Truly Native

Colorado Parks and Wildlife (CPW) biologists have discovered a unique genetic lineage of the Colorado River cutthroat trout in southwest Colorado that was thought to be extinct.
Cutthroat trout at the Durango Fish Hatchery
Cutthroat trout at the Durango Fish Hatchery.

Colorado Parks and Wildlife (CPW) biologists have discovered a unique genetic lineage of the Colorado River cutthroat trout in southwest Colorado that was thought to be extinct. The agency will continue to evaluate the findings and collaborate with agency partners to protect and manage populations of this native trout.

The discovery was officially recognized earlier this year thanks to advanced genetic-testing techniques that can look into the basic components of an organism’s DNA, the building blocks of life. This find demonstrates the value of applying state-of-the-art genetic science to decades of native cutthroat conservation management and understanding. 

“Anyone who just looked at these fish would have a difficult time telling them apart from any other cutthroat, but this is a significant find,” said Jim White, aquatic biologist for CPW in Durango. “Now we will work to determine if we can propagate these fish in our hatcheries and reintroduce them into the wild in their historic habitat. It’s a great conservation effort and a great conservation story.”

Eight small populations of these trout have been found in streams of the San Juan River Basin within the San Juan National Forest and on private property. The populations are in isolated habitats and have been for decades sustained through natural reproduction. U.S. Forest Service staff and landowners have been cooperative in CPW’s effort; they will also be instrumental in further cutthroat conservation efforts.

In August, north of Durango, crews from CPW and the U.S. Forest Service hiked into two small, remote creeks affected by the 416 Fire and removed 58 fish. Ash flows from the fire could have severely impacted these small populations. These fish, now in the Durango Fish Hatchery, will be used as brood stock to start propagation. Last spring, cutthroats found on private land north of Pagosa Springs were spawned, and young fish from that operation are now developing in the Durango Fish Hatchery.

Cutthroat trout
Cutthroat Trout

Cutthroat trout originated in the Pacific Ocean and are one of the most diverse fish species in North America with 14 different subspecies. Three related subspecies are found in Colorado: Colorado River cutthroat trout found west of the Continental Divide; greenback cutthroat trout in the South Platte River Basin; and the Rio Grande cutthroat trout in the San Luis Valley. A fourth, the yellowfin cutthroat trout native to the Arkansas River Basin, went extinct in the early 1900s. Cutthroats from each of these areas have specific and distinctive genetic markers. CPW propagates the three remaining subspecies and actively manages their conservation and recovery throughout the state.

White and other biologists — including Kevin Rogers, a CPW cutthroat researcher based in Steamboat Springs, and Mike Japhet, a retired Durango CPW aquatic biologist — have been surveying remote creeks in southwest Colorado for more than 30 years looking for isolated populations of cutthroat trout. They found some populations in remote locations long before advanced genetic testing was available. The biologists understood that isolated populations might carry unique genetic traits and adaptations, so they made sure to preserve these collected samples for genetic testing later. Significant advances in testing technology over the last 10 years were instrumental in finding the distinct genetic markers that identify the San Juan lineage trout as being unique. 

Although that might seem like a long time, the discovery of this fish goes back more than 100 years. 

In 1874, naturalist Charles E. Aiken collected and preserved samples of fish found in the San Juan River near Pagosa Springs. Two of those trout were deposited in the Smithsonian National Museum of Natural History in Washington, D.C. These samples were forgotten until 2012 when a team of researchers from the University of Colorado was hired by the Greenback Trout Recovery Team to study old trout specimens housed in the nation’s oldest museums. When the researchers tested tissue from the two museum specimens, they found genetic markers unique to the San Juan River Basin. Armed with the knowledge of these genetic “fingerprints,” CPW researchers and biologists set out to test all the cutthroat trout populations they could find in the basin in search of any relict populations. 

Photo of a museum specimen found in the Smithsonian.
Photo of a museum specimen found in the Smithsonian.

“We always ask ourselves, ‘What if we could go back to the days before pioneer settlement and wide-spread nonnative fish stocking to see what we had here?’” White said. “Careful work over the years by biologists, finding those old specimens in the museum and the genetic testing gave us the chance, essentially, to go back in time. Now we have the opportunity to conserve this native trout in southwest Colorado.”

Developing a broodstock will be a key conservation strategy for increasing their distribution into suitable habitat and ensuring their long-term stability. Protecting the fish from disease, other nonnative fish, habitat loss and overharvest are important factors that will be considered in a conservation plan that will be developed over the next few years.  

Over the decades, CPW has worked with many partners throughout the state to find and conserve distinct cutthroat populations. Many of these efforts were conducted with assistance from the U.S. Forest Service, conservation groups and private property owners. CPW also works on projects with both the Colorado River Cutthroat Trout and Rio Grande Cutthroat Trout conservation teams.  

All native cutthroats have been adversely affected by a variety of issues, including reduced stream flows, competition with other trout species, changes in water quality and other riparian-habitat alterations. Consequently, the various types of native cutthroats are only found in isolated headwater streams. To ensure continued conservation of Colorado’s cutthroats, CPW stocks only the native species in high lakes and headwater streams. That stocking practice started in the mid 1990s. 

CPW has also conserved cutthroats in headwater streams by working with the U.S. Forest Service to build barriers to prevent upstream migration of nonnative trout, removing nonnative trout and subsequently stocking them with native trout. The conservation group, Trout Unlimited, has provided valuable assistance with many of these projects.

John Alves, Durango-based senior aquatic biologist for CPW’s Southwest Region, said the discovery shows the dedication of CPW aquatic biologists. 

“These fish were discovered because of our curiosity and our concern for native species,” Alves said. “We’re driven by scientific inquiry that’s based on hard work and diligence. This is a major discovery for Colorado, and it shows the critical importance of continuing our research and conservation work.”

Joe Lewandowski is the public information officer for CPW’s Southwest Region. He’s based in Durango.

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