But the California seals aren’t the oddballs they seem to be, according to Koch, an earth scientist, and Gifford-Gonzalez, an archaeologist. By studying old seal bone collections in new ways, the two have recently reached surprising new conclusions. The bones tell them that until 800 years ago, countless northern fur seals actually crowded the shores of northern California. For thousands of years, the research suggests, the animals lived in California year-round and established large breeding grounds, called rookeries, on the mainland.

“Now we know something about the seals that we didn’t know before,” says Koch. “The habits of surviving northern fur seals are misleading. The seals have the capacity to survive on California’s mainland—they don’t need to go someplace cold.”

So why did the animals vanish from California beaches? Some scientists think they retreated due to natural causes, such as changes in climate. Other researchers believe that predators on the mainland, such as bears, forced the seal population to seek a safer home. But Koch and Gifford-Gonzalez aren’t so sure. They suspect that early human hunters, driven to hunt the creatures heavily during lean times, are responsible for California’s current dearth of northern fur seals. Indeed, the fur seals may be just one example of a more general shift of pinniped species—a group including seals and sea lions—from the Pacific Coast mainland to offshore island refuges.

The UCSC scientists’ theory not only challenges the current dogma, but also raises fundamental questions about the seals’ future. If humans forced the animals offshore, Koch says, then perhaps humans should help the seals back onto the mainland.

Definitive answers about why the seals vanished won’t come easily, says Gifford-Gonzalez. Just as in some criminal investigations, the scientists need to rely upon many indirect clues. “If you want to know who the perpetrator was, you must look at how many lines of evidence point to a common cause,” she says. Thanks to the UCSC team, that proof is mounting.

ONE OF THE “crime scenes” under investigation is Año Nuevo State Reserve, 55 miles south of San Francisco. Here, rolling sand dunes stretch for miles before ending in a low, rocky point that juts into the Pacific Ocean. Año Nuevo is home to the world’s biggest mainland colony of northern elephant seals, the more hulking relatives of the fur seals. Thousands of people flock to this shore each winter to gawk at the two-and-a-half-ton elephant seals that come to breed. They put on quite a show. Males hurl their massive bodies and stretch their necks toward the sky, battling with one another for mates. On the brink of extinction only decades ago, elephant seals have made a remarkable comeback. They are a conservation success story at a time when many other animal species are dying out at unprecedented rates.

Closer inspection of the Año Nuevo dunes, though, reveals ancient mounds of shell and bone that hint at a distinctly different history. Evidence recently collected by graduate student Seth Newsome and archaeologist Mark Hylkema point toward a vision of Año Nuevo’s past in which northern fur seals were the dominant marine mammal on the beach. “In the past there was a really healthy population, and 800 years ago, it crashed,” says Newsome.

The shell and bone are the remnants of the original human inhabitants of the coast, the Ohlone people. The Ohlones lived in the San Francisco Bay Area for thousands of years before Europeans arrived in North America. They dwelled in houses of reed and willow, and subsisted on the fruits of the land and sea: acorns and berries, as well as deer, mussels, fish, and seals.

The mounds at Año Nuevo are ancient heaps of Ohlone kitchen scraps dating back three thousand years. But their trash is gold to the scientists. Careful excavation at Año Nuevo and other sites in central California has uncovered many bones of northern fur seal adults, juveniles, and sometimes even pups too young to swim—a striking find, given the absence of the animals in those coastal areas today.

Unlike other tribes in the Pacific Northwest and southern California, the Ohlone never became blue-water sailors; they hunted and fished close to shore. That suggests fur seals must have bred on the California coast. What’s more, when Koch’s team looked at trash piles older than one thousand years, they found that northern fur seals were the most common seal among the remains—accounting for up to 80 percent of seal bones in any given mound. So far, within this time period, elephant seals haven’t made an appearance.

Thanks to a knack for geochemical wizardry, Koch and Newsome are able to use the discarded bones to pry further into the past lives of California’s northern fur seals. Their brand of magic relies on a simple and familiar idea: You are what you eat. The main clues are the basic chemical elements, principally carbon and nitrogen. Each of these elements come in different versions called isotopes, which have slightly differing atomic weights. The isotopes end up preserved within an animal’s bones in varying proportions depending upon its diet.

For instance, according to data gathered from living seal populations by UCSC graduate student Rob Burton, the bones of seals feeding close to shore are laced with more “heavy” carbon and nitrogen than the bones of those foraging in deeper waters. Similarly, marine mammals that spend their days at middle latitudes carry more heavy elements in their bones than animals hunting in colder northern waters. Thus, analyses comparing carbon and nitrogen levels in ancient and modern seal bones can pinpoint shifts in where the seals lived and dined.

In Koch’s lab, small zipped plastic bags hold the yellowed skeletal remains of long-dead California northern fur seals: ear bones, bits of rib, maybe even a toe. The researchers crush and dissolve the bone samples into amorphous clumps of collagen fiber. Then they convert the collagen globs into even more basic parts inside an incinerator, which, in a flash of fiery orange, vaporizes the bone fibers into carbon dioxide and nitrogen gas. The incinerator sends the gases directly to an instrument, called a mass spectrometer, that sorts the isotopes of each chemical in turn. For example, carbon dioxide is sorted into molecules of three separate atomic weights, in quantities reflecting the proportion of different carbon isotopes in the bones. The researchers simply sit back and watch the results appear on a computer screen as a series of red and blue peaks—each representing a separate isotope.

