Backcrossing to the Future

In New Mexico’s Gila National Forest, biologists use genetic intervention to save imperiled trout.

In the summer of 2018, a pair of fish biologists and a pair of horse packers embarked on an arduous 13-hour trek through a remote section of the 3.3 million-acre Gila National Forest in southwestern New Mexico, not far from the Arizona border.

“We rode mules the first five or so miles,” recalls Jill Wick, who managed the native fish program for the New Mexican Department of Game and Fish, “but had to continue on foot for the last several miles, basically bushwhacking our way through because there was no trail.”

hand holding gila trout
Listed as an endangered species in 1967, the Gila trout was one of the first fish to receive federal protections, even before the Endangered Species Act was enacted in 1973. Photo by Craig Springer/USFWS.

Eventually, Wick and company made their way to a primitive old Forest Service cabin on a ridge at the head of the deceptively named Big Dry Creek, where they spent the night. At dawn, as the first rays of sunlight streamed through the forest canopy, they hiked down to the water and dispersed across the stream, sporting waders and electrofishing gear. Before long, fish, temporarily stunned, began to float sideways to the surface, exposing iridescent gold sides.

By late afternoon, the team had collected about 50 fish in net pens. Eventually, a small helicopter arrived and descended onto a clearing near the creek. After being loaded into a 70-gallon aluminum tank attached to a 150-foot longline secured to the chopper, the fish were whisked off through the azure sky.

For those watching from the ground below, the hope was that some of these fish might help restore genetic integrity to a lineage of one the rarest trout species in the United States.

Listed as an endangered species in 1967, the Gila trout was one of the first fish to receive federal protections, even before the Endangered Species Act was enacted in 1973. The fish inhabits mountain streams within the Gila River and San Francisco River drainages in New Mexico and Arizona, though the extent of its historical distribution is not known with certainty. By the 1950s, though, severe habitat degradation and displacement by non-native trout had reduced its range to just five streams in New Mexico.

Today, conservation of the fish is guided by the US Fish and Wildlife Service’s Gila Trout Recovery Plan, last revised in 2003, and by a recovery team with members from the Service, the New Mexico Department of Game and Fish, the Arizona Game and Fish Department, the US Forest Service, and the University of New Mexico. Collaboratively, the team makes recommendations for conservation and recovery that are carried out on the ground by biologists and many others from the various partner agencies.

At the center of Gila trout recovery is the Mora National Fish Hatchery in northern New Mexico, where biologists maintain and breed captive populations of Gila trout. The work also includes an intensive regimen of stream restoration prescriptions in the wild. Measures include removing nonnative species and constructing barriers to prevent them from reinvading before returning native Gila trout to their ancestral streams. Altogether, such efforts have helped to fortify five remnant, genetically distinct lineages of Gila trout populations in 17 streams in New Mexico and five in Arizona. These lineages have evolved to accumulate variations in their genomes that, collectively, help the species as a whole.

In the last decade especially, though, conservation approaches have had to adjust to some extreme circumstances. In 2012, the largest wildfire in New Mexico state history, known as the Whitewater-Baldy Complex Fire, consumed nearly 300,000 acres in the Gila National Forest and destroyed half of all existing Gila trout populations on the landscape, which necessitated a series of urgent fish collection and captive breeding efforts.

Wick describes an apocalyptic scene the year after the fire, with the charred skeletons of trees and burnt stumps littering the landscape. “The ground was covered in ash, or bare rock almost everywhere, and in most places, there were just bare, dead trees as far as you could see,” she says. “The creeks were completely blown out — meaning no diversity in habitat, just a flat gravel bed with about an inch or two of water running over it. No pools or riffles, no vegetation, just bare.”

Fisheries specialist moving fish
In 2012, the largest wildfire in New Mexico state history, the Whitewater-Baldy Complex Fire, consumed nearly 300,000 acres in the Gila National Forest and destroyed half of all existing Gila trout populations on the landscape, which necessitated a series of urgent fish collection (pictured above) and captive breeding efforts. Photo by KC Shedden / USFS.

