So Fliris contacted an outsider: Richard M. Kocan, a fish disease expert at the University of Washington. Lining up a federal grant, Kocan began to test the fish in 2000, the same year the king salmon run suffered an unexpected temporary collapse that forced the closure of the river's commercial fishery.
The same proportion were infected at midriver near Tanana, about halfway to the Canadian border. But here, nearly a third of the fish showed the salt-like flecks on their hearts and other organs, and their mealy flesh released the telltale smell of putrid fruit.
Kocan went upstream to the spawning grounds near Whitehorse, Canada, and found that the proportion of infected fish dropped dramatically. But why? It didn't seem logical that the fish were recovering during the last part of their stressful 2,200-mile swim, accomplished over many weeks without eating.
"The working hypothesis," Kocan said, "is that they died before they made it to the spawning grounds."
Tracking what happens to these fish is difficult. The Yukon turns mocha-brown in the summer, when its swift waters carry a load of rock flour released by rock-pulverizing glaciers and other sediment. Salmon that perish sink out of sight.
To test his theory, Kocan set up a laboratory experiment that compared the swimming stamina of infected rainbow trout with that of healthy trout. He used a chamber with water swift enough to exhaust a healthy fish in about 10 minutes. The infected fish lasted about two minutes. "It's like asking someone with heart disease to run a 10K race," Kocan said. "He's not going to do very well."
That left a question: Why did the previously undetected disease show up in the late 1980s and resurface every year since?
Kocan and his students scrutinized all the potential variables and found only one significant change: Average river water temperatures had been rising over the last three decades. The warming began earlier each spring, following an earlier breakup of the river's ice. The June temperatures showed the greatest increase, about 6 to 8 degrees warmer, and June is when king salmon return from the ocean and begin their long upriver migration to spawn.
Unlike warm-blooded animals, the body temperature of salmon fluctuates with the temperature of surrounding waters. Laboratory studies of Ich infections in trout, a close cousin, have revealed that the incidence of disease and death rises as water warms, especially above 59 degrees.
Kocan spent five summers on the Yukon River studying the parasite, creating an uproar among fishermen by sharing his findings directly with them, rather than allowing state Fish and Game officials to review the data first.
He suddenly found his funding drying up after objections from Alaskan representatives on the committee that doles out research dollars.
"I've essentially been blackballed from working on the Yukon," said Kocan, whose work has since been accepted and published in peer-reviewed journals. "There's one fellow specifically who does not like our results: Gene Sandone. He doesn't want to hear the story and change his management practices."
Sandone denied playing any part in this: "I didn't blackball Richard Kocan. Dr. Kocan is free to put in a proposal and argue his point. He just has to get it through the technical committee."
The clash comes over the implications of Kocan's thesis. He believes that as much as 20% of king salmon are dying en route to the spawning grounds. If so, fisheries managers would have to cut back the commercial catch by at least that amount to keep the run healthy.
Sandone has an alternative theory, which has not been tested. He believes that the sick fish, weakened by the parasite, swim along the slower-moving edge of the river, where a disproportionate number get caught by fishing nets and fish wheels that line the banks.
In other words, subsistence fishermen like Pat Moore are simply catching most of the sick fish. The healthy ones swim just out of reach, deeper in the river, headed straight for Canada.
"That's my theory -- that they are not dying on the way," Sandone said. "Even if they are dying on the way, so what?" His department limits the catch based on how many fish escape all the nets and make it to the spawning grounds to reproduce.
That's been going well, he said, except for last year, when the number of fish that made it to Canada fell 50% below the minimum spelled out in a U.S.-Canadian agreement.