Click the link to read the article on the High Country News website (Christine Peterson, Photography — Louise Johns):

January 1, 2025

The prairie dog caught in Trap 69 was angry. And who could blame her? After waking up in her burrow on a mid-September morning, she’d waddled innocently outside for a breakfast of mini marshmallows and carrots, only to find herself stuck in a wire cage and carried across the prairie. Then a pair of human hands had gripped her like a burrito while two more hands put a black rubber tracking collar around her neck. 

The situation was worse than she realized: Prairie dogs are among the most maligned and persecuted animal species in the Western U.S. So maligned, in fact, that a 2020 survey in northern Montana found that well over half the area’s landowners believed prairie dogs should not live on public land. 

To make matters even grimmer, this particular prairie dog had fleas. And those fleas could have been carrying the bacteria that causes plague — the Black Death. “It’s not great,” commented researcher Jesse Boulerice as he adjusted his gentle grip around her midsection.

The rodent responded by biting into Boulerice’s leather glove, hanging on with her two front teeth while researchers swiped a black streak of Clairol’s Nice’n Easy hair dye down her back. 

Though black-tailed prairie dogs have a long-standing reputation as pests, their ingenious tunnel systems and industrious prairie pruning make them one of the West’s primary ecosystem engineers. Some researchers call them the “chicken nuggets of the prairie”; if a prairie species eats meat, it almost certainly eats prairie dogs. Without prairie dogs, black-footed ferrets would never survive outside zoos and breeding facilities, and we would have far fewer mountain plovers, burrowing owls, swift foxes, and ferruginous hawks. 

Before 1800, an estimated 5 billion prairie dogs lived from Canada to Mexico, covering the West with underground apartment complexes that shifted over the centuries like sand dunes. The Lakota, Dakota and other Indigenous peoples of the prairie shaped and depended on the ecosystems prairie dogs created. Some relied on prairie dogs for nourishment during thin times, or used them as a ceremonial food. 

But European settlers were remarkably effective at shooting and poisoning prairie dogs and plowing up their burrows. Today, the five prairie dog species occupy just 2% of their historic range, and some occupy even less. 

Prairie dogs still survive in many of their historic territories: Black-tailed prairie dogs, known for their especially large, dense colonies, persist in isolated pockets of the prairie east of the Rocky Mountains from Canada to Mexico. White-tailed prairie dogs live in parts of Montana, Wyoming, Utah and Colorado. Gunnison’s prairie dogs eke out an existence in southern Colorado, and Utah prairie dogs live in, well, Utah. Mexican prairie dogs still hang on in small slices of northern Mexico. But many of these populations are too small to serve their ecosystems as they once did.

Within this familiar story of colonization and species decline, however, are more hopeful stories of creativity and adaptation: Researchers are using pedometer-like devices to map prairie dogs’ underground tunnels, remote-controlled badgers to understand prairie dog alarm calls and Kitchen-Aid mixers to craft solutions to deadly disease. After decades of restoration work by tribal wildlife managers, prairie dogs, black-footed ferrets, swift foxes and bison are once again roaming the Fort Belknap Indian Reservation in north-central Montana, one of the few places in the world where all four species coexist. Some private landowners, meanwhile, are finding ways to tolerate the rodents. Together, these researchers, managers and landowners are striving to conserve the West’s remaining prairie dogs and the prairie that depends on them. 

ONCE THE COLLARED prairie dog was returned to her Tru Catch wire cage to await release, Boulerice reached into the next trap in line. 

Boulerice is part of a team from the Smithsonian’s National Zoo and Conservation Biology Institute that is collaring and tracking prairie dogs at American Prairie — formerly the American Prairie Reserve — in central Montana. Each collar measures the animal’s acceleration and angle; by triangulating with locations picked up by sensors posted on poles throughout the colony, researchers can determine where and how far the prairie dogs travel both above and below ground. The Clairol dye patterns provide one more way to tell who’s who in a colony of look-alikes. 

