It’s a late September day, threatening to rain, and the mountainsides around Whitefish, Montana are popping with red huckleberry leaves, mountain ash, and maple. “We’re almost to the whitebark zone,” Melissa Jenkins announces as the ski lift ascends over Whitefish Mountain Resort and the air temperature drops. As we near the summit, she points out the towering, gray skeletons of dead trees poking out of the shrubby understory.

Jenkins explains that whitebark pines (Pinus albicaulis) once dominated the upper mountain here. The trees make a living in the higher elevations of the Sierra Nevada, the Cascades, and in the Rocky Mountains as far south as Wyoming. But in the 1920s, a rust fungus introduced from Asia started appearing in the northern Rockies. Blister rust (Cronartium ribicola) hit whitebarks hardest in northern Montana and Idaho, southern Alberta, and British Columbia. By the time Jenkins, who oversees forest management activities on the Flathead National Forest, arrived in 2008, blister rust had killed 80 percent of the region’s whitebark pines.

The species’ outlook has grown increasingly dire over the past 20 years. Blister rust has been a big part of that problem. So have unprecedented, climate-driven outbreaks of native bark beetles. Fire suppression has also allowed shade-tolerant tree species to crowd out whitebarks. In 2011, the whitebark pine became the first widely distributed tree considered for protection under the Endangered Species Act. Although the U.S. Fish and Wildlife Service said the tree warranted listing as a threatened or endangered species, limited resources have kept it from being prioritized for protection. Canada declared it endangered under the Species at Risk Act in 2012.

Despite the multiple threats, some trees have survived, and that’s where whitebark conservation scientists and forest managers see hope. Jenkins points out a few of the survivors on the way up the mountain. They are conspicuous even to an untrained eye because silver mesh cages stick out of their broccoli-shaped crowns. The cages protect the cones from birds and squirrels until a tree climber can scale the branches and collect their precious genetic cargo. Although these trees have been exposed to blister rust, they are still alive and reproducing. The whitebark pine research and management community calls these survivors “plus trees,” because they appear to have exceptional defenses against blister rust, and foresters have spent more than two decades harvesting seeds from more than 1,300 of them.

Forest managers are using those plus trees to repopulate national parks, tribal lands, and national forests with thousands of rust-resistant whitebark seedlings. It’s the beginning of a massive gardening effort to give the tree a fighting chance. “We’re actually speeding up the natural selection process,” says Jenkins, 57, who, in true forester fashion, is unfazed by the raindrops now flattening her stylish blond hair and soaking her purple jacket.

By trying to save whitebark pines, managers and scientists are also pioneering approaches to large-scale restoration work on some of North America’s wildest landscapes, where direct and sometimes heavy-handed interventions may be the only way to maintain ecosystems facing multiple human-caused threats.

Whitebark pines capture the imaginations of the people who know and appreciate them because they represent the toughness and persistence necessary to thrive in harsh landscapes. But they are more than wilderness symbols; they are key ecological players at the heart of their ecosystems, with fatty, pea-sized pine nuts that serve as a superfood for grizzly bears, black bears, red squirrels, and birds.

In the 1970s curious ecologists like Diana Tomback, now a professor at the University of Colorado Denver and the director of the Whitebark Pine Ecosystem Foundation, ventured into the high country to learn the ecosystem’s secrets. Tomback was the first to document how the whitebark pine depends on a single bird species for seed dispersal. Raucous gray-and-black Clark’s nutcrackers (Nucifraga columbiana) can carry up to 100 seeds at a time in a unique throat pouch. Tomback estimates that a single bird can bury some 35,000 seeds a year. It’s the nutcracker’s way of storing food for the lean winter, but inevitably, some of those caches are never recovered, and the seeds sprout to become the next generation of whitebark pines.

Just as scientists were uncovering the richness of this wild ecosystem, they began noticing the orange cankers of blister rust creeping up into whitebark stands from lower-elevation western white pine (Pinus monticola) forests. Their concern grew as the disease progressed. In the early 1970s, Stephen Arno, a forest researcher stationed at the U.S. Forest Service Rocky Mountain Research Station in Missoula, Montana, surveyed blister rust infection in northwest Montana’s whitebarks. He returned to those transects in 1991 to see how the trees had fared. “It was shocking,” Arno, now retired, recalls. In 20 years, 42 percent of the trees had died.

By the early 2000s Arno had seen so many dead and dying trees, he didn’t think there were enough survivors left for the species to come back on its own. He simply couldn’t see how natural processes could maintain what was left of the whitebark ecosystem, much less restore it. “It was just super bleak,” he says. “The only thing that could possibly work would be a very concerted and successful effort to restore whitebark with human intervention.”

Managers knew they would need to plant a lot of whitebark for it to remain part of a healthy, fully functional ecosystem, not simply an open-air museum specimen. In 1999, the U.S. Forest Service started a whitebark pine genetic restoration program. Instead of waiting for natural selection to generate rust resistance, foresters decided to cultivate it. The goal was to establish orchards of blister rust-resistant trees, and crank out a steady supply of seeds from those trees to be used for restoration.

The program’s leader, geneticist Mary Frances Mahalovich, had experience restoring another tree hard hit by blister rust: western white pine. Still, no one knew if it would be possible to do the same for whitebark.

As Mahalovich and her team worked on the uncertain task of growing the whitebark pines of the future, the decline worsened. Mountain pine beetles (Dendroctonus ponderosae) are a natural part of western forests, and outbreaks occur periodically, but starting in the late 1990s, beetles irrupted further north and in higher elevations than ever before. Entomologists studying the outbreak found the fingerprints of climate change. Drought stressed the trees and warmer winters helped more beetles survive. Whitebark managers rushed to protect their rust-resistant plus trees from beetles using insecticide sprays and pheromone packets tacked to the tree trunks. Between 2000 and 2014, when the outbreak finally subsided, beetles killed more than 20 percent of the plus trees in Mahalovich’s program.

