An Ancient Case of the Plague Could Rewrite History

A 4,900-year-old skeleton has turned the accepted story of the disease on its head.

An excavation of human remains
The remains of the young woman in Sweden whose tooth was found to contain the DNA of plague bacteria (Karl-Göran Sjögren)

The troublesome teeth belonged to a woman buried in Sweden. She lived 4,900 years ago, and she died young. Archaeologists found her at the turn of the last millennium, her bones jumbled up with dozens of others in a limestone tomb. Geneticists sequenced her DNA a few years ago, revealing her to be, unsurprisingly, one of the Neolithic farmers who occupied Europe at the time.

Only when scientists reexamined DNA from two of her teeth last year did they notice something shocking: Her DNA was in there all right, but so were genetic sequences from Yersinia pestis, the bacterium that causes plague. The plague is known to have swept through Europe in later times—most infamously as the Black Death during the Middle Ages. But scientists thought the disease had originated thousands of miles away in Asia. What was it doing this far west, in Sweden, this long ago?

“It was really unexpected,” says Nicolás Rascovan, a genetics researcher at Aix Marseille Université. The answer, he and his co-authors suggest in a new study, is that the plague actually originated in Europe. And the bacteria from the woman’s teeth might be the earliest evidence of a continent-wide epidemic, one that explains a sudden and mysterious collapse in the European population.

It’s a lot to conclude from just a few ancient teeth.

The team had set out looking for evidence of plague in publicly available genetic data sets. Getting DNA from ancient bones and teeth is still a fairly new procedure, and it has largely focused on the stuff from humans. But modern sequencing techniques pick out all the genetic material in a sample, which frequently includes a lot of contaminating bacteria. For this reason, “normally 95 percent, 99 percent of the data was just thrown into the Dumpster,” Simon Rasmussen, who studies pathogen evolution at the Technical University of Denmark and co-authored the study, told me. The idea was to look through all this genetic detritus for signs of Yersinia pestis. When people die of the plague, their blood has high levels of bacteria, which leave a distinct genetic signature in the dental pulp inside teeth.

Rascovan ultimately sorted through the genomes of about 100 ancient individuals found throughout Europe. When he found Yersinia pestis in the teeth of the 4,900-year-old woman in Sweden, he looked at other people buried in the same tomb. Up to 78 people were buried around the same time, suggesting a surge in deaths that could have become an epidemic. Indeed, a young man in the tomb also had fragments of plague bacteria in his teeth. The strain of Yersinia pestis in the grave site was distinct from all others ever sequenced. The team thinks that it diverged from other known strains 5,700 years ago.

Rasmussen and others had previously found plague bacteria in ancient human remains all over Eurasia. Prior to this discovery, the oldest and most genetically distinct strain had been found in Central Asia. This fit a neat narrative: Steppe pastoralists from Eurasia began migrating into western Europe around 4,900 years ago, and they could have brought the plague with them. The disease seemed to explain how they were able to supplant the farmers—like the Swedish woman—already living in Europe. In the span of a few centuries, the steppe pastoralists would replace 70 percent of the population in Central Europe and 90 percent in Great Britain. In fact, modern Europeans derive most of their ancestry from steppe pastoralists who came during this period.

But now, the dates don’t match up. If the Swedish plague strain diverged from Central Asian ones 5,700 years ago, but human migration to the region didn’t start until 4,900 years ago, how did plague get to Sweden? Rascovan and Rasmussen turned to their archaeologist colleagues, who saw that this development fit into another pattern: Populations in Europe were falling even before people from the steppes migrated there.

Around 6,000 years ago, mega-settlements as big as 10,000 to 20,000 people sprang up in what is now Moldova, Romania, and Ukraine. The settlements were regularly abandoned and then burned. Perhaps, the new study argues, plague spread through these sites. At the same time, innovations such as wheeled transport and metallurgy allowed distant trade routes to emerge, possibly connecting mega-settlements with far-flung villages like those in Sweden. Thus, some populations were dense enough for a new pathogen to emerge, and trade routes helped spread it across the continent. “This might actually be one of the first plague epidemics,” Rascovan says.

This is all quite speculative. “They’ve obviously got neat DNA results. They’re building a story about it, and it’s an interesting and potentially plausible story,” says Stephen Shennan, an archaeologist at University College London who has studied Europe’s population collapse. But no evidence exists of plague in the mega-settlements themselves. Finding that evidence won’t be easy. “We actually don’t know what they did with their dead,” says David Anthony, an anthropologist at Hartwick College. They didn’t build tombs or establish cemeteries, so ancient-DNA researchers have no bones to analyze for signs of the plague. There is one cave site associated with the mega-settlements, says Anthony, where skeletons might yield some clues.

These are still early days for the study of ancient pathogens. Data points are so few and far between that it’s like making sense of a photograph from just a handful of pixels. With a few teeth, you can lob bombs at previous hypotheses, but you can’t yet make a solid case for an alternative idea.

The next step is to find more ancient plague samples. Many teeth have likely already been sequenced, but not yet analyzed for plague. It’s probably smart to look in samples found across a wide geographic area, too. “In terms of where plague originally emerged, we really don’t know at this point,” says Kirsten Bos, who studies ancient pathogens at the Max Planck Institute. “We’re finding a genome in Sweden. Who would have thought we’d find something that far north?”

Scientists are already hunting for other pathogens such as hepatitis B, Salmonella, and tuberculosis in ancient DNA. In the past decade, ancient human genomes have told us a great deal about how people migrated around the world; now they’re telling us about the pathogens they carried, the lives they lived, and the deaths they died.

The story of how plague got to Sweden 4,900 years ago is likely still incomplete. But the disease seems to have been there. At the end of our conversation, Rasmussen began conjuring up such a past, in which death came without warning. “Imagine you live 5,000 years ago in a small farming village with only 20 to 50 people. Then all of a sudden, one of them brings home food or has been in another village trading. They get ill and die a few days later.”

“And,” Rascovan added, “they had to wait 5,000 years to know exactly what happened.”