he said.

(Kocan pieced together his temperature data on the lower river from a number of incomplete records, but stands by the numbers.)

Some fishermen in Tanana said they hardly saw any infected fish at all.

Stan Zuray, who moved from Boston to Tanana in 1973 and has fished near there for decades, said he thinks Kocan is “right on.”

Zuray helped Kocan and Hershberger with their research, and learned from Kocan how to apply for grants and do research. Zuray started diligently tracking fish at a site 40 miles upriver from Tanana and created a Web site for information on Yukon River salmon.

“Right now I’m a voice in the wilderness,” he said last fall. “There’s a couple of us that are voices in the wilderness. . . . This stuff needs to be brought to someone’s attention, and that’s what I’m doing.”

In 2004, the Department of Fish and Game did its own research on Ichthyophonus. Nearly a fifth of the kings they sampled at Emmonak had the disease. The rate went up in the Chena River, a spawning stream that branches off the Tanana in Fairbanks, but down in the Salcha River, another spawning stream off the Tanana.

The researchers agreed with Kocan that infected fish could be dying, but suggested the fish could be spawning somewhere else, or that the data could be biased somehow.

Kocan and Hershberger continued their own research back in Washington. They infected rainbow trout with Ichthyophonus and tested their swimming stamina in a tank with simulated river current. Stamina went down by about two thirds in infected fish.

The findings offered a possible explanation for why infected salmon on the Yukon seemed to be dying before spawning, they wrote in a paper published in the Journal of Fish Diseases. “Many of these fish migrate between 1620 and 3240 [kilometers] in fresh water and have to negotiate numerous hydraulic challenges,” they explained. “Fatigue resulting from extended upriver migration, depletion of lipid reserves, elevated water temperatures during migration and cardiac damage could result in cardiac failure of heavily infected fish.”

“It clearly affects their ability to swim upstream with a load of eggs without eating,” Kocan said later.

Cooler waters

Four hundred miles south of Tanana on the southern end of the Kenai Peninsula, streams are already warmer than ideal for salmon.

Sue Mauger, a stream ecologist with the conservation group Cook Inletkeeper, started looking at water temperatures there 10 years ago to see if bark beetle damage was affecting salmon streams. The streams seemed warm, so in 2002 Mauger installed recording thermometers to get more data.

What she found surprised her. Water temperatures in many streams were consistently above the limits set by the state to protect fish.

The limits said spawning areas shouldn’t be above 55 degrees Fahrenheit, migration routes shouldn’t exceed 59 degrees, and at no time should water temperatures top 68 degrees.

In 2004, Mauger saw temperatures above 72 degrees.

In 2005, the Anchor River topped the state limit for migration routes on 65 separate days.

The high temperatures affect salmon like they affect humans, Mauger said later. “When it gets really hot, we have trouble breathing and feel pretty lethargic — same with them.”

Warm spots can lead to bottlenecks in migration routes as salmon wait for hours or days for the water to cool, she said.

There isn’t much evidence at this point linking warm waters to poor salmon runs, but there is some. The Department of Fish and Game attributed a poor run of pink salmon near Juneau in 2006 to warm waters two years earlier, when the returning fish were hatched, and Canadian biologists have blamed high water temperatures for a disastrous run of sockeye salmon on the Fraser River in British Columbia in 2004, when more than a million fish were deemed “missing.”

Other species seem to be on the move as well. Pollock fishermen report finding fish further north in recent years, and king and silver salmon are showing up on the North Slope in places like Barrow. Fishermen in the Gulf of Alaska report catching strange, warm-water fish.

While climate-related diseases will likely have a significant impact on Alaska’s fish, warmer waters themselves will most likely have the larger impact. Warming temperatures are expected to strain freshwater species and could eliminate some completely. According to the Intergovernmental Panel on Climate Change, fish moving into arctic waters will likely outcompete existing species for local food sources and bring parasites or diseases. Northern fish species like whitefish, char, grayling, inconnu, and cisco will probably shrink in numbers of completely disappear from the state.