Though other researchers have studied prairie dogs’ aboveground lives, no one really knows what they do underground. Satellite imagery can be used to track Arctic terns over Alaska or grizzly bears deep in the wilderness, but it can’t penetrate the Earth. Decades ago, researchers laboriously excavated a white-tailed prairie dog burrow in southern Montana, revealing features like “sleeping quarters,” hibernacula, and a “maternity area” — but such work is invasive and yields little data on the animals’ movements. 

At American Prairie in September, the Smithsonian team was joined by researchers from Swansea University in Wales who had developed the tracking collars Boulerice used. The collars were originally designed to study penguins underwater, an environment similarly resistant to conventional satellite tracking.  

Prairie dogs aren’t the only occupants of prairie dog burrows. The mazes of tunnels and rooms also provide shelter for black-footed ferrets, swift foxes and untold numbers of insects. Burrowing owls shimmy their puffball bodies into the tunnels, where they raise their chicks on the plentiful bugs. Prairie rattlesnakes, tiger salamanders, horned lizards and badgers use them, too. 

And as climate extremes become more common aboveground, these burrows may become even more important. 

“By creating tunnels, they’re also creating a thermal refuge,” said Hila Shamon, the director of the Smithsonian’s Great Plains Science Program and principal investigator of the colony-mapping project. “The prairie can be so hot in the summer or brutally, brutally cold in the winter. You don’t have any shade or place to hide from the cold … and conditions in the tunnel systems are consistent.”

Prairie dogs spend much of the day and all night in their burrows, living in family coteries composed of one male, three or four females and the year’s young. Their tunnel systems, which can extend across an area larger than  a football field, are like bustling apartment complexes where every family has its separate unit. Residents periodically pop out of doors to grab food, gossip about the neighbors and scan for danger. 

“In the prairie,” Shamon said, “there’s a whole world that’s happening beneath the ground that we can’t see. But it exists, and it’s very deep, and it’s important.”

Aboveground, the effect of prairie dogs on the landscape is more obvious. “Prairie dogs create an entirely novel habitat type,” said Andy Boyce, a Smithsonian research ecologist. “They graze intensely. They increase the forbs and flowering plants, and they clip woody vegetation. They will eat and nibble on a new woody plant until it tips over and dies.”

The landscape created by prairie dogs may look barren, but the reality is more nuanced. A healthy prairie isn’t an uninterrupted sea of grass; it’s  made up of grass and shrubs, wetlands and wildflowers and even large patches of bare dirt that allow prairie dogs — and other species — to spot approaching predators. 

Bison like to wallow in the dirt exposed by prairie dogs, and graze on the nutritious grass and plants that resprout after a prairie dog pruning. Mountain plovers and thick-billed longspurs frequently nest on the grazed surface of prairie dog towns. (Both birds have declined along with prairie dogs; the mountain plover has been proposed for protection under the Endangered Species Act.) 

Prairie dog colonies may also provide other species with a home-alarm system. “You have 1,000 little pairs of eyeballs constantly searching for predators all around you and then vocalizing loudly when they see them,” Boyce said. To test this hypothesis, Boyce’s Ph.D. student Andrew Dreelin attached a taxidermied badger to a remote-controlled car and drove it near long-billed curlew nests in Montana prairie dog colonies. He then measured how nesting curlews responded to the badger with and without a warning from the prairie dogs. 

Results are pending, said Dreelin, but he’s certain that “we’ve only just started to scratch the surface on the multifaceted ways that prairie dogs could shape the lives of birds on the prairie.” 

IN EARLY OCTOBER, about 500 miles south of American Prairie, Colten Salyer also donned thick leather gloves to protect himself from an angry mammal’s teeth. Then he opened a cat carrier filled with paper shavings and a member of a species once considered extinct. 

The young black-footed ferret inside bared its long white canines. Bred at the National Black-Footed Ferret Conservation Center in northern Colorado, she was one of 20 about to be reintroduced to southcentral Wyoming’s Shirley Basin.

