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KALISPELL – A controversial project aimed at restoring native cutthroat trout to a chain of alpine lakes above the South Fork Flathead River drainage has passed its halfway mark, and state fisheries biologists are already seeing evidence of the program’s success.

Jim Vashro, regional fisheries manager for Montana Fish, Wildlife and Parks, said the Westslope Cutthroat Trout Conservation project is likely to become one of those rare, self-sustaining programs that restores a native species to an ecosystem on the brink of genetic corruption.

“It would be ideal if we could walk away from those lakes and let the fish run this themselves,” Vashro said last week.

The decadelong project, which has entered its sixth year and is funded by the Bonneville Power Administration, targets 21 alpine lakes with outlets flowing into the South Fork Flathead drainage, considered the best remaining stronghold for Montana’s state fish.

To prevent the hybridized cutthroats from dribbling downstream, the lakes are either poisoned with a toxin called rotenone, the source of the early controversy, and then restocked with genetically pure hatchery westslopes; or the hybrids are genetically swamped, meaning the lakes are densely stocked each year with genetically pure trout in an effort to dilute and overwhelm the hybrid population.

So far, 16 of the 21 lakes have been managed — either with rotenone treatment or through genetic swamping – and five of the most remote and logistically challenging lakes remain.

The most salient marks of success, Boyer said, are reports from anglers who say the treated lakes are fishing well, and evidence that natural reproduction is already occurring among genetically pure cutthroat populations in several of the lakes.

“We are beyond the halfway point and the really exciting part now is that we are seeing the fruits of our labors,” Boyer said. “Anglers are catching fish, we are seeing natural reproduction and the lakes are being restored back to genetic purity.”

Biologists have closely monitored the effects of the rotenone on the lakes’ subspecies, like amphibians and zooplankton, and say trout appear to be the most sensitive to the treatment while the subspecies are unaffected.

“Trout are pretty wimpy in that respect,” Boyer said. “They are the first to go because they are the most susceptible to toxins, so we have a treatment that kills trout and not other subspecies, keeping the ecosystem intact.”

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Wild populationsof westslope cutthroat trout have been devastated by decades of habitat loss and more than a century of interbreeding with non-native species like rainbow trout and Yellowstone cutthroat. The native trout now occupy just 9 percent of their historic range and have lost much of their genetic diversity.

First proposed in 2001, the conservation project finally got under way in 2007 after four separate environmental reviews, beginning with the poisoning of Black and Blackfoot lakes in the Jewel Basin Hiking Area.

In 2008, Lower Big Hawk Lake was treated, followed by Clayton and Margaret lakes in 2009, Wildcat Lake in 2010, and the Necklace Lakes chain in 2011.

The remaining lakes will be among the most challenging to access, Boyer said, and genetic swamping of Lick Lake in the Bob Marshall Wilderness is slated for this spring, with Lena, Koessler, Sunburst and Handkerchief lakes to follow.

The project was born of concern that hybridized fish populations would find their way into the South Fork drainage over time and create a proliferation of hybridization.

The South Fork Flathead comprises 50 percent of the westslope range-wide, “which is a significant component of their habitat,” Boyer said, and illustrates why it is critical to conserve a species that evolved here. The project sets a goal of wiping out hybridized trout in the watershed by roughly 2017, and replenishing the lakes with multiple broodstocks to maintain genetic diversity.

Currently, the pure genetic strain of westslope cutthroat trout, certified for natural population restoration in Montana, are raised at Washoe Park Hatchery in Anaconda.

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The captive brood stock was built using fish caught in the Clark Fork River and the South Fork of the Flathead, which Boyer said remains Montana’s purest refuge of westslope cutthroat trout.

Biologists in the Flathead have been working to replicate another population of genetically pure cutthroat in the Bob Marshall Wilderness, on Danaher Creek, and spawned those fish for the first time last year. After treating the Necklace Lakes chain, biologists will restock them using the Danaher Creek brood.

“The simple thing to do would be to put the state broodstock fish everywhere, but the downside is that you homogenize all the diverse populations in the South Fork by planting broodstock from a genetically identical stock,” Boyer said. “A better approach from a conservation standpoint is to achieve genetic variation by using multiple sources.”

The project’s biological rewards have paid off in terms of conservation, Boyer said, but the project has also been socially rewarding.

“We have a number of people who, while staunchly opposed to this project initially, have now become some of our biggest supporters,” he said.

“The opportunities for true ecosystem restoration are not exceedingly common and this is one project where we have a real shot at accomplishing ecosystem-wide restoration for a native species,” Boyer said.

Missoulian Flathead Valley Bureau reporter Tristan Scott can be reached at (406) 730-1067 or at tscott

@missoulian.com

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