A Cook Inlet sockeye salmon comes ashore/Craig Medred photo

For decades now, Cook Inlet fishermen of all stripes have been feuding bitterly over shares of the annual return of sockeye salmon, and now comes an indication that all that time they were getting collectively ripped off by another fishery.

An Alaska Department of Fish and Game genetic stock analysis has fingered a previously unquantified fishery annually scooping up as many 636,000 Inlet-bound sockeye.

For comparison sake, that’s about 100,000 more than were caught in the sometimes controversial Kenai River personal-use dipnet fishery in the record year of 2011. Dipnet harvests in recent years have been in the range of 350,000 to 380,000 – around a half to two-thirds of the harvest in what up to now has a been a ghost fishery, at least data wise.

The fishery’s newly calculated 2012 catch of 626,473 sockeye would have amounted to more than 10 percent of the commercial catch of sockeye in the Inlet that year. 

The mystery fishery picking off Inlet sockeye?

The Kodiak purse seine fishery operating off the capes of that island 50 to 100 miles south of the entrance to the Inlet.

Surprising non-surprise

Alaska Department of Fish and Game biologists and others studying Alaska salmon have long known the Kodiak fisheries intercepted salmon from all around the Gulf of Alaska. Tagging studies began telling that story decades ago.

But until recently there was no way to determine the size of the intercepts. There is now. Scientists can take tissue samples from salmon, tease out the DNA, and in that way fingerprint the “stock” from which the fish originated.

Random sampling of the fish from a known-size catch allows them to then determine the percentage of  the harvest coming from various stocks. Some simple math – the percentage times the total harvest – allows for a pretty accurate calculation on how many salmon from each stock have been caught.

Fish and Game this month released its look at the genetic make up of the Kodiak fishery as part of its “Fishery Manuscript Series.” The “Genetic Stock Composition of the Commercial Harvest of Sockeye Salmon in the Kodiak Management Area, 2014-2o16” is sure to get more than a few people talking in the lead up to the Alaska Board of Fisheries set to start in Anchorage on Feb. 23. 

Inlet salmon are on the agenda, and the process of allocating the catch between five different Inlet user groups is always contentious. Sockeye salmon are the key player in the game, too, because collectively the form the tail that wags the Inlet dog.

In a blender

The Inlet’s commercial fisheries in one regard mirror those off Kodiak; they are all mixed stock fisheries. Kodiak targets not only salmon spawned in streams flowing off the 4,000-square-mile rock in the Gulf of Alaska, but also fish born in streams draining into Cook Inlet, Prince William Sound and Chignik Lake.

Inlet fisheries catch almost solely Inlet sockeye, but those fish traces their roots to stocks in dozens of streams. State fishery managers have spent years trying to manage Inlet runs to minimize the harvest of weak sockeye, Chinook and coho salmon  stocks while maintaining large catches of strong sockeye stocks.

They have not always been successful. Efforts to maximize the commercial catch of Kenai sockeye, in particular, has often led to significant catches of non-target salmon.

Mixed stock fisheries are not easy to manage well, which is why salmon managers around the globe have tried to phase them out when and where they can. That isn’t always easy because so many salmon fisheries are mixed.

Even the rod-and-reel fishery in the Kenai River is a mixed stock fishery. An angler hooked into a sockeye in Soldotna could be battling a Kenai River fish, a Russian River fish, a Hidden Lake fish, a Quartz Creek fish, or a fish from any of a number of smaller streams.

The danger is mixed stock fisheries is that if fishermen catch too many fish from the weakest stock they can wipe out a run. Kodiak fishermen can argue that because their harvest is comprised of so many fish from so many places the odds of the worst happening are low.

It’s a good argument, but whether it will sell with Inlet fishermen about to discover they have been sharing a sizable chunk of their catch with folks of they didn’t know will be interesting to see.