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Rising to the Future

Conservation efforts to re-establish genetically pure cutthroat populations pioneer a path to protection

On a recent summer evening as the waning light danced over the South Fork Flathead River, a flash of red burst onto an angler’s mayfly pattern and a native westslope cutthroat trout rose through the slippery surface, its speckled mosaic of colors suspended in brilliant relief against the valley’s steep, fire-scorched banks.

Wallpapered with a mix of blackened lodgepole and clusters of radiant fireweed, the charred remains of last year’s Bear Creek wildfire offered a stark contrast to the river corridor’s oasis of crystalline water, burnished bottom stones and wild, purebred trout.

And yet here they thrive.

In these cold, clear waters, the fish are hardwired to persist in often harsh but pristine conditions, equipped with genetic adaptations they’ve adopted over the course of millennia, and which vary from one neighboring tributary to the next. Although morphologically indistinguishable, cutts caught in either Danaher Creek or Young’s Creek—the two main tributaries that form the South Fork at its confluence—possess genetic markers so divergent it’s like comparing a Chihuahua to a Dalmatian.

Scientists now recognize that these drainage-specific genetic adaptations are critical to the species’ survival, and rescuing, preserving and propagating their genetic diversity is the new end goal and the driving force behind a suite of cutting-edge management plans and research studies.

In Northwest Montana, fisheries managers have spent decades working to reverse the deleterious effects of legacy stocking of nonnative species while fine tuning the interplay between science-based manipulation and nature in order to protect one of the last remaining strongholds of cutthroats in the lower 48.

Today, those efforts are beginning to show signs of success, despite a host of new challenges foisted on the native trout species by climate change and other human stressors.

Native westslope cutthroats found in the South Fork Flathead River and elsewhere are precious gems, each fish equipped with the genes and genetic wiring of its ancestors, traits developed specifically for survival in a harsh northern Montana climate.

Westslope cutthroat trout have lived in post-glacial western Montana for thousands of years. During that time, the species has been able to survive catastrophic fires, massive floods and severe droughts. And yet in the two centuries since Lewis and Clark first inscribed the species into the nation’s vernacular during their famed 1805 expedition—the trout’s scientific name is Oncorhynchus clarki lewisi—the cutthroat’s range has dwindled and genetically pure populations have come under siege. The population decline is due to stream siltation, dams, overfishing, and competition from—and hybridization with—introduced nonnative fish such as rainbow and brook trout, a phenomenon exacerbated by the warming world.

But a new era of fisheries management has taken root, and efforts to re-establish, jumpstart and bolster genetically pure populations are gaining ground, while the potential for applications in other historic strongholds is bright. Massive, landscape-scale conservation efforts are in the works, including translocation of native species, drainage-specific stocking, eradication of invasive species, and rearing of genetically pure trout.

Working in concert, management agencies and researchers are developing a clearer understanding of the trout’s evolutionary history, overall genetic diversity, conservation challenges, and reproductive success.

And still, despite all of the time and resources exhausted trying to save native trout populations, one question persists.

So what? Isn’t a trout a trout?

“I get that question all of the time,” said Chris Downs, fisheries biologist for Glacier National Park, where a new blueprint for fish management is in the works, and for the next two decades will serve as a guiding document for native trout conservation.

“I think it’s a very fair question, and I think we are demonstrating the answer,” he continued. “Beyond the ecological value, there is a cultural and social value. That is why you see as many rod cases as suitcases at our airport. They are here to fish our native trout.”

Trout fishing brings in tens of millions of dollars in Montana alone, and many anglers are especially eager to catch native cutthroats—they’re as selective about their trout as the trout are about spawning in their natal waters. Westslope cutthroat are among western Montana’s original salmonid inhabitants, a subspecies that has been designated the state’s official fish, treasured for their sport and beauty.

“I can talk all day about the biological value, their enhanced fitness and how they have adapted to certain niche environments, but there is also an intrinsic value to having native fish on the landscape,” said Matt Boyer, science program supervisor for Montana Fish, Wildlife and Parks. “They are our state fish. They are iconic. This is a species that has been on the landscape for tens of thousands of years. They have survived floods, drought and wildfire. They have the specific genetics that have carried them through these events, and hopefully they will have the genetics to carry them into the future.”

Charred trees remain after the Bear Creek fire burned through the Bob Marshall Wilderness along the South Fork Flathead River in August, 2015. Greg Lindstrom | Flathead Beacon

Charred trees remain after the Bear Creek fire burned through the Bob Marshall Wilderness along the South Fork Flathead River in August, 2015. Greg Lindstrom | Flathead Beacon

Yet less than 10 percent of the species’ historic range still exists, and the fish is considered a state-listed “species of concern” in Montana and “threatened” in Alberta.

