When the last ice age ended 12,000 years ago, the boreal forests that had extended into the Southeastern U.S. followed the cooler climate north into Canada or migrated to higher elevations. Today, vestiges of natural communities of a time long past, such as the stately red spruce and the tiny northern flying squirrel, cling to high peaks in the southern and central Appalachians.

Early in the 20th century, logging and fires drastically reduced what little spruce remained, shifting the forest to a northern hardwood community. Some red spruce stands endure, however, in protected or particularly rugged areas. The rare Virginia subspecies and the endangered Carolina subspecies of the northern flying squirrel still occur in these isolated spruce patches, their only habitat south of the Adirondack Mountains.

The two flying squirrel subspecies eat truffles — the fruiting bodies of fungi that occur in symbiosis with the roots of spruce. The fungi help the spruce take up nutrients; the trees provide carbohydrates to the fungi. The fungi depend on the squirrels to disperse spores, signaling when they are ripe with peculiar odors that attract the squirrels. It is only in the last decade that the squirrels’ dependence on spruce forests and associated fungi has been fully documented.

Mark Ford, who has been studying squirrels for 20 years, calls the spruce-squirrel habitats “islands in the sky.” Now the leader of the U.S. Geological Survey’s Virginia Cooperative Fish and Wildlife Research Unit at Virginia Tech, Ford’s work with agency and university partners contributed to the removal of the Virginia subspecies from the endangered species list in 2013. Corrine Diggins, a former Virginia Tech fish and wildlife conservation doctoral student and now post-doctoral research associate, continues to monitor the Virginia squirrel’s status, and she and Ford started similar research with the Carolina squirrel in 2012.

Surveying squirrels is hardly a walk in the woods. It is a trek, mostly off trail, hauling cumbersome equipment. “You go out during the day, when the squirrels are snug in their dens,” Diggins said. “You carry a gigantic ladder because the artificial nest boxes to survey the squirrels are 15 to 20 feet off the ground. You find a nest box, then very quietly, lean the ladder against the tree and sneak up.”

The surveyor plugs the box’s exit hole and taps it to see if it is occupied. If so, a net is placed over the hole and the box is shaken until the squirrel shoots out. The researchers weigh, measure, tag, and radio-collar the squirrel, then return it to the nest box and plug the hole until the animal calms down. “You don’t want a nocturnal animal taking off into the forest during the day just to get eaten,” Diggins explained.

Finding squirrels in nest boxes is hit or miss, so data collection requires repeated trips. After locating a squirrel’s den, the researchers return at night. “We set up simultaneous listening stations to estimate their foraging locations based on where the radio directions converge,” she said. “Some of the forests are so dense that we would never be able to follow them by foot.”

Ford’s work with flying squirrels began when he was a wildlife biologist for the Westvaco Corporation (now WestRock) in the 1990s. He found what he thought was a common southern flying squirrel in a nest box but soon realized it was a then-endangered Virginia northern flying squirrel. “It was a great day until I had to tell my boss that I had found an endangered species on company land,” he recalled. “Fortunately, the company realized that the discovery allowed us to show what careful forest stewardship can do for wildlife.”

Upon joining Virginia Tech in 2010, Ford began building on earlier work, analyzing two decades of capture data and habitat information. The results were two models that predicted where the Virginia subspecies occurred in the Allegheny Mountains in West Virginia and how different sites were spatially related. “The work led to additional surveys of likely habitat, revealing the presence of the squirrels across a million-acre landscape,” he said. In addition, he helped devise approaches to improve the quality of red spruce habitat using active forest management, such as selectively thinning competing hardwoods to release red spruce.

In North Carolina, the Southern Appalachian Spruce Restoration Initiative — a partnership between The Nature Conservancy, the U.S. Forest Service, the North Carolina Wildlife Resources Commission, and other parties — has begun the task of helping to restore 150,000 acres of red spruce forest. “Unlike the Virginia subspecies, which occurs over a relatively large, connected landscape, the Carolina northern flying squirrel remains critically endangered, being scattered among the high mountain ranges miles apart and surrounded by a sea of inhospitable hardwoods,” Ford said.

Ford’s experience with the Virginia subspecies drew the interest of Christine Kelly, lead for the Carolina northern flying squirrel project with the North Carolina Wildlife Resources Commission. “We had low captures and recaptures in North Carolina, and we needed insight on analyzing the data,” she said. Ford and Kelly began to collaborate to create a predictive habitat model.

Advances in GIS technology allowed the team to look at the Carolina subspecies relative to terrain shape as well as elevation and forest community. “We discovered that the best places for the squirrels are sheltered ravines on north-facing aspects,” Ford said. “These spots have high moisture and deep organic soil layers where red spruce and their symbiotic fungi grow best.” The research team created a predictive model for the area that helps managers assess the landscape and prioritize areas for spruce restoration.

Acoustic surveys offer another method for surveying squirrels. Michelle Gilley, an assistant professor at Mars Hill University working with Ford and Kelly, discovered that flying squirrels vocalize above the level of human hearing, meaning they could be “heard” by commercially available bat acoustic detectors.

“Nest boxes haven’t allowed for density estimates because capture rates are low and the process is time-consuming,” Diggins explained. “Acoustics allows us to differentiate between rare northern and common southern flying squirrels without having them in hand, as their vocalizations differ in duration and modulation.” But the research is still preliminary. “We are exploring how useful the method will be. Bioacoustics works with bats because navigation requires them to constantly vocalize, but squirrels are usually quiet. We have to iron out the nuances.”

Why save a tiny flying rodent and its evergreen home? “Red spruce and northern flying squirrels cannot move further up the mountains to escape climate change,” Ford said. “So we monitor the subspecies to see where both passive and active forest management can work to perpetuate this community while we develop strategies to cope with changing conditions. It tells us about the health of the forest and the whole Appalachian ecosystem. It only takes one visit to a red spruce forest to know these are special places worthy of managing for future generations.”