The 16 listing decisions made in June 2005 by the NOAA Fisheries Service, following ESA status reviews, were challenged in U.S. District Court by the Alsea Valley Alliance.

The Oregon-based organization, represented by the Pacific Legal Foundation, said the reviews did not give genetically similar hatchery fish the same status as naturally produced salmon in determining the overall health of the stock. The group claimed the resulting protective regulations do not exhibit equity for hatchery fish.

PLF filings in Judge Michael R. Hogan's court also said the new listings improperly included salmon populations in the same ESA groupings that do not interbreed.

"Congress did not specify how NMFS should conduct a species review," Hogan's Aug. 14 ruling said of the Alsea challenge to NOAA's method for assessing hatchery salmon's role.

The federal agency included in listings hatchery populations that are closely matched genetically with fish that were born in the wild, and judged the risks and benefits represented by hatchery-born stocks that might stray onto the spawning grounds.

"While reviews commenced with the BRT's evaluation of natural populations within historic ESUs, the listed ESUs include hatchery stocks," Hogan said, referencing the biological review team assembled for the status reviews.

"NMFS made its listing determinations after assessing the effects of artificial propagation programs and existing protection efforts," according to the order. "Plaintiffs do not contend that NMFS improperly excluded any hatchery populations from a listed ESU, as occurred in Alsea I."

The Alsea Valley Alliance was successful in an earlier challenge of the Oregon Coast coho salmon listing. Hogan in 2001 ruled that NOAA had defined the coho population -- the "evolutionarily significant unit" -- to include both hatchery and natural born populations, then improperly included only the wild fish in the actual ESA listing.

The federal government chose not to appeal the decision. Instead it created a new "hatchery listing policy" and employed it in determining the status of salmon and steelhead stocks. The 2005 salmon determinations include fish from 133 hatchery programs. Only one, the Central Valley Spring-run Chinook ESU -- does not include hatchery stocks.

In challenging the salmon listings, the PLF has said that the overall hatchery-wild abundance should be the determining factor.

"Federal law says that all the salmon should be counted, and all the salmon should count," according to PLF attorney Sonya Jones. "Regulators do not have license to pick and choose which salmon they''ll pay attention to and which ones they'll ignore. For this reason, the case is not over. We're appealing, so that the federal officials will be required to do their job under the ESA."

"Not only does the law say that regulators can't do a low-ball estimate of salmon, science and common sense argue against leaving hatchery salmon out of the equation," Jones said. "Hatchery salmon are real salmon. They're biologically the same as stream-spawned fish. Most stream-spawned salmon are descended from hatchery fish."

"The standard is getting lower and lower and lower," Jones said.

The Hogan order was welcomed by NOAA Fisheries.

"It certainly removes a lot of uncertainty on more than a dozen salmon species" for which recovery plans are being developed, said agency spokesman Brian Gorman.

The 16 stocks range from the Canadian border, through the Columbia basin, to the central California coast. They include the Snake River spring/summer and fall chinook stocks, the Upper Columbia spring-run chinook, the Lower Columbia chinook and Upper Willamette chinook, Snake River sockeye, Lower Columbia chum and Lower Columbia coho.

A coalition of fishing and conservation groups applauded the Hogan decision.

"Hatcheries never were meant to be a replacement for self-sustaining populations of salmon in healthy streams," said Earthjustice attorney Jan Hasselman. Earthjustice represented the fishing and conservation groups, which joined the proceedings as a defendant-intervener.

The groups say that science has revealed that hatchery and wild salmon are different in important ways and that many hatcheries have helped push wild salmon closer to extinction.

The hatchery policy says that "hatchery fish will be included in assessing an ESU's status in the context of their contributions to conserving natural self-sustaining populations."

Their presence can be positive" by contributing to increasing abundance and productivity of the natural populations in the ESU, by improving spatial distribution, by serving as a source population for repopulating unoccupied habitat, and by conserving genetic resources of depressed natural populations in the ESU.

"Conversely, a hatchery program managed without adequate consideration of its conservation effects can affect a listing determination by reducing adaptive genetic diversity of the ESU, and by reducing the reproductive fitness and productivity of the ESU," the policy says.

"The ESA does not prohibit this approach," Hogan said.

He also supported the new listings' protective rules, which applied "take" prohibitions to "natural and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their adipose fin removed."

"In the absence of a challenge to NMFS's scientific conclusions, the ESA does not require that protective regulations treat natural populations and hatchery stocks equally," Hogan wrote.

The order also said NOAA's ESU groupings met ESA standards. The PLF has argued that some ESUs include far-flung populations that do not interbreed as the law requires.

"In the absence of a challenge to NMFS's scientific conclusions, NMFS's determined population segments for listing under a permissible construction of the ESA's definition of 'species,'" Hogan said.

"Plaintiffs' position that actual interbreeding is required would prohibit the agencies from listing the United States population of an animal that is abundant elsewhere in the world," Hogan said. "Congress intended otherwise."

"Substantively, defendants argue that the words 'interbreeds when mature' reflect Congress's intent that members of the same species, subspecies or distinct population segment be capable of interbreeding when mature.

"Defendants further argue that NMFS accounts for interbreeding between populations within ESUs by requiring that ESUs be reproductively isolated from other conspecific populations," Hogan said.

NOAA's interpretation of what constitutes an ESU is "within permissible limits under the ESA," Hogan concluded.

The PLF is girding for a renewed fight.

"This case has important real-world consequences for the people and the economy of the Northwest," said Jones. "When regulators put their hands over their eyes and act as if a large segment of the salmon population doesn't exist, they're more likely to impose harsh regulations on property owners and businesses, to 'protect' a species because they've deliberately underestimated its population."

The PLF is a public interest legal organization dedicated to property rights, limited government, and a "balanced approach to environmental protection."

A copy of the Hogan decision can be found at: www.earthjustice.org

With the decision, NOAA Fisheries can claim one victory in an increasingly complex fight.

In June, a Seattle-based federal judge declared NOAA's new hatchery policy illegal and ordered the restoration of "endangered" status for Upper Columbia steelhead stocks. The NOAA re-evaluation had resulted in the steelhead's downlisting -- from endangered to threatened.

Judge John C. Coughenour said the hatchery policy mandates that "status determinations be based on the entire ESU…," which includes hatchery fish.

"The status determination for the Upper Columbia River steelhead ESU provides a clear example of how an evaluation of the entire ESU distracts from the risks faced by natural populations and departs from the central purpose of the ESA," he said.

The PLF has since appealed Coughenour's ruling in the U.S. Court of Appeals for the Ninth Circuit.

NOAA spokesman Brian Gorman said the agency has until Aug. 28 to file an appeal of the decision if it so desires.

"Findings and Recommendations" issued last month by U.S. District Court Magistrate Janice M. Stewart take to task the 2006 NOAA decision to leave the Oregon Coast coho off the list. She said NOAA's withdrawal of that listing proposal hinged on an Oregon assessment of the coho's ability to persevere that is "based on assumptions plagued by uncertainty, lack of data and potential bias…."

The July 13 findings said the NOAA decision is arbitrary and capricious under the ESA because it fails to consider the best available science. She recommended that NOAA "be ordered to issue a new final listing rule consistent with the ESA within 60 days of the court's decision." Any objections to Stewart's findings are to be filed by Monday.

Ultimately a district court judge will accept Stewart's findings, modify them or reject them.

In Eastern California's U.S. District Court, a judicial decision is due on PLF challenge of five steelhead listings. That argument is based on the same premise presented in the Alsea case, that hatchery and naturally born fish should be treated as equals.