The black-footed ferret is North America’s only native ferret and one of only three ferret species in the world. And if there’s one thing black-footed ferrets need, it’s prairie dogs. They eat them almost exclusively, and they use their tunnels to live, hunt and reproduce, slipping in and out of burrows as they move like water across the landscape. 

In 1980, black-footed ferrets were declared extinct, most likely extinguished by disease, development and endless prairie dog poisoning campaigns. But in 1981, a northern Wyoming ranch dog proudly presented his owners with his most recent treasure: a dead ferret. A local taxidermist confirmed that it was, in fact, a black-footed ferret, a member of a tiny remnant population. 

The newly discovered ferrets lived in the wild until 1985, when biologists discovered that disease had killed all but 18. At that point, they scooped up the remaining ferrets and took them to captive breeding facilities. Only seven successfully reproduced, but those seven now have more than 11,000 descendants. In 2020, researchers used DNA from a wild-caught ferret with no surviving offspring to produce the first cloned ferret. Since then, they have created two more cloned individuals, and this past November, the U.S. Fish and Wildlife Service announced that one had given birth to healthy kits.

Captive-bred ferrets have now been released across the West. But to survive long-term, they need prairie dog colonies. And prairie dogs aren’t popular with their human neighbors. 

Because they eat the same grass cows do. And they make holes. 

“I was running to rope a yearling once, and I stood up in the saddle and was about to open my hand — and all of a sudden the horse’s front end disappeared,” said Salyer, a ranch manager in Shirley Basin who volunteered to help with the releases. His horse had sunk a hoof into a prairie dog hole, a misstep that sent Salyer tumbling to the ground.  

Both Salyer and his horse were fine, and he shrugged after telling the story.But most ranchers have, or have heard, similar stories, many of which end with a valued horse breaking a leg. There’s no way to know how frequently horses injure themselves in burrows, but the stories spread as fast as a prairie fire. 

What’s certain is that prairie dogs eat grass. Quite a bit of grass: A single prairie dog can devour up to 2 pounds of green grass and non-woody plants every week, according to Montana State University. For ranchers who use that vegetation to feed their cows, prairie dogs look like competition. Researchers, however, say the effects of prairie dogs on livestock forage are mixed. Black-tailed prairie dogs’ propensity to clip and mow, for instance, results in plants with higher fat and protein and lower fiber. “Across years, enhanced forage quality may help to offset reductions in forage quantity for agricultural producers,” a study published in 2019 by Rangeland Ecology and Management reported.

This uncertainty has led to some bureaucratic contradictions. The Wyoming Department of Agriculture labels prairie dogs as pest species and offers training in properly using pesticides to kill them; at the same time, the Wyoming Game and Fish Department lists the black-tailed prairie dog as a species of greatest conservation need. 

Until the 1990s, said Randy Matchett, a Fish and Wildlife Service biologist in central Montana, prairie dogs were so despised in places like Phillips County, Montana, that the Bureau of Land Management produced maps of their colonies designed for sport shooters. Attitudes haven’t changed much: In 2020, 27 years after an initial survey of attitudes toward black-tailed prairie dogs and black-footed ferrets in Montana, researchers found that feelings about them had barely budged. 

Matchett said that when he tells his Montana neighbors that only 2% of prairie dogs remain, a common attitude is: “What the hell’s the holdup getting rid of that last 2%?”

Chamois Andersen, a Defenders of Wildlife senior field representative, has spent decades working with landowners in prairie dog-rich places, and she’s persuaded some to allow researchers to survey their land for black-footed ferrets in exchange for funds for noxious weed removal. She speculates that younger generations of ranchers are more open to prairie dog conservation and to partnerships with public agencies and wildlife groups.

Matchett is less optimistic. Even the U.S. Forest Service and National Park Service, which together manage one of the largest black-footed ferret colonies in the world in South Dakota’s Conata Basin, poison some prairie dogs on federal land to prevent the population from moving onto private property.

