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The Nevada Independent

One recovery effort, two strains of fish. The complex comeback of Lahontan cutthroat trout

Once-endangered fish is recovering along the Truckee River — but is it sustainable without human intervention?
Amy Alonzo
Amy Alonzo

It’s spawning day at the Lahontan National Fish Hatchery Complex, and volunteers clad in rubber boots and jackets move quickly around the south Gardnerville building, fishing nets in hand.

They swoop the nets into giant pools of water chilled to mimic temperatures found in local waterways, extracting mature male Lahontan cutthroat trout one at a time. The fish, which are sedated but still active, squirm as they are carried across the hatchery.

There, a group of biologists waiting to handle the fish reach into the nets, gently extract a fish, and begin massaging its abdomen from head to tail, manually extracting milt — the semen-filled fluid of male fish. The milt is stored in small vials marked with letters and numbers like a game of bingo — G83, H24, F17 — and is later manually mixed with the eggs of fish deemed genetically compatible.

The biologists handle each fish for only a matter of seconds, but there are hundreds of trout, and the process takes hours.

“We know what male is spawning with what female, which doesn’t normally happen in a hatchery,” said U.S. Fish and Wildlife Service project leader Lisa Heki. “It’s not random.” 

It’s a scene that plays out once a week from early February through mid-May in an elaborate effort to breed pure Pilot Peak Lahontan cutthroat trout, a unique strain adapted to grow large and live long. According to the service, the Pilot Peak strain directly descended from trout that once swam in Pyramid Lake before the fish were believed to be extirpated from the Truckee River corridor. 

Miles from the hatchery and much closer to the original spawning grounds of the Lahontan cutthroat trout, members of the Pyramid Lake Paiute Tribe spawn trout of their own.

The fish don’t spend their lives in a hatchery. Instead, each spring they swim upstream from Pyramid Lake, blocked from going further than 3 miles up the Truckee River by the Marble Bluff Fish Passage and Research Facility. 

Although the facility has a passageway for fish to move upstream, only select Lahontan cutthroat trout raised at the Gardnerville hatchery move past Marble Bluff. Fish that were raised by the tribe instead swim into a manmade channel, where staff net and spawn them before returning them to Pyramid Lake 

The federal and tribal spawning operations are vital in the ongoing recovery of a population of fish that is culturally significant to the tribe and valuable to sportsmen, but it’s unclear whether the fish — once listed on the federal endangered species list and since downgraded to threatened — can continue to rebound without such intensive human intervention.

Preserving populations

Lahontan cutthroat trout are the only trout native to the Tahoe Basin. The largest cutthroat trout species in the world, they grow half an inch per year in the wild and are known for reaching 4 feet in length.

They evolved in ancient Lake Lahontan, which spanned more than 8,600 square miles of the western Great Basin. As the lake dried up thousands of years ago, the trout persevered in the region’s remaining waterways.

Prior to European settlement, it is believed the fish occupied more than 7,400 miles of streams and numerous lakes. As Europeans settled in the region, the fish population steadily declined due to the introduction of nonnative fish, overharvesting, mining, water diversions and dams.

The 1905 construction of the Derby Dam on the Truckee River proved particularly devastating to the trout. It diverted nearly 50 percent of the river’s water, and the last natural run of Lahontan cutthroat trout down the Truckee River was in the 1940s.

For decades, there were few, if any, Lahontan cutthroat trout in Pyramid Lake, according to Chris Crookshanks, fisheries division administrator for the Nevada Department of Wildlife. But in the 1970s, Lahontan cutthroat trout were pulled from other Northern Nevada lakes to build up the population at Pyramid Lake and, in 1973, Pyramid Lake Fisheries was formed. 

Around the same time, a federal biologist discovered fish in remote Morrison Creek on the Nevada-Utah border that looked like trout — but not the Bonneville cutthroat trout he was looking for. They looked like Lahontan cutthroat trout, yet they weren’t in a waterway considered part of their native range.

There were no live samples to compare DNA with, so samples were compared to museum specimens of Lahontan cutthroat trout harvested between 1872 and 1911. Genetic testing confirmed the remote desert fish were descendants of the Lahontan cutthroat trout that once called Pyramid Lake and the Truckee River home.

