Plummeting numbers of several salmon and trout species have conservationists looking more and more to hatcheries—where fish are reared in comfortable captivity and then released into natural bodies of water. But this strategy may hurt wild populations, according to a paper published this week in Biology Letters.

Researchers at Oregon State University (O.S.U.) found that not only do hatchery-raised steelhead—a Pacific trout sharing the same genus, Oncorhynchus, as salmon—produce relatively fewer and weaker offspring once back in a natural environment, but so do their wild-born spawn.

"Captive breeding programs are a popular and efficient strategy to save declining populations, but the genetic impact must seriously be taken into account," says Hitoshi Araki, a co-author on the paper who recently moved from O.S.U. to the Swiss Federal Institute of Aquatic Science and Technology. "Otherwise, wild populations can be at risk of extinction."

Araki and his colleagues looked at the Hood River steelhead supplementation program in Oregon and found that trout fry raised by two hatchery-reared parents had just 37 percent of the reproductive success of those with two wild-born parents, even though both sets of offspring were born in wild waters. If the fry had a mix of one wild and one hatchery-raised parent, then it had 87 percent of a pure-bred wild fry’s reproductive fitness.

And this effect may not be limited to fish. Araki speculates that it could be relevant for "any supplementation or captive-breeding program that ends up stocking and releasing [animals] in the wild for conservation efforts."

Dramatic drops in the reproduction rates of released hatchery fish were previously reported in a 2007 issue of the journal Science. The study noted the effects could be explained by a natural selection that favors characteristics useful in a sheltered, predator-free artificial environment over those necessary in the more hostile natural world. Of the large numbers of eggs laid by the released mothers during spawning, only a small fraction ever reached adulthood—the few that were best suited for survival in wild conditions.

The new study, which sampled from the same Hood River program as did the 2007 study, is the first to look at the survival and reproductive effects on the next generation: their wild-born offspring. "If fitness could drop that quickly in one generation, some expected that the reverse would be the same—that in the next generation of natural rearing, fitness could recover. Why not, right?" says Araki, who was also an author on the 2007 paper. "Unfortunately, we found that was not the case."

Their results leave many questions unanswered. "Something is changing," says Araki. "But we don't know what trait, what gene, is responsible for these changes." He adds that when and if they do find an answer, it might be possible to "mitigate those effects."

In the meantime, overfishing, water diversions and habitat destruction continue to impede restoration efforts for the 28 Pacific salmon and steelhead populations listed under the Endangered Species Act. Araki acknowledges that there may be instances where a hatchery program is necessary to save a local population from extinction.

Peter Moyle, a fish biologist at the University of California, Davis, agrees. "We can't just stop," he says. "We are dependent on hatcheries to maintain fisheries." But Moyle also understands the risks the strategy can pose on the fitness of wild fish in the long run: "Studies like this make us go, 'Hmmm, are we creating domestic animals here?' It's like putting cows from pastures into the mountains."