Not all prairie dogs are equally reviled. White-tailed prairie dogs like those in Shirley Basin live at lower densities and tend to clip plants farther up the stems, making them less obvious to the casual observer. Landowners, as a result, are often more tolerant of them than their black-tailed cousins, said Andrew Gygli, a small-carnivore biologist for Wyoming Game and Fish. 

Bob Heward, whose family started ranching in Shirley Basin more than a century ago, understands that a disliked species can also be useful. 

He invites recreational shooters to target prairie dogs on his land, but he won’t use poison to kill the rodents because he knows they provide food for other species. Prairie dogs are a “nuisance,” he said, but they’re also as inevitable as the wind: “We’ve learned to live with them. They’ve been here longer than I have.”

THE MALE SWIFT FOX at the end of the trap line was chunky, at least by swift fox standards: Though he weighed only about 5 pounds, his belly was round beneath his fluffy fur. His black eyes carefully followed Smithsonian researcher Hila Shamon as she loaded him into the backseat of her four-door pickup, covering the trap with a blanket as she prepared to transport him from this ranch north of Laramie, Wyoming, to a new home on the Fort Belknap Indian Reservation in Montana. 

Unlike black-footed ferrets, swift foxes can survive without prairie dogs, but when prairie dogs are scarce they suffer from the loss of food, Shamon said, and are deprived of the shelter they find in prairie dog burrows. So they, too, declined as prairie dogs were exterminated and prairie habitat was converted into cropland. By the early 1900s, they had disappeared from Canada, Montana, North Dakota, Nebraska, Kansas and Oklahoma. 

But swift foxes still live in parts of the West — and in some places, their populations are being restored. For the last five years, Shamon and her team have trapped swift foxes in Wyoming and Colorado and trucked them to Fort Belknap. This rectangle of grassland, buttes and prairie breaks near the Canadian border is home to the Nakoda (Assiniboine) and A’aninin (Gros Ventre), both Great Plains peoples. Today, it is one of the only places in the world where prairie dogs, swift foxes, black-footed ferrets and bison co-exist. 

Montana State Sen. Mike Fox (Gros Ventre), D, who served as Fort Belknap’s director of Fish and Wildlife from 1991 to 2001, oversaw early efforts to restore buffalo, swift foxes and black-footed ferrets to the reservation. The goal was to “create a steady, healthy population of native animals that were driven to extinction because of the different uses of the land,” he said. “Like when they started poisoning the prairie dogs off in the ’30s and ’40s and wiped out the ferrets that were native here, and the same with the swift fox. We want to make as complete an ecosystem as we can, along with the buffalo.”

The tribes worked with the Fish and Wildlife Service to reintroduce black-footed ferrets, and, with researchers at the Smithsonian, World Wildlife Fund and other organizations, to bring back the swift fox. The collaborators spent two years planning the swift fox capture and translocation, Shamon said, considering factors like habitat quality, community attitudes and the overall risk to a re-established population. 

Swift foxes had already been reintroduced in parts of Alberta and Saskatchewan and on the Blackfeet and Fort Peck reservations. The reintroduction at Fort Belknap continued the tribes’ restoration efforts and added a possible point of connectivity for other populations. 

Tribal members living on and near the Fort Belknap Reservation have largely supported the reintroduction of native prairie species, especially after prairie dog numbers were diminished by an outbreak of disease in the late ’90s, Fox said. Now that the population is recovering and has started to clear larger areas of grass, however, some tribal members who raise cattle have begun expressing frustration to the tribal council. 

“Wildlife and cattle will graze prairie dog colonies because of the new growth coming back throughout the year,” said Fox. “It makes it look even worse because it’s attractive to wildlife and domestic cattle, and they do their part. When it starts looking like a moonscape is when we get people noticing the most.”

He tells people that the little grass-eating rodents are necessary, and notes that the “moonscapes” aren’t as widespread as they may seem. But like non-Native ranchers across the West, some tribal members equate abundant prairie dogs with fewer cows. Fox doesn’t believe the council will allow widespread prairie dog poisoning on tribal lands — especially since the reservation now hosts black-footed ferrets — but he does worry that opposition could intensify.

