There are thousands of salmon swimming through the lazy currents of the Mokelumne River. In an industry where numbers have faltered for several years, this should be good news.
But a recent study says these fish are almost all born as a result of human intervention. Wild salmon populations are still dwindling.
The study compared salmon bred at the Mokelumne River Fish Hatchery with wild salmon born in the river, using data from 2004.
"Hatchery production was radically sweeping natural production in this year," said J.D. Wikert, a biologist with the Anadromous Fish Restoration Program run by the United States Fish and Wildlife Service who contributed to the study.
That's a problem, according to fisherman Bill Fererro. Hatchery fish don't have the same genes as wild salmon.
"You always want the wild genes to continue in the breeding process with these stocks of fish," said Fererro, who runs Mokelumne River Outfitters.
Without those wild genes, fish lose their natural instincts. These instincts are essential for salmon to fin their way home to natal streams for breeding.
With those wild, instinctive fish populations shrinking, rivers are left with fish who end up in the wrong streams and breeding suffers even more.
A new microchemistry technique was used for this study, involving the bones of fish.
Biologists removed otoliths, or ear bones, from salmon carcasses and studied how calcium and sulfur built up in the bone.
As a fish ages, calcium deposits around the bones like tree rings marking time.
Fish bred in a hatchery are fed a diet high in sulfur. As adults, hatchery fish have much more sulfur in their bones than wild fish, so it's a definitive way to tell them apart.
The findings were striking: More than 90 percent of the salmon spawning in the Mokelumne in 2004 were born and bred in the hatchery.
But staff at the hatchery say the numbers aren't a surprise.
"You can't manipulate the water systems to the extent that we have and expect any other outcome. This is what happens," said Bill Smith, hatchery manager.
Salmon in the river can't reach more than 80 percent of natural salmon breeding grounds. They're cut off by dams and canals and other structures. Hatcheries exist to boost salmon populations that would otherwise flounder.
Unless changes are made to address water diversion and loss of habitat, options are limited. Either accept dwindling salmon numbers overall, or be prepared for all hatchery-bred fish.
Wikert says this is an indicator that the Department of Fish and Wildlife might need to be thinking differently about managing hatchery populations. Tagging the fish has worked in the past, but now it's complicated.
Right now, only 25 percent of hatchery-bred fish are marked by clipping the small adipose fin. That means for every marked fish, three more are swimming about that look like wild salmon.
Fishermen are instructed to catch and release wild salmon and keep only those with a clipped adipose fin. With so many hatchery fish remaining in the rivers, it's easy for their populations to overwhelm the system.
Also, the marking isn't consistent. Twenty-five percent of fish bred for production are marked, but 100 percent of fish bred for yearling and ocean enhancement are also marked at Mokelumne River Hatchery.
"We need an opportunity to sort them somehow, in real-time," said Wikert.
In the Pacific Northwest, hatcheries mark all the fish they release. The downside is that makes for a lot more work. There's more data to keep track of. The costs add up to tag all the fish, then collect the tags and enter the resulting information into a database.
Smith agrees that tagging more fish might not be the answer. During the past few years when salmon populations were stricken, the hatchery tagged all of the two million fish they released.
This past fall, 14,000 tagged fish returned to the hatchery.
It's a lot of work to tag so many in the first place, then process all the returning data.
"If somebody's got the money to fund that for all the programs, go for it, but you're talking about a lot of money," said Smith.
The study was published in PLoS One, and online scientific journal associated with the Public Library of Science.
Contact reporter Sara Jane Pohlman at email@example.com.