Did a new form of plague destroy Europe’s Stone Age societies?

Nearly 5000 years ago, a 20-year-old woman was buried in a tomb in Sweden, one of Europe’s early farmers dead in her prime. Now, researchers have discovered what killed her—Yersinia pestis, the bacterium that causes plague. The sample is one of the oldest ever found, and it belongs to a previously unknown branch of the Y. pestis evolutionary tree. This newly discovered strain of plague could have caused the collapse of large Stone Age settlements across Europe in what might be the world’s first pandemic, researchers on the project say. But other scientists contend there isn’t yet enough evidence to prove the case.

“Plague is starting to seem like it’s everywhere,” says Kyle Harper, a historian at the University of Oklahoma in Norman who studies how the disease affected human societies. Ancient plague genomes, such as the one in the new study, show “we have a really long history with this germ,” he says.

Until now, the oldest known strain of plague came to Europe with the Yamnaya, herders from the central Eurasian steppe who swept into the continent some 4800 years ago. That was followed, several thousand years later, by the strain that led to both the Justinian Plague, which afflicted the Roman Empire in the sixth century C.E., and the Black Death, which killed half of Europe’s population in the 1300s.

The discovery of the new strain was fortuitous. A team led by Simon Rasmussen, a computational biologist at the University of Copenhagen, and Nicolás Rascovan, a biologist at Aix-Marseille University in France, were scanning publicly available ancient DNA datasets for the genetic sequences of common human pathogens. They found Y. pestis sequences in the teeth of the 20-year-old woman, who was buried in the Frälsegården grave in western Sweden, and in the teeth of another person buried in the same grave, they report today in Cell . Both were farmers from Scandinavia’s Funnel Beaker culture, and neither had any trace of Yamnaya ancestry—meaning a form of plague was present in Europe before the steppe migrants arrived. That the bacterium was preserved in their teeth means it was circulating in their blood and very likely killed them, Rasmussen says.

The newly discovered Neolithic bacterium belongs to a branch of the plague family tree separate from the later, better-known strains. It split off from a common ancestor about 5700 years ago, Rasmussen and Rascovan say. But it’s not the common ancestor itself, meaning it doesn’t reveal where or when plague originated, says Johannes Krause, a geneticist at the Max Planck Institute for the Science of Human History in Jena, Germany, who has also studied ancient plague. “I’m not sure we have a good sense of how far back [plague] goes,” agrees Anne Stone, an anthropological geneticist who studies ancient pathogens at Arizona State University in Tempe.

Rasmussen and Rascovan have an idea. During the Neolithic, the region in Eastern Europe that today includes Moldova, Romania, and parts of Ukraine was home to large “megasettlements” of tens of thousands of people belonging to what archaeologists call the Trypillia culture. Though their settlements weren’t complex enough to qualify as cities, their residents still lived in close quarters with poor sanitation and stores of grain that would have attracted rodents, Y. pestis’s wild host. “These megasettlements are the textbook example of a place where a pathogen could evolve,” Rasmussen says.

But about 5400 years ago, many of the megasettlements collapsed. Residents died or moved away, and the buildings they abandoned were burned. Rasmussen and Rascovan propose their new strain of plague might be the culprit. “Maybe this is the first time that a huge society collapses based on plague,” Rasmussen says. And because these megasettlements were connected to other communities all over Europe by trade routes, the bacterium could have easily spread to places such as Sweden. “This could in principle be the first pandemic,” Rasmussen says.

Still, the only way to know for sure would be to find evidence of Y. pestis in the collapsing megasettlements themselves. Without that, it’s “highly speculative,” Krause says. And this early strain does not have the genetic adaptations that made later ones so easy to catch, such as their ability to spread from rodents to humans through fleas. “Does this particular branch of Y. pestis have what it takes to cause a pandemic?” Stone wonders. Without knowing more about this strain, exactly how the 20-year-old woman caught the disease—and whether she was a victim of a wider pandemic—may remain a mystery.

*Correction, 6 December, 2:27 p.m.: This article originally stated that the ancient plague strain likely didn't affect the lungs. In fact, it could have caused pneumonic plague.