Bronc Speak Thunder (Assiniboine), director of the Fort Belknap Buffalo Program, has also heard people complain about prairie dogs, though he added that “people complain about a lot of stuff.”

The tribes aren’t actively restoring prairie dogs, he said; they’re simply refraining from poisoning and shooting them. He sees that prairie dogs benefit tribal land by creating more habitat for ground-nesting birds and serving as food for swift foxes, coyotes, hawks and eagles. They also encourage the growth of nutritious grass for bison. “Like life, it’s a big circle, and that’s where it fits,” he said. “They’re part of the ecosystem that exists, and if you take something out, it throws everything off.”

WHEN I MET Randy Matchett, the Fish and Wildlife Service biologist, he sported a cowboy hat and graying horseshoe mustache and carried a handful of Smurf-blue flea-control pellets, each slightly smaller than a marble. The pellets, which Matchett produced in his workshop at the Charles M. Russell National Wildlife Refuge headquarters in Lewistown, Montana, are his latest attempt to protect prairie dogs from a fatal disease.

The pellets contain Fipronil, an insecticide used in treatments likeFrontline to keep fleas and ticks away from household pets, and are flavored with peanut butter and molasses to increase their chances of ending up in prairie dog bellies. Matchett dyes them blue because research shows prairie dogs are attracted to the color, and because the dye stains their feces, making it easy to estimate how many animals have consumed the pellets. Once ingested, Matchett hopes, his “FipBits” will kill the fleas that land on and bite prairie dogs, including the fleas carrying the bacteria that causes plague. 

Yes, that plague. The bacte-ria Yersinia pestis causes bubonic plague, which became known as the Black Death after it killed at least 25 million Europeans during the 14th century.

In 1900, the disease arrived in North America via San Francisco, carried by rats stowed away on ships. During the following decades, the development of antibiotics controlled the disease in humans, but plague continued to spread among rodent species, affecting black-footed ferrets, rabbits and squirrels. First detected in prairie dogs in 1936, it devastated populations already hit hard by the conversion of the prairie to agriculture — and it remains a major threat to prairie dogs.

“Once colonies have plague, they can disappear in two weeks,” said Shamon. “There will be thousands of acres chirping with thousands or tens of thousands of animals and in two weeks, you will go map it, and they’re gone.”

A plague vaccine does exist, and is used to protect highly endangered species like black-footed ferrets. But it’s simply not possible to jab every prairie dog in the West. Matchett, who as a Fish and Wildlife biologist is responsible for conserving endangered species, got involved in plague prevention in the early 1990s, initially dusting prairie dog colonies for fleas. In 2013, he began testing oral vaccines in Montana colonies, working in parallel with researchers in seven other states. The first-generation vaccines were red, peanut-butter flavored cubes with a biomarker that tinted prairie dog whiskers pink. Matchett and his colleagues in Colorado also developed vaccine pellets that they mass-produced using a Lithuanian carp bait-making machine. Matchett helped craft a pellet shooter that could be bolted to the front of a four-wheeler.

With the new vaccines primed to launch, Matchett felt hopeful. The World Wildlife Fund, which helped fund some of the work, felt hopeful, too. But in 2018, after years of trials with thousands of prairie dogs, he and other researchers concluded that even when a colony was given oral vaccinations, the number of prairie dogs that survived a plague outbreak was too small to support a black-footed ferret population. 

So Matchett pivoted. If he couldn’t inoculate prairie dogs against plague, maybe he could kill the fleas that carried the bacteria. What if he could persuade prairie dogs to eat Fipronil? 

He made a new set of pellets with the same bait machine, this time using his wife’s grandmother’s Kitchen-Aid mixer to blend various types of flour, vital wheat gluten, peanut butter, molasses and other food-grade ingredients with a soupçon of flea killer. Early results have been promising: While adult fleas aren’t affected until they bite a prairie dog that’s ingested a pellet, not every flea needs to be killed; studies have shown that in general, fleas don’t trigger plague outbreaks until they reach a critical mass. And flea larvae appear to die when they crawl into or consume treated prairie dog poop, suggesting that the pellets could tamp down flea reproduction as well as kill the adult insects. 

