Editor’s Note: This story accompanies the May 2016 issue of National Geographic magazine, devoted entirely to America’s first national park. Find more at natgeo.com/yellowstone.

At its birth in 1872, Yellowstone National Park was viewed in great part as an oversize zoo, its diverse animals managed like captives in a menagerie. But in the decades since, much has changed.

Yellowstone Superintendent Dan Wenk summed up today’s more expansive view in a recent interview: “Rather than manipulating wildlife to do what we want it to do, we strive now to secure habitat to let wildlife do what it needs to do—to let natural processes play out as best we can.”

Indeed, the arrival of the modern environmental age has brought many dramatic changes to the Greater Yellowstone Ecosystem. Take the case of the black-footed ferret.

A camera trap at a watering hole caught grizzly and black bears bathing, splashing, and frolicking.

Within circles of conservation biology, there are animals known as “Lazarus species,” those believed lost to extinction that seem, miraculously, to rise again.

Mustela nigripes, a member of the weasel family, was believed to have gone extinct by the 1980s. The ferret preys on prairie dogs, and when those rodents were deliberately annihilated from much of the West to make way for livestock in the 20th century, ferret numbers dwindled and appeared to wink out.

Until 1981, when a dog owned by Lucille Hogg carried a dead ferret home. The sudden, unexpected event took place in rural Meeteetse, Wyoming, on the eastern side of the Greater Yellowstone Ecosystem—and it led to the discovery of a few dozen ferret survivors. Today a captive-breeding program has yielded a wild population of a thousand individuals.

View Images There were times in the 1970s and ’80s when the Greater Yellowstone Ecosystem held as few as perhaps 140 grizzlies, and the population seemed doomed, says Chris Servheen, a U.S. Fish and Wildlife Service official who coordinates grizzly recovery. Today 700 to 1,000 live there, including these two hulks tangling near the Firehole River. Photograph by Michael Nichols

The comeback of a surprising number of other animals can be linked to Greater Yellowstone’s role as a refugium for species that have been doomed in parts of the United States by habitat destruction, market hunting, and poaching.

Today, Dan Wenk says, Greater Yellowstone exists as a flagship for “rewilding.” It not only hosted the reintroduction of wolves—a lost species—but also served as a critical reservoir in the recovery of grizzly bears, bison, elk, Rocky Mountain bighorn sheep, sandhill cranes, and trumpeter swans. The area is the only essentially intact bioregion in the country—and one of the few in the world that still are home to all of their original mammals and birds.

View Images Tracking grizzly bears with radio collars in the 1950s and ’60s, John Craighead and his twin brother, Frank, discovered just how far bears roamed beyond the boundaries of Yellowstone and Grand Teton. The two championed the idea that the parks should be managed as part of a Greater Yellowstone Ecosystem—an idea that took decades to catch on. Now 99, Craighead spends a lot of time in a tepee outside his house in Missoula, Montana. Frank died in 2001. Photograph by Erika Larsen

And as bison, elk, bighorn sheep, and swans have recovered, their descendants have been used as seed stock to help revive their prospects in other parts of the country.

“This ecosystem is considered a fountainhead for conservation and wildlife abundance,” says Yale University professor Susan G. Clark. She is founder of an independent research organization in Jackson, Wyoming, called the Northern Rockies Conservation Cooperative, and she was involved in the ferret recovery 35 years ago.

But nothing is as simple as it seems. Clark asks an intriguing question: What does having a lot of anything really mean?

View Images

“When we talk about 5,000 wild Yellowstone bison, yes, it’s a lot compared to the two dozen still left standing after near annihilation. But there were once 35 million in the West. We have 800 grizzlies today in Yellowstone and close to 2,000 in the entire northern Rockies—yet there were 50,000 in the lower 48 historically, and today grizzlies are gone from 95 percent of their former range.”

Which is to say, these populations exist at pretty much bare minimums. “What’s important,” Clark says, “is not just having a checklist of species and calling it good, but preserving these animals’ natural histories, protecting migration patterns, and turning grass into meat—which is then recycled across the landscape in the food chain.”

In other words: habitat, habitat, habitat.

“To ensure that wildlife have sufficient habitat for population persistence into the future, and to confer resilience in the face of climate change and land use change, there must be an adequate amount of protected habitat available among the spectrum of lands that are accessible to those wildlife,” writes Lance Craighead, a biologist who operates a research station in Bozeman, Montana. Craighead is the son and nephew of famous bear researchers and conservationists Frank and John Craighead, active in Yellowstone in the 20th century.

View Images After being nearly eradicated by trappers in the mid-1800s, beavers are making a comeback in the West, including in Grand Teton National Park. As climate change creates more variable weather, these wetland engineers are holding more water in the landscape, thereby bolstering biodiversity. Photograph by Charlie Hamilton James

View Images The interior of a beaver lodge in Grand Teton National Park, Wyoming Photograph by Charlie Hamilton James

Greater Yellowstone, Craighead explains, isn’t a monolith; rather it’s an amalgamation of rich habitats stretching from mountaintops to valley floors. And, as Clark says, it’s the best example of ecosystem protection that supports big, wide-ranging animals that don’t recognize artificial boundaries created by humans.

But Clark, like many, is concerned. Although natural processes still play out in grand fashion in Yellowstone, human population pressures and climate could cause things to unravel.

Michael Finley, president of the nonprofit Turner Foundation, is the only Park Service veteran to have served as superintendent of three major national parks: Everglades, Yosemite, and Yellowstone.

“There seems to be an ideological belief,” Finley says, “that little impacts on the environment don’t adversely affect the park. In Yellowstone, however, it will be the cumulative effects of a thousand seemingly little assaults upon the ecosystem that will render the real damage to the park and its surrounding wildlands in the future.”

View Images Cutthroat trout, seen here spawning in the Gros Ventre River, are highly prized by anglers. Adapted to cold water, they’re threatened by a warming climate—and in Yellowstone Lake, by non-native lake trout. Photograph by Charlie Hamilton James

View Images A weasel blends into snow in Grand Teton. In spring it will molt and turn light brown. Photograph by Charlie Hamilton James

Despite ongoing conflict and endless complications, “the miracle of Yellowstone is the reintroduction of the wolf and the biological cascade that has occurred by restoring a keystone species,” Finley says.

Michael Soulé, considered by many to be the godfather of conservation biology, raises an optimistic voice: “Greater Yellowstone is the center of the Wild West that remains. The challenge is trying to connect the ecosystem to other ecosystems, to let it serve as a source for rewilding other places.”

But, Finley says, only a continuation of hard-nosed conservation vigilance will hold the gains that have been made.

View Images The carcass of a bison that drowned in the Yellowstone River became a feast for an alpha female of the Mollie’s wolf pack and her two year-old offspring. Bringing down a live bison is dangerous; Yellowstone wolves far more often target elk, which make up 85 percent of their winter diet. Photograph by Ronan Donovan, National Geographic