That's a very good question. Fortunately, I just attended a presentation by Dr. Andrew Trites on this exact subject in terms of the Fraser sockeye. What he said was twofold. One is that they pick up the scat from seals and analyze what these seals have been eating. In general, for the harbour seals of British Columbia, 3% of their diet is salmon, which is very small.
But there are specific locations and river mouths. Seals are like dogs: they're very smart, and if they get onto something, they'll stick with it. In some instances, there are seals that have learned to target certain populations of salmon, in which case, as I understand it, they are doing enormous damage. But these are very localized situations that would need to be addressed individually. If you were to go out and kill all the seals today, you would not be protecting salmon, because what they are actually eating is different fish.
One thing he brought up is that one of the fish they prey heavily on, hake, is actually a predator of juvenile salmon. So the seals are helping reduce another predator. You have to be very careful with these natural systems. But no, seals are simply not responsible for what's happened to the Fraser sockeye.