FipBits aren’t the only way to reduce the toll plague takes on prairie dogs, but Matchett believes they’re the most likely to work. In his office, perched on stacks of files, are the remnants of another of his many assaults on the problem: dozens of vials of alcohol, each containing bits of prairie dog ears. In 2007 and 2008, Matchett and his colleagues collected the snippets from prairie dogs that had survived plague outbreaks, hoping genetic analysis would explain their fortitude. The material has yet to be analyzed owing to a “combination of lack of funding, interest, time and capability,” Matchett said, but he hopes new funding will allow him and his collaborators to return to the project.

Despite the setbacks, Matchett believes researchers can find a way to control plague in prairie dogs. Human intolerance, as he sees it, is a more stubborn problem. Places like Fort Belknap and the Conata Basin of South Dakota — where prairie dogs are, at least for now, allowed to flourish — remain few and far between. 

DRIVE SOUTH from Fort Belknap down Highway 191, head east on a straight gravel road, and you’ll find one more place where prairie dogs are left in peace.

American Prairie began in 2001 as an effort to protect and restore Montana’s grasslands. The nonprofit now manages more than 527,000 acres of private land and federal and state leases. Its ultimate goal is to connect 3.2 million acres of prairie, providing habitat for an array of species from bison to mountain plovers to black-footed ferrets. To the casual observer, American Prairie’s lands may already look like intact prairie, though ecologists like Daniel Kinka can’t help noticing the nonnative crested wheatgrass and the hundreds of miles of fencing. 

“This is kind of like the Field of Dreams model: If you build it, they will come,” said Kinka, American Prairie’s director of rewilding. “A better habitat houses more wildlife, and the wildlife that are here are perfectly capable of restoring themselves.”

American Prairie prohibits the poisoning and shooting of prairie dogs on its land, and it regularly hosts research projects such as the Smithsonian’s burrow mapping — which may help explain how plague spreads within colonies — and Matchett’s tests of plague-mitigation tools. Prairie dogs, said Kinka, are the “unsung heroes of a prairie ecosystem,” important to all the other species American Prairie is trying to foster. And as researchers have found, the woody plants that prairie dogs chew down to clear their line of sight tend to be replaced by nutritious grasses and wildflowers, suggesting that even cattle may benefit from their presence. 

The possibility that prairie dogs could be good for cattle, or at least not as bad as generally believed, is met with skepticism by American Prairie’s neighbors, many of whom see the nonprofit as a threat to ranching. Signs posted along highways in Phillips County, Montana, read “Save the American Cowboy. Stop American Prairie Reserve.” For now, Kinka isn’t trying to convince anyone to like or even appreciate prairie dogs, aiming instead for tolerance.

The black-tailed prairie dog complex studied by the Smithsonian team at American Prairie is a noisy place, filled with the barks and trills of hundreds of creatures. As I stood beside researcher Jesse Boulerice, listening, it was easy to imagine that the rodents were doing just fine. But they’re not. Will they ever be allowed to exist in numbers like this throughout their historic range?

Boulerice surveyed the surface of the colony, which was covered with dried plant nubs and bare mounds of dirt, and said he wasn’t sure. 

Then he released a collared prairie dog who wagged her chubby butt in the air as she scurried into a nearby hole. She promptly popped back up, chirping out a message we’ll never understand. Perhaps she was warning her colony-mates to watch out for those marshmallows and carrots; they hide a nasty trap.

Or maybe she was scolding us — telling us exactly what she thought of our species before she disappeared into her burrow, leaving us to decide the future of hers.   

This story is part of High Country News’ Conservation Beyond Boundaries project, which is supported by the BAND Foundation.

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This article appeared in the January 2025 print edition of the magazine with the headline “The prairie dog conundrum.”