Like many foresters in the region, Jenkins helped identify plus trees and collected their cones for Mahalovich’s program. During the outbreak she worked on a forest closer to Yellowstone National Park, where the beetle outbreak was at its worst. One summer she climbed a healthy new plus tree to protect its cones with cages, only to return in September to find it dying and overrun with pine beetles. The dual threat of blister rust and beetles challenged Jenkins’s resolve. “I was down for a while,” she says. “The scale of the problem was so big, and our efforts were so small in those days. It was like, ‘Are we even making a difference?’”

Throughout the bark beetle outbreak, foresters continued collecting plus tree cones and pollen. They also collected blister rust spores from infected trees that nursery staff would use to test seedling resistance. It took three years to grow the seedlings, and another five to watch for signs of rust resistance. Then, because whitebarks don’t typically set their first cones until they are around 30 to 50 years old, foresters have a trick to get the seeds earlier. They climb back up the mother tree, cut off a cone-bearing branch, and graft it onto the smaller seedling. Only then is a rust-resistant seedling finally ready for the orchard.

As someone who has spent her career around whitebark pines, Jenkins has had many memorable wilderness encounters with the trees. But her favorite story is from her first tour through one of those whitebark orchards in northwestern Montana. After years of laboring alongside her colleagues to protect whitebark, she spotted a new cone on a shin-high seedling. “That little conelet was the culmination of all this work we’d gone through—from when we started finding the plus trees in 1999, and collecting the cones, and doing the whole rust-screening process,” she says. That conelet also held the genetic material of future forests, and tangible potential for keeping the whitebark pine ecosystem alive. It was enough to bring a tear to her eye.

In the last five years, federal managers in Montana, Idaho, and Wyoming have restored, on average, 283 hectares (700 acres) of whitebark pine forest annually. Whitebark restoration now has more traction than ever, but there are still questions about whether it will be enough, and if it will hold up in a changing climate. Considering federal agencies have replanted only 1 percent of the trees that were lost in the bark beetle outbreak between 2001 and 2014, these are still early days for restoration.

Tomback once estimated the cost of replanting the U.S. whitebark pine’s range with rust-resistant seedlings at $11.4 to $13.9 billion, which is more than the entire U.S. Forest Service’s annual budget. Whitebark conservationists are well aware of the disparity between the size of the problem and the size of the federal budget for such work. Tomback says the Whitebark Pine Ecosystem Foundation, which supports science and restoration, recognizes that agencies need to identify and focus on core areas, especially those where whitebarks are most likely to survive climate change. “Once the trees are mature and produce cones, these core areas will serve as dispersal centers, thanks to the nutcracker, for gradually moving the forest out to sustainable habitat,” she says.

But figuring out exactly what climate change means for the species is no easy task. Over the past few years, several modeling studies have sought to predict the whitebark pine’s prospects under climate change. The forecasts look bleak. According to a 2014 study, the area suitable for whitebark pine in the Greater Yellowstone Ecosystem is expected to fall by more than 80 percent by 2100—and that’s under a moderate global warming scenario.

While those models, known as bioclimatic envelope models, are the best estimates we currently have, ecologists like Tomback know they’re imperfect. The models don’t, for example, account for topographic variation, like cooler north-facing slopes that may still harbor trees in the future. They also don’t account for ecological interactions like seed-dispersal, or the adaptive capacity that comes with genetic diversity, which remains high in whitebark pines. In the field, scientists continue to find examples of how much we still have to learn about the species. Last year, a researcher discovered a whitebark pine forest in Montana pushing its way downhill into more arid sagebrush habitat, going against every expectation about how whitebarks should behave in a warmer climate.

While most of the whitebark pine research and management community is onboard with the current restoration plan, there’s a minority questioning whether focusing on blister rust is the best strategy. When the bark beetle outbreak started decimating whitebark pines in the 2000s, Diana Six, an entomologist at the University of Montana, almost quit studying the tree because she thought it might simply blink off the landscape throughout most of its range. She’s concerned that the focus on rust resistance is coming at the expense of helping the trees adapt to other stressors. Specifically, she worries that covering the landscape with trees hand-picked for rust resistance may override adaptation that could have happened in response to climate change and bark beetles—and that, she says, could leave forests vulnerable to future climate conditions.

The idea that the trees may be adapting to climate change and bark beetle outbreaks is what helped her stick with whitebark research. Amid the beetle-killed forests, she started noticing a few healthy trees that millions of beetles had ignored, and wanted to know why. Now, she thinks there’s a connection between a pine’s ability to survive beetle outbreaks and its ability to survive a warmer, drier climate. “We think that the beetle has been a big natural selection agent, wiping out trees that are adapted to old wetter, cooler conditions,” she says. “[The beetle] took those out because they were struggling.” Earlier this year, she began looking for genetic markers that could help identify trees that will do better under climate change. She hopes that forest managers might eventually use those markers to take stock of whitebark genetics in the future.

For Six and others, whitebark forest restoration looks less like a problem isolated to the mountains, and more like an indication of the changes ecosystems may face on a larger scale. “I think some of the first systems to tip are those that are in the harshest and most difficult situations,” she says. She’s seeing it happen in the euphorbias she studies in Africa, and in saguaros and Joshua trees too. “Even if there’s no exotic species present, those things that are kind of on the margins go first. This is just a harbinger of things to come.”