Using what they knew about the influence of nutrition on the bone makeup of living seals, Koch’s research team has decoded the bone chemistry of the ancient seals into information about their prehistoric dietary habits. The isotope studies reveal, not unexpectedly, that the creatures fed in deeper offshore waters. But the bones show no evidence that seals strayed to higher latitudes—confirming the idea that some colonies of ancient northern fur seals stuck around California all year, rather than seasonally trekking down from the icy waters of Alaska.

To learn the cause of this drastic shift, the scientists looked at the leading suspect —ocean climate change—again with the aid of geochemical tools. The Ohlones snacked on mussels and tossed their shells in the trash heaps along with the fur seal bones. Luckily for Koch and his associates, mussels, which live two to ten years, serve as natural recorders of ocean conditions. As they grow, their shells thicken and form annual growth rings like those found in trees, so that the chemical makeup of each shell layer reflects the climate conditions in a given year. By measuring the amount of oxygen and carbon isotopes in each layer, the researchers are reconstructing the temperature and nutrient composition of ocean waters off California over time, and identifying periods of major climate change.

So far, after poring over 3,000 years’ worth of Ohlone mussel scraps the researchers have yet to find any sign of unusual changes in ocean climate. The usual suspect seems to be off the hook. Prehistoric Ohlone hunters became the prime suspects instead.

According to Gifford-Gonzalez, drought conditions on land may have led to overhunting of fur seals. Evidence from tree rings suggests that California got warmer and drier 1,000 years ago. A shortage of their standard fare—acorns and grains —may have left the Ohlone little choice but to target more of the rich, fatty seals, she says.

Indeed, says archaeology grad student Newsome, contents of the Ohlone trash heaps show an increase in marine scraps around the time the seals disappeared, possibly indicating that other food resources were drying up. And seal bones from the mounds suggest selective hunting of females, which are smaller and less threatening than males.

The practice of targeting females would have put the fur seals at greater risk of extinction. Successful male seals are quite the playboys, forming harems of up to 40 females, while the other males just hang out on the sidelines and may not mate at all. So most males fail to contribute pups to the next generation, and are irrelevant to population growth. On the other hand, the loss of females directly spells fewer young seals the following year.

ALL IN ALL, the bone studies by Koch and Gifford-Gonzales’ crew provide irrefutable evidence that northern fur seals once thrived on California’s mainland. “It challenges longstanding ideas about pinnipeds’ limitation to offshore islands,” says Dan Costa, a seal ecologist at UCSC who isn’t involved in the bone research. The findings highlight the value of a deep time perspective. Ecologists tend to think in terms of decades, while an animal’s true history extends over centuries and even millennia. “The way the seals are now may be an artifact of human habitation and disturbance—not to mention lots of environmental change,” Costa says.

However, Costa has doubts about the importance of Koch’s mainland fur seals to the species as a whole. The number of seals that made their home on California’s mainland centuries ago can’t be guessed from the Ohlone bone fragments. Maybe, mainland fur seals were just small populations on the outskirts of their ideal habitat range, says Costa. One line of evidence fuels his skepticism: Today’s California seals wean their pups in just 4 months, a feat uniting them with Antarctic seals. This leads Costa to conclude that northern fur seals belong in the icy waters where they mainly live today.

Koch sees his point, but maintains that fur seals weren’t a rarity in California. Studies over the last decade have found that they were the most common seal species at many archeological sites, from Santa Barbara to the Oregon border. But until the number of ancient seals that lived onshore is well established, the importance of California’s mainland fur seals will remain a matter of debate.

In the meantime, should the seals’ ancient history alter how ecologists work to protect them today? A precedent for applying archaeological proof to questions of conservation has already been set, in Yellowstone National Park. Opponents of the reintroduction of wolves to the park argued that the wolves weren’t a crucial part of the community, says National Park Service archaeologist Ken Cannon. But fossil evidence contradicted their story. “Tens of thousands of wolves once roamed Yellowstone,” he says. So wolves were let back in.

Similarly, Cannon says, northern fur seals could be brought back to the mainland at sites specially designated for them, much like the dedication of Año Nuevo to the northern elephant seal. At the very least, any conservation plan should consider all the information available so that wildlife managers and the public can make an informed decision. “Whether or not we reintroduce a species becomes a larger societal issue about what people want,” he says.

However, according to Costa, the odds run against a successful re-colonization of fur seals. The animals are stubborn, typically giving birth within a few meters of where they themselves were born. Young females sometimes strike out for new ground, but the world’s population is shrinking. “Seals generally move to new areas when the core population increases,” Costa says. “In a declining population, you don’t expect to see new areas developing.”

Even so, it isn’t impossible. Northern fur seals have proven they can make it in the waters of coastal California. In 1968, a crew of them found its way south to establish the breeding colony off the coast of Santa Barbara, on San Miguel Island. And 1986 marked the first year in recent times that a new pup was born on the South Farallon Island, near San Francisco. According to Peter Pyle, a Point Reyes Bird Observatory researcher, that island’s population of 20 seals is showing signs of growth. But the creatures are sensitive to human activity, Pyle cautions. “If they were to re-colonize the mainland, it would have to be somewhere remote —where there were no people. These days, it’s hard to find that.”

Other seals, as well as sea lions, may face a similar predicament, Koch says. “In Oregon, the abundant pinniped is the Steller sea lion; in southern California, the Guadalupe fur seal,” he says. “Today, all of them breed offshore. There may have been other seal rookeries on the mainland.” Did these pinnipeds get evicted from Pacific beaches like the northern fur seals did? Koch hopes scientists will start studying that question.

Koch sees a broader lesson here. Humans have made their mark on nature since prehistoric times, though the rate of environmental change has risen rapidly in the modern era. Since the goal of conservation is to preserve species well into the future, management efforts stand to benefit from consideration of the distant past.