Prior to the 2012 fire, Mora had been maintaining two Gila trout lineages, says Trevor Luna, project leader at the Mora facility. “Since then, we’ve been maintaining fish from all five.”

Of those five lineages, one — “Spruce Creek” — was nearly wiped out completely by the fire. When wildfire decimates a fish population, the genetic diversity of the remaining population is proportionally diminished. And of the Spruce Creek fish, biologists have noted that they’ve been “very difficult to maintain and rear in captivity,” says Wick, adding that many have exhibited deformities, suggesting the lineage’s genetic makeup may be less than ideal. “They don’t look like high-quality fish.”

That’s part of the reason Wick endeavored to take some from Big Dry Creek two years ago, which was then the only stream that still contained the lineage. After the fish were airlifted out of the forest, some were translocated to their namesake waters in nearby Spruce Creek in order to repopulate it. Others were delivered to Mora to augment captive breeding efforts there — as well as to be included in an experiment intended to restore diversity to the strain.

Indeed, genetic analyses subsequently confirmed that these wild fish were no more diverse than the hatchery’s brood-stock, which originated from fish taken just after the 2012 fire. The lineage was deemed “genetically depauperate” in ichthyological vernacular — and in need of intervention.

Set on some 640 acres in the rural dairy farm country of New Mexico’s southeastern plains, in the town of Dexter (population 1,239), the Fish and Wildlife Service’s Southwestern Native Aquatic Resources and Recovery Center includes a fish culture facility, 76 fish culture ponds, and more than a million fish representing 14 different threatened and endangered species. The facility also houses a suite of laboratories with state-of-the-art equipment such as a MiSeq Next Generation Sequencer, which performs small genome sequencing and targeted gene sequencing; a bioanalyzer, used to analyze the quantity of RNA, DNA, and protein in a sample; and a real-time polymerase chain reaction system, which quantifies the number of DNA copies in a sample during replication.

Typically, the genetic project workflow starts when the lab receives tissue samples from a partner. In fish, this is typically a small fin clip preserved in 95 percent ethanol, explains Wade Wilson, a fish geneticist who serves as the deputy director for the Center.

“Before they get stored in upright freezers at -112 degrees Fahrenheit, fish samples are cataloged and given unique names to describe the species, whether the samples are wild or captive, year collected, and population name or facility name,” explains Wilson. For example, he points out the sample name “OgigW12LGC_001” which describes the first Oncorhynchus gilae (Gila trout) sample collected in the wild in 2012 from Langstroth Creek.

Wilson, in fact, has made Gila trout work a priority. The fish’s five lineages are important because their genetic distinction from each other makes the species, collectively, more capable of avoiding extinction, he explains. Because the five lineages each evolved in different watersheds over hundreds to thousands of generations, they adapted to what’s optimal for survival in their various areas. During this process, variations in their genomes accumulated.

“These genetic variations may be associated with water flow, water temperature, spawning time, proteins to digest or absorb certain food sources, or to fight disease, to name a few,” Wilson says. “Historically, there may have been a few individuals that could move from one population to another, but mostly the lineages were separate and evolved independently — with enough genetic differences to provide managers evidence that the lineages should be managed separately.”

But, as is said, desperate times, desperate measures. In relation to the beleaguered Spruce Creek lineage, the recovery team decided that, while still working to preserve the population’s distinctness, it was necessary to inject a measure of diversity into the gene pool. They agreed, females from the Spruce Creek lineage would be spawned with males from the “Whiskey Creek” lineage, which was selected for both its genetic diversity and its “middle-ground” proximity to Spruce Creek fish on the “family tree.” And, to preserve the unique Spruce Creek lineage genetics going forward, the new, more diverse offspring would subsequently be spawned back with pure Spruce Creek individuals.

“This is called backcrossing,” says Wilson. “Individuals from a mixed lineage are crossed back to one of the two pure parental lineages, in this case Spruce Creek and not Whiskey Creek.”

