For millennia, owls have roosted in Homestead Cave, west of Utah’s Great Salt Lake, coughing up the remains of their prey in slow-growing piles on the dusty floor. The bones, preserved in a deposit at least 2 meters thick, represent what the birds have munched on for nearly 13,000 years. Now, scientists have used those remains to show that human changes to the landscape over the last 100 years may have thrown the area’s small mammal community out of whack in a way that even the rapid, natural climate change at the end of the last Ice Age could not.

“This is … the first time that we have, I think, really good insights that suggest that how these ecosystems have functioned [over time] has really changed. And it’s happened really recently,” says S.K. Morgan Ernest, a community ecologist at the University of Florida who was not involved with the study.

Located on an Air Force testing range in the Great Basin desert, the cave is on the edge of a landscape increasingly engineered by humans. Scrubland has given way to range land, and invasive plant species like cheatgrass are taking over the environment. These changes—along with the impacts of climate change—make the Great Basin one of North America’s most threatened ecosystems. Just last Friday, President Obama protected a large swath when he turned roughly 704,000 acres in central Nevada’s Basin and Range environment into a national monument.

Given the changes wrought by humans, paleoecologist Rebecca Terry at Oregon State University and University of New Hampshire, Durham, community ecologist Rebecca Rowe decided to use the owl vomit—pellets of undigested bones, hair, and teeth—to see how different the present-day small mammal community was from its past counterparts. They compared more than 63,000 bones from the ancient owls’ meals—stretching back 12,800 years—to those from the cave’s modern owls, which contain nearly 1700 specimens from animals like kangaroo rats, mice, and weasels from the last 100 years.

The duo tracked how energy flow—a measurement of the amount of energy needed to sustain a group of animals over a period of time—had changed. Energy is always flowing through the environment, passed along from the sun to the plants to the rest of the creatures in the food web. So, in essence, the scientists figured out how the energy stored in the bodies of the small mammal part of the food web changed through time. Such a measurement gave them a bird’s-eye view of how the entire community was changing that studying individual species could not.

“The paleontological data makes the study really unique,” Ernest says. “You just don’t see that ability to go almost continuously from modern times back to the last Ice Age. It allows the scientists to do some really powerful analyses you normally can’t do.”

The analysis revealed that total energy flow in the small mammal community was relatively stable for thousands of years, despite major environmental changes at the end of the last Ice Age when the region’s lakes dried up, and its vegetation morphed from forests and sagebrush steppe to desert shrublands. The total amount of energy in the system stayed nearly the same because even as the species that didn’t fare well under the altered environment declined, others who enjoyed the warmer, drier climate took their place, Terry says.

“It’s amazing how long the system was able to hold energy flow stable with all of the shifts going on in the community,” Ernest says. “It wouldn’t be interesting at all if you had the exact same species for 13,000 years. That’s trivial. It’s the fact that the community is changing, but those changes all seem to balance out for thousands of years.”

The last century, however, was a different story. The researchers found that over the last 100 years, the amount of total energy in the small mammal community had declined substantially in a way it had never done before, suggesting the animals are not adapting as well today to their once again altered environment as in the past, the authors reported online this week in the Proceedings of the Natural Academy of Sciences. “When we saw just how different the modern [community] was, it was really shocking,” Terry says.

Small mammals are crucial in the desert environments of the Great Basin. They store energy from plants and other foods and then pass that energy along to the larger mammals that prey on them, including owls and coyotes. One implication of the reduced energy flow is that predators may have to work harder to obtain the energy they need to sustain themselves. And recent studies have shown the creatures may have a more important role in helping disperse the seeds of plants than was thought.

For the moment, however, the overall effect of having a dramatically different small mammal community on the entire ecosystem is unknown. Because of limitations to analyzing paleontological data, the scientists can only say that the amount of energy in their sample of animals’ remains is much lower than what it used to be.

Still, there may be some good news to come out of the research. When the climate changed roughly 11,000 years ago, it warmed 5 or 6 degrees in just a few decades, a faster rate than what is currently expected for manmade warming, and the small mammal community coped, says Felisa Smith, a paleoecologist at the University of New Mexico who was not involved in the study.

That resilience suggests that the direct impacts humans have had on the small animals’ habitats—through increasing pastureland or spreading invasive plants—are the driving force behind the recently unbalanced system, independent of climate change.

While having the community thrown out of its previous balance may mean the rodents will be less able to cope with manmade climate change, addressing those more local, human impacts is perhaps an easier challenge in the short term than dealing with climate change, Terry says. “Perhaps it means we can make a quicker difference in repairing the system just by focusing on habitat restoration. Maybe that’s a silver lining to all of this.”