With that in mind, FWP set out more than a decade ago to preserve and restore the westslope fishery in the pristine South Fork, which meanders through a large swath of protected wilderness, the Bob Marshall Wilderness Area.

Recognizing the pressure of hybridization, the architects behind the South Fork Flathead Cutthroat Conservation Project have been systematically removing non-native fish and replacing them with pure westslope cutthroat since 2007. FWP identified 21 lakes in the Bob Marshall Wilderness and Jewel Basin, and every fall one lake after another has been chemically treated with a piscicide called rotenone and then re-stocked with genetically pure strains of westslope cutts. Only two lakes remain: the 51-acre Handkerchief Lake on the Flathead National Forest, set for fall of 2016, and the largest lake on the list, the 148-acre Sunburst Lake in the Bob Marshall Wilderness in the fall of 2017.

Boyer, the state’s lead biologist for the project, says the effort has proven to be biologically successful and general public acceptance has come around, despite strong contention at the project’s outset.

“This project is one of a kind in terms of scope. It’s a landscape-scale effort, and it employs cutting edge techniques,” Boyer said. “There’s not really anything quite like it. Certainly not at this scale and certainly not with an eye toward genetic conservation.”

The genetic conservation component wouldn’t be possible without the revival of the Sekokini Springs Fish Hatchery near West Glacier, an experimental state fish hatchery that raises wild, genetically pure, drainage-specific strains of westslope cutthroat trout.

The hatchery allows biologists with FWP to raise genetically diverse populations of wild westslope cutthroat trout, hold them in isolation until they are certified genetically pure and pathogen-free, and then introduce them to Montana’s lakes and rivers where the fish have historically thrived.

Prior to Sekokini Springs coming online, the only pure genetic strain of westslope cutthroat trout certified for natural population restoration in Montana was the “M012,” a “cookie-cutter” strain raised at Washoe Park Hatchery in Anaconda.

With the advent of the experimental hatchery of Sekokini Springs, fisheries managers can raise drainage-specific strains of cutthroat and plant them in the mountain lakes where they evolved and are best suited to persist.

“It’s kind of like the ark,” said the FWP’s Brian Marotz, the impetus behind the $1.8 million project, funded by Hungry Horse Dam mitigation. “And if we do our job really well, this precludes the need to list the species under the Endangered Species Act.”

Preserving the species’ genetic variation is critical to its long-term success, Marotz said, with their genetic makeup and landscape-wide population distribution serving as the best defense against wildfire, drought and other stressors.

“A lot of these local adaptations involve multiple genes or gene complexes working together, and hybridization breaks that stuff up,” Boyer said. “Often times local adaptations involve not just a single gene, but multiple genes working in concert. Hybridization has the potential to disrupt that.”

Hatcheries manager Scott Relyea said the success of Sekokini Springs and the South Fork Lakes Project has piqued the interest of managers in other corners of Montana, and the facility is expanding to accommodate new isolation tanks and rearing ponds.

“We’ve had enough success here that the same application we used in the South Fork will be used in the Stillwater and in Glacier National Park,” Relyea said.

Hatchery manager Scott Relyea holds a saucer of westslope cutthroat sac fry. Greg Lindstrom | Flathead Beacon

Hatchery manager Scott Relyea holds a saucer of westslope cutthroat sac fry. Greg Lindstrom | Flathead Beacon

In Glacier, where Downs and park staffers are working to complete a comprehensive park-wide fisheries management plan, they’ve assessed every drainage to determine how to best manage them in the future.

The biggest problem is that Glacier’s lakes and streams are a veritable stew of nonnative species, particularly as invasive lake trout have radiated out of Flathead Lake, colonized the lakes and out-competed native species like cutthroat and bull trout.

Historically one of the last best strongholds for native cutthroat and bull trout, Glacier Park has seen its wild populations decimated by the explosion of invasive lake trout, reducing Montana’s aquatic darlings to imperiled icons and pushing the species toward the brink of extinction.

But park biologists along with the U.S. Geological Survey have pioneered a new effort to suppress lake trout in remote backcountry lakes and reintroduce dwindling native trout populations, with recent results showing strong evidence of success, and indicating that the efforts could be applied to other invaded habitats and broader ranges.

In 2009, biologists with Glacier Park and the USGS began an experimental project on Quartz Lake, located in the park’s remote northwest corner, where lake trout invasion was still in its early stages of invasion. The aim was to reduce or eliminating lake trout by gillnetting, a project that required a boat to be helicoptered in and all of the supplies to be hauled in by biologists and mules.

