In the 1990s, rainbow trout in Colorado died. A lot of them. Millions of them.

Whirling disease, an imported aquatic disease first discovered in Germany in 1893, left young trout swimming in circles. Nearly entire generations of rainbow trout died with kinks in their tails, catastrophic deformities from a nearly invisible parasite.

The Colorado River in Grand County lost 98% of its wild rainbow trout population.

In other river systems, the devastation wasn’t as bad, but the disease still took its toll.

The rainbow trout population in the Lower Gunnison River from Delta to Grand Junction, crashed from 2,000 adults per mile in the 1980s and early ’90s to 300 per mile by 2000.

That density dipped to about 170 adults per mile in 2014, said Eric Gardunio, an area aquatic biologist with Colorado Parks and Wildlife in Montrose.

But since 2014, the rainbow trout population in the Gunnison has rebounded.

In 2019, 630 adult rainbows scattered every mile of the Lower Gunnison, a more than threefold increase thanks to CPW’s decades-long effort to restore rainbow trout across the state.

CPW’s endeavor to build back rainbow trout populations has been time consuming and costly. In 2018, CPW was spending $3.8 million every year to stock rainbow trout across the state. For decades, CPW researchers have studied whirling disease and resistant trout to try to find a solution.

Yet, the continued success of CPW’s whirling disease program has highlighted the importance of genetic research for conservation efforts across the state at a time when invasive species and climate change are an ever-increasing threat.

“Without incorporating those (genetic) resistance characteristics into rainbow trout, we probably would not be where we’re at in terms of recovering the rainbow trout populations across the state,” said Eric Fetherman, an aquatic research scientist and whirling disease expert with CPW.

The story of how whirling disease made its way to Colorado’s rivers and ravaged rainbow trout before CPW’s genetic initiatives saved the day sounds like a fisherman’s tale.

Whirling disease, which targets young fish disrupting the development of their skeletal system, was brought to the U.S. by frozen fish products or brown trout imported from Europe, according to a 2002 paper by the American Fisheries Society.

Once it reached the U.S. in the 1950s, the disease began to spread. It was first detected at two public and two private trout hatcheries in Colorado in 1987 before making its way into all of the major river systems in the western half of the state.

As the disease fanned out and rainbow populations declined throughout the 1990s and 2000s, CPW began searching for solutions.

In 2002, CPW learned that German researcher Mansour El-Matbouli had discovered whirling disease resistance in a genetic strain of domesticated rainbow trout at the Hofer Trout Farm in Bavaria, Germany.

Researchers at the University of California-Davis imported the fish to the U.S., and subsequent experiments confirmed the “Hofer” rainbow trout strain was resistant to whirling disease.

George Schisler, an aquatic wildlife researcher with CPW, imported the Hofer trout from California and another resistant strain of lake and reservoir rainbow trout from Harrison Lake in Montana to CPW’s Fish Research Hatchery near Fort Collins.

Researchers immediately began assessing them for their genetic potential and started breeding the Hofer trout with the wild Harrison Lake trout and CPW’s own wild Colorado River rainbow trout.

“What we started really incorporating into the hatchery system were these crosses of the Hofer and these wild-strain rainbow trout, hoping that we could create a fish that was retaining the resistance of the Hofer, but (that) also retains the characteristics of those wild fish so they could continue to survive well in Colorado’s waters,” Fetherman said.

As they studied the offspring, researchers found that the first generation of rainbow trout, with a Colorado River and a Hofer parent, were best suited for wild streams while retaining their resistance to whirling disease.

Around 2004, CPW started its selective breeding program and the agency began stocking the 50% Hofer/50% Colorado River rainbow trout to see how they would do in river systems.

The results were mediocre, and few of the fish survived to pass on their whirling-disease-resistant genes to the wild population. The problem was the domestic background of the Hofer strain.

“We were seeing them not surviving very well in the wild, not because of whirling disease, but they couldn’t compete very well with brown trout,” Gardunio said. “They just couldn’t figure out how to live well out in the natural environment because they’re such a domesticated strain.”

In 2006, CPW began stocking the 50% Hofer/50% Colorado River rainbow trout in the east portal of the Gunnison River in Curecanti National Recreation Area. The east portal of the Gunnison was one of the few locations in the state where the impacts of whirling disease had been comparatively mild and researchers hoped the introduced fish would survive and reproduce better.

Stocking continued through 2013, and as Fetherman and other scientists collected genetic data, they realized the fish had spawned with the wild Gunnison River rainbow trout initially in the river.

“We did actually learn that those trout had spawned in that system, and those Hofer resistant characteristics had been incorporated into the genetics of those wild fish,” Fetherman said. “They were just maintaining the resistance genes from the Hofer and then everything else was wild trout genetics.”

Gardunio watched as the rainbow trout population in the east portal of the Gunnison began to rebound.

“When you put (the Gunnison River rainbow) in a river that’s filled with other fish like brown trout, they can compete with those fish and be successful,” he said. “They’re really what we’d been looking for for a long time.”

Gardunio and CPW immediately began collecting Gunnison River rainbow trout eggs to build a brood stock that the agency could raise in its hatchery and begin stocking in rivers hit hard by whirling disease.

Since 2014 when the program began, CPW has collected about 100,000 eggs per year from 100 female trout in the east portal. From 2014 to 2019, CPW stocked 80,000 to 100,000 Gunnison River rainbows every year, primarily in the Gunnison and Arkansas rivers.

But now that the fish CPW initially brought in to create its brood stock are reaching reproductive maturity, those numbers have grown.

In 2020, CPW stocked 279,000 across the state. This year, the agency released almost 592,000.

In Southwest Colorado, CPW stocked about 58,000 Gunnison River rainbows in the Animas, San Juan and Piedra rivers, with the Animas receiving about 68,000 since efforts began in 2019.

The genetic ingenuity has paid off.

Jim White, a CPW aquatic biologist, said in a September news release that the rainbow trout in the Animas were the best CPW had seen for years after whirling disease and the 416 Fire, which killed 80% of the fish in the river.

“We’ve definitely been seeing some positive results,” Gardunio said. “We’re hopeful that will continue and that (the Gunnison River rainbow trout) can really help us as a state rebound from this whirling disease issue and get our wild rainbow populations back.”

“The goal is eventually to get back to where the rainbow trout are self-sustaining and we don't have to be reliant on stocking anymore,” Fetherman said.

Fetherman, Gardunio and CPW’s genetic ingenuity may provide a blueprint for future efforts to conserve aquatic wildlife in Colorado.

Climate change and other diseases continue to pose a threat to trout populations in the state.

In 2015, a bacterial disease at CPW’s Glenwood Springs Hatchery wiped out the entire Hofer/Colorado River rainbow trout strain researchers had developed.

“Really over about a decade, which isn’t that much time, this population with a little help from us was able to develop that (disease) resistance,” Gardunio said.

“What’s amazing to me is how adaptive these fish are,” he said. “If it is the kind of impact that doesn’t kill everything, that selective process can happen relatively quickly and these populations can change to overcome hurdles.”

“The whirling disease issue taught us a lot about how we should be monitoring and watching for these things,” Fetherman said. “And so we're trying to learn from past occurrences so that we can try to prevent anything like this from happening in the future.”

ahannon@durangoherald.com