What is killing the pacific salmon?

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A sockeye salmon

A sockeye salmon

The great sockeye salmon run from the Pacific Ocean to Canada’s Fraser River was for decades an example of nature’s fruitful bounty. Some 60 million fish returned annually to spawn. But starting in the 1990s, the sockeye’s productivity declined precipitously—and in 2009 only 1 million fish returned to the run.

That led the Prime Minister of Canada to launch a judicial inquiry into the salmon collapse—wild salmon is worth over $1 billion to the economy of British Columbia.

As head of the inquiry, British Columbia Supreme Court Justice Bruce Cohen found a wealth of scientific data on the sockeye salmon; in fact, his office received so much information—more than 30 reports and over 700 recommendations—that it recently had to call for an adjournment to digest the huge volume of material. But despite all that research, scientists still don’t have a grasp as to what caused the decline.

(See TIME’s list of the best photos of the natural world from 2002).

That might be changing. Writing in the latest edition of the journal Science, Canadian biologists say that they have identified a key genetic signature among fish that die on their way upriver that indicates they are suffering from metabolic and immune-related stress. What’s more, this signature appears in the fish before they enter the river for the journey. Although the research doesn’t reveal the cause of this stress, the scientists speculate that a viral infection may be responsible.

Co-author Scott Hinch at the University of B.C. says that the infection probably starts at sea, before the fish make their run upriver, a phenomenon he describes as “dead fish swimming” in an interview with the Vancouver Sun today. He said the virus may be associated with leukemia and lymphoma.

“There is no doubt there is some form of pathogen involved,” Hinch said.

Climate change may be exacerbating the problem, too. Seven of the past 10 summers were the warmest on record for the Fraser River, and biotelemetry revealed high losses of salmon in regions of the river with elevated temperatures. Previous studies on salmon migration has shown that warmer water reduces the delivery of oxygen to the tissues of the fish and allows more rapid development of infections.

(Click here to read how to save the world’s fish.)

In recent years Canada has imposed substantial reductions on fishery harvests. The strategy may be working. In 2010, scientists recorded an estimated run of 30 million salmon—the largest run of the century. Even so, scientists warn that the 2009 run marked such a shocking decline that it’s too early to assume that the fish have guaranteed a sustainable future. To ascertain that, scientists must first get to the bottom of what caused one of nature’s great rituals—the sockeye salmon run— to so precipitously decline. This new study marks an important step in that journey of discovery.