Extinction isn’t always final: Rediscovery of the native trout of the San Juan basin

The rediscovery of the San Juan cutthroat trout is a celebration of basic conservation principles and shows why implementing conservation measures is so critical for perpetuating the wildlife resources.
San Juan Cutthroat Trout
A handsome male San Juan cutthroat trout in full spawning colors.
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By Kevin B. Rogers

In 125 years of perpetuating the wildlife of Colorado, our aquatic biologists have learned an important lesson: “extinction” isn’t always final.

And that’s especially true when it comes to Colorado’s native cutthroat trout, which are especially prized by anglers and conservationists alike. 

As the only native trout of Colorado, cutthroats get special attention from Colorado Parks and Wildlife aquatic biologists and researchers. Over the decades, our knowledge of them has grown, particularly as new genetic testing methods continue to expand the boundaries of discovery.

These recent scientific advancements have shown that Colorado is home to more distinct lineages of cutthroat than we ever knew, and lineages believed to be extinct still survive, though not always in their ancestral waters.

An important example was a DNA study published in 2012 that revealed six distinct lineages of cutthroat trout historically called Colorado home. The native ranges of these lineages align with Colorado’s major drainage basins. 

Two of these lineages were thought to be extinct, the yellowfin cutthroat trout native to the headwaters of the Arkansas River and the San Juan cutthroat trout, the subject of this story, native to the gin-clear headwaters of the San Juan basin. Fortunately, that was not entirely correct. But it took decades of work by CPW biologists and their partners to sort out the truth.

This story begins in 1874, not long after the end of the Civil War and before Colorado became a state. George Wheeler, an 1866 West Point graduate commissioned as a lieutenant in the U.S. Army Corps of Engineers, was tasked with leading a surveying expedition to map the territories ceded to the U.S. by Mexico in 1848. 

Charles Aiken, a taxidermist by trade and an accomplished ornithologist, accompanied Wheeler on a five-year expedition known as the Wheeler Survey. (Ultimately, the findings of the Wheeler Survey, along with the Clarence King and John Wesley Powell Surveys, became the foundation of the U.S. Geological Survey.)

Aiken, a naturalist at heart, collected a pair of trout specimens from the San Juan River near Pagosa Springs when the survey crew passed through the area. He included these specimens with bird samples he collected and shipped them off to the Smithsonian National Museum of Natural History in Washington D.C. where they remained largely forgotten about for over 100 years.

trout specimen found in the Smithsonian
Trout specimen at the Smithsonian National Museum of Natural History in Washington D.C.

The San Juan cutthroat’s story picks up again in 1978 when Mike Japhet headed west through a blizzard over Wolf Creek Pass to begin a position with the then Colorado Division of Wildlife as the first aquatic biologist based in Durango. His charge was to address sport fishing issues in the southwest region of the state but also to conserve native trout, something he was passionate about.

The playbook for cutthroat trout conservation at that time was pretty thin, but Japhet was inspired by his supervisor Lloyd Hazzard who had pioneered conservation work for native Rio Grande cutthroat trout. Japhet leaned heavily on Aldo Leopold’s conservation ethic. Leopold’s first rule of intelligent tinkering – “to keep every cog and wheel” resonated deeply with him. 

During routine conservation work, Japhet’s crew discovered a population of cutthroat trout in a very remote headwater stream. He did not have the genetic tools of today to assess whether these were pure fish or what their heritage might have been. Cutthroat trout look similar to each other in outward appearance, but the remote habitat they occupied suggested that they might be native and worthy of protection. 

Japhet knew that replicating this population on the landscape would help ensure its long-term survival. So he partnered with the U.S. Forest Service to use a helicopter to transplant some of these fish to a fishless stream nearby that had good habitat and was protected by an impassable downstream waterfall. This unidentified population of cutthroat trout thrived in their new habitat. 

Biologist Jim White and Mike Japhet
Biologist Jim White (front left) and his predecessor Mike Japhet (immediately behind Jim) probe the remote streams south of Pagosa Springs on their quest to find new populations of San Juan cutthroat trout

This little-known conservation story went unnoticed for 30 years until 2009 when Jessica Metcalf, who had just completed her doctoral studies at CU-Boulder in the Martin Lab, dusted off Charles Aiken’s 130-year-old specimen jars containing those two trout Aiken plucked from the San Juan River near Pagosa Springs. 

Metcalf hoped to collect DNA samples from the fish for a survey of native trout distributions in Colorado before European settlement. She examined Aiken’s specimens and discovered they were genetically distinct from cutthroat trout known to call the San Juan drainage home at the time. 

Unfortunately, a screening of existing trout samples revealed no modern matches to Aiken’s fish. At that point, Metcalf and her team concluded the trout was extinct. 

With the study revealing a previously unknown lineage of cutthroat trout native to the San Juan basin, an intensive search was launched to determine if any relict populations remained tucked away in the corners of the rugged San Juan Mountains of southwest Colorado.

Colorado Parks and Wildlife biologist Jim White shared Japhet’s passion for native trout. After he retired in 2008, White picked up where Japhet left off. Armed with access to powerful new molecular tools, he set out with hopes of rediscovering this fish. 

White and his crews scoured every stream in the San Juan basin, collecting fin clips from trout along the way for DNA analysis.

White’s efforts paid off, with a half dozen small trout populations he sampled sharing the genetic fingerprint with Aiken’s specimens collected over a century ago from Pagosa Springs. Two of those populations were ones that Japhet had secured 30 years earlier. The San Juan cutthroat trout was not extinct after all!

The rediscovery of the San Juan cutthroat trout is a celebration of basic conservation principles and shows why implementing conservation measures is so critical for perpetuating the wildlife resources of our great state. Without the dedication and passion of people like Aiken, Japhet, Metcalf, and White, one of Colorado’s cherished native fish might have slipped through the cracks and been gone forever.

Learn more about Colorado cutthroat trout conservation efforts on Colorado Parks and Wildlife’s website.

CPW 125th Anniversary Logo

Colorado Parks and Wildlife is celebrating its 125th Anniversary throughout 2022 to honor the legacy of our agency and the talented staff who make fulfilling CPW’s important mission possible. For more stories like this, please visit the Colorado Parks and Wildlife’s 125th Anniversary web page!


Written by Kevin Rogers. Kevin is an aquatic research scientist for Colorado Parks and Wildlife

2 Responses

  1. This is great! I’m a fly fisherman and this article makes me proud to be part of this great state. Thank you CPW.

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