In 1995, fertilized eggs from the remote fish — dubbed the Pilot Peak strain after a nearby mountain — were transported back to Northern Nevada. That effort was the start of the now expansive hatchery program in Gardnerville. In 2006, the U.S. Fish and Wildlife Service and the Pyramid Lake Paiute Tribe restocked the Pilot Peak strain back into Pyramid Lake.

The next year, a fire burned through the Morrison Creek area. Few Lahontan cutthroat trout survived, according to Danelle Lloyd, hatchery manager.

“That is why these types of programs can be instrumental in preserving these populations,” she said.

Map of the Truckee River Basin. (Courtesy U.S. Geological Survey)

Maintaining genetic diversity

Each spring, hundreds of thousands of Lahontan cutthroat trout — both Pilot Peak strain and not — are stocked into water across Nevada and Eastern California, including nearly a half million in Pyramid Lake alone. 

The fish were listed as endangered in 1970, but in 1975, they were reclassified as threatened, opening them to recreational fishing, and the lake, as well as the Truckee River, are now renowned angling destinations. 

The Gardnerville hatchery’s broodstock — the mature, genetically sorted fish used for breeding — will never be planted in Pyramid Lake or Tahoe. Those fish will be used as broodstock for the duration of their lives — about five to six years at the hatchery — to continue producing what Heki describes as genetically strong offspring.

Each of the hatchery’s mature fish is tagged and has a clipped fin. Before the fish spawn, fin clippings are sent to a lab in Montana that determines the best crosses to get maximum genetic diversity and prevent inbreeding of the fish.

“We’re not directing the genetics here, but we are trying to maintain the genetic diversity,” said Jason Smith, the hatchery’s broodstock coordinator.  

The hatchery has done a good job maintaining that diversity, said Jason Barnes, a biologist with Trout Unlimited who focuses on Lahontan cutthroat trout. 

“In the wild, those genes would plummet,” Barnes said. 

After the milt is extracted from the males and eggs are extracted from females, the two are mixed in plastic bags and the fertilized eggs are placed in trays where they develop into “eyed eggs” — eggs that appear to have tiny eyes in them — and then fry. As fry — tiny fish — they live in large troughs filled with grooves that mimic the protection that gravel and small rocks would provide in the wild.

About 150 of the thousands of new offspring produced this year will be kept on-site and raised to replace the broodstock that is aging out, separated, as are all the fish, by age and gender. By about 3 years of age, they will be ready to spawn. 

The Gardnerville hatchery’s process is effective but goes against nature, according to officials from the Pyramid Lake Paiute Tribe. The fish that swim into the tribe’s channel are those that nature has chosen, they say, rather than those that are artificially selected by scientists, and their reproduction and survival should not hinge on humans. 

Brandon Brady, right, a Pyramid Lake Paiute Tribe member, sorts fish during spawning activities at the hatchery at Pyramid Lake in Sutcliffe on April 4, 2024. (David Calvert/The Nevada Independent)

Locked out of the Truckee River

Pelicans swoop overhead and buzzers sound at the Marble Bluff Fish Passage Facility. Just 3 miles upstream from Pyramid Lake, the facility plays a pivotal role in which Lahontan cutthroat trout can spawn upstream and which can’t. 

Prior to the 1900s, Lahontan cutthroat trout would travel as far as the Sierra Nevada to spawn — more than 100 miles upstream.  

After Derby Dam was built, Truckee River water was diverted throughout the region, resulting in lowered flows to Pyramid Lake. With the lowered flows, a large sandbar formed at the mouth of the river, blocking upstream migrations except in high flow years.

In 1975, Marble Bluff Dam was built 3 miles above Pyramid Lake to help manage the sandbar problem. Its associated facility allows fish to move upstream through a passageway with a contraption similar to an elevator, added to the facility in 1998. The elevator can hold up to 3,000 cui-ui, a type of sucker fish found only in Pyramid Lake, or up to 120 of the much larger Lahontan cutthroat trout. 

But the elevator doesn’t just move the fish upstream — that could be accomplished with a simple fish ladder. Instead, the elevator deposits them into holding pens, where biologists measure their length, weight and sex. They also note which trout were raised in the hatchery, and which were not.