A caveat: “Once you spawn one lineage with another, you cannot fully recover what was unique,” Wilson says. “You can backcross to the lineage of interest, but the genomes will forever be combined to some degree.”

In the meantime, the backcrossing effort will require patience. The first generation of backcrossed fish were hatched last spring. Subsequent generations are expected once annually. And these fish will provide Wilson and his team with genetic samples to be catalogued and archived. According to Wilson, it will take some time to gauge the success of the backcrossing effort “since the genetic rescue of the lineage is expected to take several generations.”

At the same time, adds Wilson, “we as a team are still gathering information about what is or was on the landscape in Arizona and New Mexico, what is currently at Mora, and what cryopreserved milt [semen] we have available to us.” (The Fish and Wildlife Service’s Warm Springs Fish Technology Center, in Georgia, stores Gila trout milt in a cryopreservation lab.) “Each year we will take this information and adapt our original plan as needed to keep the lineage moving forward. Recovery of the species is a challenging and adaptive process.”

Wick readily agrees that recovery work for the species has had to adapt. “We focused more on replicating single lineage populations in the past but as we learn more about these fish, as we lose more individuals and encounter difficulties propagating them, and as we discover the loss of genetic diversity encountered after the fires, of all lineages, we’re beginning to realize that mixing lineages may be a more appropriate way to conserve the species as a whole,” she says. “Backcrossing is an experiment, we don’t really know if it will work, but it’s something worth trying and it has worked for other species.” (The strategy has been used to help conservation of the Florida panther, among other species conservation efforts.)

Like Wick, Wilson is cautiously optimistic: “There are numerous talented, dedicated and passionate people involved in the process, so I’m hopeful recovery is moving forward in a positive way. It may not be the same path the species was on prior to the 2012 fire and subsequent fires, but it’s a path forward.”

As if mirroring nature itself, the work to conserve the species — from putting sample specimens through the automated DNA sequencing machine in Dexter; to maintaining and breeding fish at Mora; to collecting wild fish from their diminished range in New Mexico’s most far-flung streams — is likewise evolving.

“As we learn new things and encounter new obstacles, such as wildfire or loss of genetic diversity, we have to adapt how we manage and conserve the species,” Wick says. “That is an ongoing lesson and, generally, the lesson of science.”

You Make Our Work Possible

You Make Our Work Possible

We are standing at a pivotal moment in history, one in which education and advocacy around the climate emergency, public health, racial injustice, and economic inequity is imperative. At Earth Island Journal, we have doubled down on our commitment to uplifting stories that often go unheard, to centering the voices of frontline communities, and to always speak truth to power. We are nonprofit publication. We don’t have a paywall because our mission is to inform, educate and inspire action. Which is why we rely on readers like you for support. If you believe in the work we do, please consider making a tax-deductible year-end donation to our Green Journalism Fund.

Get the Journal in your inbox.
Sign up for our monthly newsletter.

The Latest

Older Black Farmers See Little Hope in Biden’s Agriculture Pick

Black farmers have been disregarded by the USDA for years. Will anything change in Tom Vilsack’s second stint?

Summer Sewell The Guardian

From Cradle to Grave

To get to a healthier pattern of consumption, to complete the cycle and close the loop, we’ve got to get used to passing things on again.

Sandra Goldmark

Wildfire, Landslides Threaten California’s Endangered Black Abalone

In the wake of a record-breaking wildfire season and an intensifying rainy season, debris flows wreak havoc on Big Sur's rocky intertidal habitats.

Anne Marshall-Chalmers

Her First Ski Home

Our child may not remember individual moments in the Alaskan backcountry, but they will wire her mind to the outside world.

Tim Lydon

Not Another Brick in the Seawall

In a beach village in Japan, surfers and scientists oppose a proposed seawall that would threaten an important coastal ecosystem.

Kim Feldmann

No, Frozen Wind Turbines Aren’t the Main Culprit for Texas’ Power Outages

Lost wind power makes up only a fraction of the reduction in power-generating capacity that has brought outages to millions of Texans across the state during a major winter storm.

Erin Douglas Ross Ramsey The Texas Tribune