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A sockeye salmon in the Adams River in Roderick Haig-Brown Provincial Park near Chase, B.C. Friday, Oct. 8, 2010.Jonathan Hayward/ The Canadian Press

After 18 months of hearings and the filing of 2,145 exhibits, a federal inquiry into the decline of sockeye salmon has ended – except for the writing of a report that could recast fisheries management on the West Coast.

The inquiry, under the direction of the B.C. Supreme Court's Mr. Justice Bruce Cohen, was struck by Prime Minister Stephen Harper after only about one million of an anticipated 10 million sockeye returned to spawn in the Fraser River in 2009.

The collapse of the sockeye run led to the closing of the once-lucrative commercial fishery for the third season in a row, and was so extreme that even native bands along the river were curtailed from making catches for food and ceremonial purposes.

Judge Cohen's task is to find out why the Fraser's sockeye population has been declining and to offer solutions. But his findings are expected to have broader implications, because it is widely accepted that as go the sockeye – which is the most commercially valuable of the five species in B.C. – then so go the rest of the stocks.

In what is expected to be an exhaustive final report, due by June 30, 2012, Judge Cohen is supposed to make recommendations for improving the future sustainability of the sockeye fishery in the Fraser, including suggesting changes to the policies, practices and procedures of the federal Department of Fisheries and Oceans.

Any hope that the Cohen Commission could find a smoking gun, and point to an easy solution, were quickly abandoned as the hearings got under way and an array of scientists began testifying about the complex and little-understood world of wild salmon.

Sockeye hatch in tributaries of the Fraser River throughout B.C. – some in the shadows of the Rocky Mountains – before rearing for a year in large lakes, then migrating up to 1,200 kilometres to the ocean.

But Judge Cohen heard that fisheries managers pretty much lose track of the young sockeye once they are in the Fraser. What happens to the fish on their journey out of the river, up the coast to the Gulf of Alaska, and on their return is pretty much a mystery.

Ocean changes that affect the amount of nutrients in the sea, climate changes that bring in warmer waters and new predators, and the possible exposure to fish of new diseases and lice, perhaps amplified by salmon in fish farms, were all raised as concerns. But there was no clear culprit, and more than once scientists referred to "death by a thousand cuts."

Some of the more intriguing evidence Judge Cohen heard was about a phenomenon that has emerged in recent years in which adult salmon die as they migrate back up the Fraser, or on the spawning beds, just days before they should have reproduced. Nobody can explain why.

In the closing days of the hearings, Judge Cohen focused his attention on infectious salmon anemia, a virus that appears to have been detected in sockeye, although scientists are at odds as to whether the tests are reliable or not.

Lawyers representing three different participant groups grilled witnesses from DFO and the Canadian Food Inspection Agency over how the government reacted to scientific findings pointing to the possible discovery of the ISA virus on the West Coast.

Instead of launching tests to try to confirm the presence of the virus, Judge Cohen heard, government officials investigated the labs that had reported the findings.

He also heard it is unclear if the virus is in B.C., and if it is, no one knows what kind of a threat it might hold for salmon.

There was no sense of drama when the hearings ended Monday.

"The hearings are complete – I hope," said Brock Martland, putting in the final word.

Judge Cohen left without comment, perhaps because he realizes the hardest work is yet to come.