Marine species are more likely to shift in range as waters warm, but are also expected to increase or decrease in numbers. According to UAF’s Kruse, who led the Department of Fish and Game’s marine fisheries research program for 16 years, the shifts will likely disrupt established fisheries. Species seeking suitable ocean conditions may have to deal with less-than-ideal habitat, and fish moving to new areas may bring competition and disease to the species already there. Pacific and jack mackerel, which compete with and prey on young salmon, have already moved north into waters off British Columbia and even reached southeast Alaska.

In the near term, salmon are likely to do well. The fall chum run on the Yukon River in 2005 was the highest since 1975, and the harvest of all salmon in Alaska in 2007 was near the all-time record. (Yukon king salmon runs have remained low compared to runs before the late 1990s.)

But warming spawning streams may already be stressing salmon in Alaska, and warming ocean waters may ultimately strain the fish off Alaska’s coasts.

When Kruse gave his presentation with the slide, “Goodbye Salmon, Hello Tuna?” he was merely posing the question, he said later.

But the question wasn’t completely out there, he added. The same warm, El Nino year that tuna showed up by Kodiak Island, salmon runs dropped in western Alaska rivers, including the Yukon.

A changing system

Scientists say a shift in the whole marine ecosystem is not out of the question as the climate warms. The productivity of the ocean and marine species depends on the smallest organisms — the phytoplankton and zooplankton that appear each year in massive blooms — and those organisms depend on arctic sea ice.

In years when the sea ice lingers into the spring (the cooler years), phytoplankton generally thrive in the layer of fresh water left at the surface when the ice melts. Zooplankton in the water below tend to do less well, so when the oceans mix later in the year, the phytoplankton largely falls to the bottom, where it provides food for bottom dwellers, such as crabs and clams.

In years when the sea ice melts early (the warmer years), phytoplankton tend not to bloom until later in the year, giving zooplankton a chance to develop. When the phytoplankton do bloom and the oceans start to mix again, much of the nutrients are taken up by the zooplankton, ultimately fueling species that live in the water column, such as salmon and pollock.

Alaska’s waters are already split between those that favor bottom dwellers — the benthic species — and those that favor species in the water column — the pelagic species. But scientists believe ecosystems now on the edge of that line could shift solidly toward the pelagic, making it harder for the whole benthic food chain — from clams to walrus.

“If the grass doesn’t grow as green, the cows don’t do as well,” said Mike Sigler, a marine biologist with the National Oceanic and Atmospheric Administration in Juneau.

Back to the wheel

By early November, all the fishing was done on the Yukon.

Chum salmon were frozen and stacked like firewood by Moore’s dog yard. Moore had let the salmon ferment in a wooden crib before chipping them apart and stacking them for the winter. (Dogs do better with fermented fish than fresh fish, he said.)

Sled dogs used to be a necessity, but now most people in Tanana use trucks and boats for work and dogs for racing. (Moore tried using a dog team to haul fish from camp once but switched back to the outboard motor.)

“I’m just wondering if the dogs are going to make a comeback,” he said, noting the skyrocketing cost of gas. “When I was a kid growing up here, everybody had a dog team.”

For now, there are plenty of salmon for the dogs. Chum salmon runs on the Yukon seem to be coming back after the bad years in the 1990s.

Moore worries more about the king salmon, which are better to eat and bring a much higher price in the market. They’ve been getting smaller in recent years, something many people attribute to fishing practices; overall runs are still low; and there’s Ichthyophonus.

About 8 percent of Moore’s king salmon had the disease last year — the lowest number in at least a decade, he said.

Another Tanana fisherman said he caught only a few fish with the disease.

Zuray measured 26.7 percent for females and 14.2 percent for males.

Despite a low return of king salmon, it turned out to be a relatively good commercial season upriver. Zuray made about $2,500 selling kings and $600 selling chums — about average for 15 years ago but high for the last five years. (Fewer fishermen were competing for the fish, he noted.)

Lord, the fisherman in Nenana, did pretty well, too. He covered his expenses, ate well, and put away lots of fish for the winter, he said later. He even started talking about opening his own processing plant.