Clint Muhlfeld, aquatic ecologist for the USGS Northern Rocky Mountains Science Center, and his team first located so-called “Judas fish,” captured and radio-tagged them, then tracked the fish to spawning areas in order to capture and remove the most dense concentrations of spawning lake trout.

In seven years, the project has shown evidence of success in reducing lake trout, and is hailed as one of the first successful projects of its kind and a leading example that lake trout suppression, once thought to be futile, is possible.

Now, biologists with both agencies have received approval to continue the federal program on Quartz, and have applied a similar method of lake trout removal to Logging Lake, which was once among the most robust bull trout fisheries in the park, but is now on the cusp of blinking out due to lake trout invasion.

A second element to the Logging Lake project involves translocation of bull trout—the first of its kind in the upper Columbia basin—where biologists moved 107 bull trout from Logging Lake to a safe haven called Grace Lake, an upstream body of water that is protected from lake trout invasion by a waterfall, which serves as a natural barrier.

“We captured as many of the remaining bull trout in Logging Lake as possible and literally put them on our backs in a bucket, hiked up a trail and released them in Grace Lake,” Muhlfeld said. “Now we’ll focus our efforts on suppressing that Lake Trout population in Logging.”

Meanwhile, a team of researchers led by Muhlfeld recently completed the park’s first comprehensive genetic assessment of westslope cutthroat trout inside the park’s boundaries, giving park managers a genetic inventory and providing baseline genetic status and distribution information that can be used for prioritizing management efforts to protect and restore the genetic integrity of westslope cutthroat trout populations in Glacier Park.

For the past five years, Muhlfeld and his team have scoured the park’s three river basins that are historic ranges to native westslope cutthroat—the Columbia, Missouri and South Saskatchewan—dispatching an army of fly-fishers into the park’s remote corners to cull genetic samples.

“My crew will probably tell you it was the coolest summer job they’ve ever had,” Muhlfeld said.

Of the 115 populations sampled in the three river basins, 34 contained hybrid samples, while 36 conservation populations were identified, 19 of which were tagged as having medium-low to medium-high risk of hybridization. Twelve populations were at high risk of hybridization, while five populations were at low risk, all of them located upstream of fish passage barriers.

Biologists like Muhlfeld have been tracking the reproductive success of hybridized trout, and recent evidence suggests they aren’t doing well.

“The hybrid offspring have greatly reduced fitness and a diminished ability to produce offspring and have those offspring survive,” he said.

In 2014, Muhlfeld led a project study that linked the rapid hybridization between native Montana trout species and invasive species in the Flathead River system to climate change.

In the past three decades, hybridization between native westslope cutthroat trout and invasive rainbow trout has rapidly accelerated in the Flathead River system, a range-wide stronghold, according to a groundbreaking study.

Although the threat from introduced rainbow trout was held at bay for decades, climate change gave rise to accelerated hybridization.

“So essentially, hybridization was a time bomb waiting to go off under the right environmental conditions,” Muhlfeld said.

Clint Muhlfeld works with a crew to collect genetic samples of trout along Midvale Creek near East Glacier. Greg Lindstrom | Flathead Beacon

Clint Muhlfeld works with a crew to collect genetic samples of trout along Midvale Creek. Greg Lindstrom | Flathead Beacon

On a recent summer morning in East Glacier, Muhlfeld humped a Ghostbusters-like electrofishing backpack along a tributary of Glacier National Park’s Two Medicine River drainage, stunning cutthroat in order to gather genetic samples.

The tributary is one of only two streams in the Missouri River drainage that contains a conservation population of genetically pure westslope cutthroat, and park managers hope to maintain its integrity.

According to Downs, the genetic assessment will help park managers prioritize conservation actions as they develop their fish management plan.

“It’s going to help us identify where we want to conduct conservation actions and further research, with the intent of being able to secure populations first and foremost, as well as restore populations that have been extirpated,” Downs said.

“Part of the fish management plan will be identifying potential projects that would benefit native fish including westslope cutthroat, and the success of the South Fork Lakes project is a pretty good model for what can be done to make some large scale gains for westslope cutthroat. I think we have similar opportunities in the park.”

Boyer said while most native trout restoration projects rely on continued suppression, the South Fork project is unique in that there is a finish line.

“Suppression is an ongoing effort. It’s mowing the lawn. Here you are able to remove the threat, introduce a self-sustaining, genetically pure population and get out,” Boyer said. “That is the beauty of this project. There is a finish line.”

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