For a few years in the early 1990s, the contamination problem was so acute that it nearly brought down the field. Eager to stake a claim in the burgeoning science, researchers raced to extract DNA from any ancient object they could find. A slew of remarkable papers quickly followed: Analyses were reported of DNA from a 7,000-year-old human brain, a dinosaur, and a 23-million-year-old insect preserved in amber. Although a few findings proved reproducible, most were embarrassingly debunked. For instance, the renowned paleobiologist Svante Pääbo, then at the University of California at Berkeley, claimed to have recovered nuclear DNA from an Egyptian mummy. Follow-up experiments showed that the mummy’s DNA was probably Pääbo’s own.
Paleobiologist Alan Cooper (top right) and two members of his team examine a recent haul from the Irish Gulch Mine in the Yukon. The bones mostly came from the limbs of prehistoric bison and horses that once roamed here in great numbers. They are beautifully preserved: Eighty percent contain salvageable DNA.
To win the confidence of the scientific community, Cooper needed a meticulously controlled environment. So while still a postdoctoral student at Oxford, he wrangled a $2 million grant from the Wellcome Trust and the British government to build a state-of-the-art laboratory. Completed last June, the Ancient Biomolecules Centre keeps a computer registry of all its employees’ DNA, drawn from hair samples. Its researchers work in disposable Tyvek coveralls, booties, shower caps, and gloves. As a final prophylactic measure, the entire building is maintained at positive pressure: Should a door accidentally open, the lab’s air will rush out, but the outside air won’t seep in.
This past summer, Cooper and graduate student Beth Shapiro revealed the results of their bison study at the Third International Mammoth Conference, in Dawson. Compared with recent studies of mammoths found in the Siberian ice fields, the bison study seemed somewhat unglamorous. By paleobiology standards, however, the results were exotic. Cooper and Shapiro recovered DNA samples from more than 400 bison and entered those sequences, with their radiocarbon dates, into a modeling program. Developed to track the evolution of viruses like hepatitis and HIV, the program uses pieces of salvaged DNA to create a genetic family tree. Joins on the tree, known as coalescence points, mark the time at which two family lines diverged—or, traveling into the past, the point at which two lineages “coalesce” back into a common ancestor.
The frequency of the coalescence points goes down as the number of bison goes up. (Roughly, the more bison there are, the greater their genetic diversity and the longer it will take to find the common ancestor of two animals chosen at random—just as one would expect residents of a small English village to be more closely related than two people picked at random from the world population.) Had the bison actually been hunted to death, as Cooper first believed, there would have been a rapid population drop-off around 12,000 years ago. Instead, the number of bison peaked about 30,000 years ago, then tanked spectacularly. From highs of tens of millions of bison, the breeding population dropped to hundreds at most. For Cooper, this was baffling not just because the bison were dying earlier than expected but because they were dying for no apparent reason—some 10,000 years before the brutal cold of the glacial maximum and some 20,000 years before the first known humans arrived. “Even if there were humans—and I wouldn’t be surprised if there were a few of them—we’re talking about a population of 10 million bison, which is bloody huge,” Cooper says. “There’s no way people could have done that kind of damage without leaving some pretty major archaeological signs. If they were driving them over a cliff or something, you’d find masses of bones at the bottom. But there’s no sign of anything like that.”
As Cooper sees it, the most likely culprit was climate—though the effects now appear to have occurred much earlier than expected. “This is not a time of extreme heat or cold, as you’d think,” he says. “Something subtler in the lead-up, such as increasing aridity and changes in vegetation, may be doing the damage.” Interestingly, the timing of the bison die-off matches another mysterious disappearance: the vanishing of Beringia’s brown bears. “There’s clearly something severe going on in the environment at this point,” Cooper says. “But so far, neither the climatologists nor the paleontologists have identified it.” It’s possible, he adds, that the few survivors, unlike some of the other megafauna, were genetically diverse enough to adapt to their new circumstances. Then humans showed up. “Humans were probably the nail in the coffin,” he says. “But it was climate that created this dead-man-walking situation, with diversity so buggered that the animals were just ready to be knocked over.”
Not every biologist agrees. Some believe that humans infected Beringia with a virulent, species-crossing disease, although no one has found clear evidence of it. Paleontologist Paul Matheus of the Alaska Quaternary Center at the University of Alaska has a broader complaint. “With ancient DNA, the flash factor is high,” he says. “There are biologists who’ve spent their lives studying the local ecology and biology, and these geneticists’ ideas don’t always agree with what we’ve found. You have to be careful or you end up with an oversimplified view of how these systems work. At worst, the attitude is, if the DNA says it, it must be true.”
Even detractors agree that Cooper is obsessed with accuracy. But ancient DNA results are notoriously tricky. Cooper recently conducted a study of Viking DNA that showed many of them to be of Middle Eastern descent, an impossible result. By tracing the problem, he discovered that the DNA extracted from the Vikings had mutated consistently at a key point that geneticists use to determine a person’s ancestry—in this case, the splitting point for Middle Eastern and European lineages.
Cooper’s efforts are more than an academic exercise. Given that our own changing climate is hotly debated, the fate of the ancient megafauna could help clarify the future as well as the past. Thirty thousand years ago, Cooper says, animals could respond to environmental changes by migrating. These days they are increasingly hemmed in by human development, so future temperature shifts are likely to cause even more rapid extinctions. In the meantime, Cooper is analyzing Beringian horse DNA to see whether it matches the bison results. The two species have only slightly different ecological needs, so comparing them should give a better idea of what killed them off. “It’s a bit twisted, really,” he concludes. “On the one hand, it looks like humans didn’t carry out the slaughter we thought they had. On the other hand, climate change seems to cause problems much earlier than anyone thought.”
Imagine what paleobiologists 10,000 years from now will say when they look back on our world.