Jack Hopkins was in charge of the cracker shells, beanbag rounds, and rubber bullets. As the leader of a bear management crew in Yosemite National Park, he fired these deterrents at food-pilfering black bears from a 12-gauge shotgun. Each spring he attached radio collars to bears trapped among the crowded campgrounds of Yosemite Valley. After three years of chasing recalcitrant bears, however, he had questions.

How many bears in the park — especially outside of the valley — associated humans and their paraphernalia with food? Did the bears he hazed in campgrounds lose their taste for human food? Was there a better way to manage the interaction between bears and humans?

Other researchers had spent years tracking the radio signals of collared bears looking for answers to these questions, but Hopkins thought he had a better idea: To use a technique called stable isotope analysis — which had been employed for decades by geologists, archeologists, and climatologists — to answer his questions about the interaction of Yosemite’s bears with its human visitors. The isotopic signature of bear guard hairs would help tell the tale.

Scientists are examining the lives of animals that are too small, too dangerous, or live too remote to study in other ways.

Stable isotope analysis relies on the fact that elements in different environments and foods contain different atomic signatures, based on the number of neutrons. For example, the ratio of a heavy nitrogen isotope to the common nitrogen isotope tends to increase as you move up the food chain from plant to predator. Oceans have an isotopic signature that is distinct from fresh water. Dry habitats have a different ratio of carbon isotopes than wet habitats. Deuterium, a heavy hydrogen isotope, tends to be proportionately high in clouds over tropical oceans. It decreases predictably the farther inland you go.

In recent years, the cost of stable isotope analysis has steadily fallen, and as a result Hopkins and other ecologists are using the technique to examine the lives of animals that are too small, too dangerous, or that live too remotely to study in other ways. Scientists are now using stable isotope analysis to piece together the migrations of dragonflies, to deduce the likely wintering grounds of songbirds, and to determine why animals feed in different areas based on pressure from predators.

“Stable isotope analysis has been adopted by ecologists recently,” says Seth Newsome, an assistant professor of biology at University of New Mexico. “Before that it was used by geologists, paleontologists, archeologists and climatologists — people who study deep time.”

Newsome, for example, has used stable isotopes to study the shifting diet of California condors from the Pleistocene era through the present by examining the ratio of the heavier carbon and nitrogen isotopes in their bones. His work has revealed that Pleistocene condors fed more on whales or other marine mammals that washed up on shore, while today’s condors show isotopic ratios consistent with a diet of land-based plant-eaters, particularly corn-fed feedlot cattle.

Stable isotopes have been used to study the shifting diet of California condors from the Pleistocene to the present.

The ratio between stable isotopes is sorted out using a device called a mass spectrometer. The sample to be analyzed — a dragonfly wing, or a hair from a bear — is sealed in a metal capsule that is smaller than a thimble, placed into the spectrometer, burned into a gas, and then shot toward a magnet. The magnet deflects each atom at an angle relative to its weight, much the way a prism refracts a beam of light into its component colors by wavelength.

In the late 1990s, before the development of tracking devices small enough to be carried by songbirds, stable isotope analysis changed the study of songbird migration from a game of chance — waiting for a banded bird to be spotted again — to a laboratory exercise. In 1998, Peter Marra, then at Dartmouth College, published the first paper linking the quality of a songbird’s wintering grounds with its survival and breeding success. Science Magazine called it “the Holy Grail of avian ecology.”

Marra, now at the Smithsonian Institution’s Migratory Bird Center, used carbon isotopes in the blood samples of small songbirds — American redstarts — arriving on their New Hampshire breeding grounds to determine which had wintered in rich, wet habitats and which had wintered in poor, dry habitats. Birds wintering in lush habitats in Jamaica and Honduras, mostly older males, arrived first. Previous studies had shown that early birds sire more offspring.

“That carbon technique is still state of the art,” Marra says of his method to link habitat and diet.