The fraction of fish that are determined by Marble Bluff biologists to be Pilot Peak strain are dropped into a tube that connects to the Truckee River upstream of the dam, where they can swim upstream and spawn; the fish of questionable heritage are deposited back in the river below the dam.

Installed in 2016, the tube is touted by federal fish managers as the key to creating a pure strain of Lahontan cutthroat trout that will repopulate the Truckee River on its own.

But to others involved in the fish’s recovery, the tube represents a hindrance that focuses too much on the Pilot Peak strain and not enough on the recovery of the species as a whole.

Mike Sevon, retired fishery supervisor for the Nevada Department of Wildlife’s Western Region, recalls more than a decade ago watching members of the U.S. Fish and Wildlife Service extract federally-raised fish from the tribal spawning channel so that those raised in the Gardnerville hatchery did not mix with non-hatchery fish. 

The Gardnerville fish come from a strain Sevon describes as “special” and “the real deal.” But he doesn’t believe they should be separated from other Lahontan cutthroat trout.

“I don’t see anything wrong with mixing up fish that traditionally were in the headwaters of the Truckee and the Pilot Peak lacustrine (lake) fish,” Sevon said.  

Letting nature prevail

Driving along Interstate 80 east of Reno, Heki, the Fish and Wildlife project leader, points to stands of cottonwoods and gravel bars. They didn’t exist when she started her career decades ago. Instead, they were developed and planted over the years to facilitate Lahontan cutthroat trout spawning and provide bank stability and shade to cool the fish — a shift in the way the river was utilized.

For much of the 20th century, the Truckee River was viewed as little more than a ditch conveying water to downstream agricultural users, Crookshanks said. Habitat and wildlife were rarely considered as more and more water was diverted for agriculture. 

That mindset shifted in the late 20th Century, as officials and lawmakers sought a balance between preserving natural resources and agricultural needs. 

Those river enhancements include efforts to aid fish seeking to move upstream. 

In 2020, a fish bypass at Derby Dam opened to allow fish to swim past the dam for the first time in more than a century. 

And last year, the Pyramid Lake Paiute Tribe secured nearly $8.3 million from the federal Bipartisan Infrastructure Law to build a rock ramp at Numana Dam, located between Pyramid Lake and Derby Dam, to help fish swim past the diversion.

But the further the fish stray from Pyramid Lake, the more likely they are to spawn with nonnative fish such as rainbow trout

Nonnative fish — including rainbow trout — were introduced to the Truckee River more than a century ago. Having thrived in the river for so long, the state department of wildlife considers them “naturalized.” 

Sometimes, rainbow trout wash down toward Pyramid Lake near the mouth of the river, Barnes said. Although the lake’s salinity prevents them from living in the lake, they can survive in the lower stretches of the river during the spring before the water temperature gets too high, allowing them to mix with some Lahontan cutthroat trout.

Further upstream, rainbow trout thrive in less saline water. As the Pilot Peak strain make their way up the river to spawn, they can mix with the rainbow. About 8 percent of recently studied river Lahontan cutthroat trout were hybridized, according to Barnes. 

There are also brown trout, which spawn in the fall and don’t represent a hybridization problem for the Lahontan cutthroat trout — but do represent a predatory threat.

“[Wildlife managers] can’t get rid of them, and the cutthroat can’t compete with them,” Sevon said. 

Moving forward, the goal is to achieve a naturally reproducing population of the Pilot Peak strain in Pyramid Lake and the Truckee River, Heki said, and rangewide to have the fish recover enough so they can be delisted.

But a self-sustaining population would negate the need of the elaborate efforts at the hatchery, which, along with the Marble Bluff Fish Passage Facility and its associated conservation office, received $6.3 million in funding last year.

Sevon said he doesn’t see a self-sustaining population coming back to the river. There are too many obstacles, including the nonnative fish in the Truckee River that threaten to spawn with the Lahontan cutthroat trout and create hybrids. 

“We tried to explain to the Fish and Wildlife Service when they proposed all of this, that their objective will never be met without using that hatchery until the end of time,” he said.

What the fish are left with is a mishmash of plans to propel their populations forward, with diverse groups each doing what they believe is best for the Lahontan cutthroat trout.

“In the end, there’s just a whole bunch of us who care about the fish,” Sevon said. 


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