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Timber Whitehouse, Area Chief Fraser River Stock Assessment , opens up a dead sockeye salmon looking for evidence of pre-spawn mortalities, a phenomenon that sometimes kills up to 50 per cent of stock before the fish have spawned.

John Lehmann/ The Globe and Mail/John Lehmann/ The Globe and Mail

What is killing British Columbia's salmon? And just where is the crime scene?

Like Agatha Christie's fictional detective, Hercule Poirot, B.C. Supreme Court Justice Bruce Cohen is faced with a mass of conflicting evidence as his federal inquiry tries to answer those questions and explain what happened to millions of salmon that have vanished at sea.

The cool, taciturn judge has handled complex cases before, but nothing like the one given him two years ago when Prime Minister Stephen Harper appointed him to investigate the decline of sockeye salmon in the Fraser River.

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During the hearings, one scientist compared the task to Murder on the Orient Express because Judge Cohen is faced with so many confusing clues and so many suspects.

For two decades, the river's sockeye population has been steadily dwindling, leading to a catastrophic collapse in 2009, when only one million fish returned, instead of the 10 million expected. (That event was followed by a big return in 2010, but fisheries managers say that was a one-off event.)

Sockeye, mainstay of the commercial fishery and a primary food source for native communities, migrate out of the Fraser each spring in the tens of millions, as one-year-olds. But few live to return as adults, and there are no signs of massive fish kills along the migration route.

After hearing from hundreds of witnesses and receiving thousands of documents in evidence, Judge Cohen's inquiry wraps up its evidentiary hearings this week, except for a two-day session in December that will hear late-breaking news on fish disease. The bulk of evidence heard so far suggests that, as he ponders the case of the missing salmon, he will focus on five key culprits.

Death by misadventure

Tracking data showed that in 2007 young Fraser sockeye (which were due to return in the disastrous 2009 run) navigated safely through Georgia Strait before heading into Queen Charlotte Sound, just north of Vancouver Island. But most didn't emerge on the other side.

One science report stated that in 2007 "extreme sea surface temperatures … and even more extreme salinity/density and wind anomalies" occurred in Queen Charlotte Sound.

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Judge Cohen also heard that juvenile fish collected in the sound by the Department of Fisheries and Oceans "had the smallest mean size since sampling began in the late 1990s."

And one expert testified that harmful algae blooms occurred in Georgia Strait coincident with the spring migration of young salmon.

In his final written submission, Government of Canada lawyer Mitchell Taylor told the inquiry: "A consensus appears to be emerging among scientists that biophysical changes in the marine environment stand out as the most strongly inferred factors explaining the pre-2010 decline."

Death by disease

Included in this category is a mysterious ailment that has yet to be identified and which appears linked to staggering death rates among adult salmon. Fish farms and the government's own hatcheries were accused of spreading diseases, but there was a lack of scientific evidence and the allegation remained unproven.

The Aquaculture Coalition, representing several conservation groups, argued the primary cause of the collapse in 2009 was disease, and "salmon farms along the path of the migrating salmon played a significant role in the origin or amplification of that disease."

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The B.C. Salmon Farmers Association, however, said there is no reliable evidence to implicate farms and that ocean conditions, harmful algae blooms, low food abundance and sea-temperature anomalies "combined to create the 'perfect storm' " that devastated the run of 2009.

A science review on the impacts of salmon farming was at odds, with Don Noakes saying "the evidence suggests that salmon farms pose no significant threat to Fraser River sockeye salmon," and Larry Dill stating "the greater the farm production, the lower the survival of the sockeye."

Some of the most intriguing evidence Judge Cohen heard came from Kristi Miller, a DFO research scientist, who has detected genomic signs indicating a new disease is afflicting sockeye. But Dr. Miller's research was stalled by a lack of funding and remains inconclusive. Complicating the picture in recent weeks have been laboratory findings that indicate infectious salmon anemia, a disease originating in Atlantic salmon, is now in Pacific sockeye and Coho. The implications are not yet clear, nor is it known how long the disease may have been present. On Friday, the Cohen Commission announced it will reconvene for two days in December to hear evidence on the ISA findings.

Before the hearings, fish farms were being blamed by environmentalists for "amplifying" sea-lice outbreaks that devastated wild salmon stocks. Researchers dismissed that as a primary cause of sockeye decline. But the inquiry also heard that the science on the subject is incomplete, which hands Judge Cohen a tough call on a divisive and controversial subject.

Death by poison

Nitrite, phosphorous, chloride, arsenic, selenium and an array of hydrocarbons are all present in the Fraser. The pollutants harm fish, but not enough to explain the epic crash of 2009. "There is a strong possibility that exposure to contaminants …has contributed to the decline of sockeye … [but that]is not the primary factor," a science report stated.

Death by degrees

Long seen as a threat to salmon, which thrive in cold water, the warming of both the ocean and the Fraser is thought to be lowering the survival rate of sockeye in all their life stages, from juveniles to adults.

Warmer water in the Fraser (up 5C in summer) is blamed for triggering earlier entries into the river by returning salmon, which puts them in freshwater longer, giving diseases and pathogens a greater chance to take hold.

Linked to the changes in run timing are increases in deaths of salmon as they migrate up the Fraser. Fish that die en route are categorized as in-river mortalities, while those that succumb on the spawning grounds, just before reproducing, are called pre-spawn mortalities. In some years, up to 90 per cent of sockeye become in-river or pre-spawn mortalities, but scientists are still struggling to understand the phenomenon.

The forensics

Just what is known, and what isn't, became a key issue in the hearings, and the need for more research was one of the few things on which all stakeholders could agree. One report concluded "there are major gaps in … our fundamental understanding of how various factors interact to affect Fraser River sockeye salmon." Information is lacking on how many salmon come out of the Fraser each spring, where they travel in the ocean, how they interact with fish farms and how they are affected by diseases, including ISA and the state of fish habitat in B.C.

It is expected Judge Cohen will call for research to address those and other knowledge gaps. And in the end, he may, like Detective Poirot, point his finger at many suspects.

In the early 1900s, the Fraser River had annual runs estimated at 100 million sockeye. Now it seldom sees more than 10 million. In 2009, it fell to one million. So the decline over time is dramatic, persistent and threatening.

Judge Cohen has spent two years trying to understand the problem. His report, which is expected to chart new directions for salmon management, is due at the end of June.

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About the Author
National correspondent

Mark Hume is a National Correspondent for The Globe and Mail, based in Vancouver, writing news and feature stories on a daily basis about his home province of British Columbia. His weekly column, which often challenges the orthodoxy on environmental issues, appears every Monday. More

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