Ecologist Jack Hopkins collects bear hair samples in Yosemite National Park for stable isotope analysis. MONTANA STATE UNIVERSITY

For tracking bird migration, data loggers now exist that are small enough to affix to a songbird. But that is not the case with dragonflies. So Marra and Kent McFarland of the Vermont Center for Ecological Studies are using stable isotope analysis to track the migration of green darner dragonflies. Green darners are large for an insect — imagine a flying blue-green cigarette — but still too small to carry a tracking device and too delicate even for the stickers that have been used to trace monarch butterfly migrations. That dragonflies migrate has been known for millennia, says McFarland. How green darners move north in the spring is still a mystery, however.

McFarland and Marra’s dragonfly research will rely on that deuterium gradient, which in North America runs roughly north to south, to trace the green darners’ journey. McFarland hopes his green darner studies will reveal important migration points for the dragonflies so that those places can be conserved, if necessary. Throughout their lives, the dragonflies maintain the isotopic signature of the pond where they were larvae. The green darner research is possible because analyzing a tiny piece of dragonfly wing in the Smithsonian’s mass spectrometer now costs only about $8 — crucial for a project that has no major funding.

When Hopkins, the Yosemite bear researcher, decided to concentrate on using stable isotopes to analyze the bears’ diets, he needed access to a mass spectrometer and a stable isotope expert. He found both in the Earth and Planetary Sciences Department at the University of California, Santa Cruz, in the lab of Paul Koch, a vertebrate paleoecology researcher wise in the ways of both stones and bones. But analyzing the hundreds of bear hair samples that he had collected by stringing barbed wire around bait stations throughout the park was not going to be as easy as popping the hair into the mass spectrometer and reading the results. First, he had to lay the groundwork.

Isotopic signatures showed there were twice as many problem bears in Yosemite Park as anyone expected.

As Marra has found, site-specific variables — such as elevation, diet, the age of the animal, and the distance from the seacoast — can confound the isotopic ratios found in different creatures. Those variables are a trap for unwary researchers, says Merav Ben-David a professor in the Department of Zoology and Physiology at the University of Wyoming who wrote several of the papers in a special feature in the Journal of Mammalogy last year on stable isotope analysis. “There are hundreds of papers out there that I consider unreliable because people didn’t quantify the underlying variations,” she says.

Hopkins — now a post-doctoral researcher at the University of Alberta and Peking University — figured out the underlying variables for his bear study by analyzing human hair samples from a barber shop in St. Louis, hair samples from Yosemite black bears known to eat human food, bears known not to eat human food, and samples of just about any food a bear might eat in the backcountry, from berries to mule deer. The various samples allowed him to compare the isotope ratios in the bear hair to the actual, natural food the bears would eat in Yosemite.

Once he compared the isotopic signatures in the hair of about 300 bears from around Yosemite, Hopkins found that there were four additional bears in the busy Yosemite Valley that were conditioned to human food that the bear managers didn’t know about, in addition to about 20 that they did know about. The big surprise was how many bears in the backcountry — 15 — were also eating human food. There were twice as many problem bears in the park than previously known. Bears that had been identified as eating human food in an earlier study stayed human-food eaters in this study; scaring or moving bears was not changing their behavior.

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Hopkins’ bear studies have provided scientific confirmation for bear-management changes already underway in Yosemite National Park. Park officials are still firing bean bag rounds at Yosemite Valley’s recalcitrant bears, but this year, among other changes, the park has increased efforts to prevent bears in the backcountry from ever tasting human food.

Ben-David says that such isotope research enables researchers to look beyond just diet to broader animal behavior. Her 2004 paper in Oecologia used nitrogen isotopes to show that female Alaskan brown bears with young cubs sometimes avoid salmon streams, forgoing a feast in order to keep their cubs safe from other bears. A 2007 study by University of Victoria conservation scientist Chris Darimont discovered that black-tailed deer pay for feeding in richer habitats by becoming more likely prey for wolves.

Ben-David admits that it is impossible to know where the cutting edge of ecological stable isotope studies will be in two years. “This field is moving very fast,” she says. So fast, that when she was recently asked to compile some papers on ecological studies using stable isotopes into a book, she refused.

“By the time it’s published,” she says, “it will be ancient history.”