Europe’s first farming populations were wiped out by plague, say researchers who have identified genomes of a 4,900-year-old strain of the plague-causing bacterium Yersinia pestis from a Neolithic burial site in Sweden.

The scientists say their discovery suggests that plague emerged and spread through Europe earlier than was previously thought — but others aren’t so convinced.

The Y. pestis sequences are as old as any known plague strain — and they sit closer than any other to the base of the deadly pathogen’s evolutionary tree. “We are at the beginning of the evolution of this disease,” says Simon Rasmussen, a computational biologist at the University of Copenhagen who led the study, published on 6 December in Cell ¹ .

Other scientists say the strain’s discovery is significant — but that it doesn’t back up the authors’ bold claims about the spread of plague through Neolithic Europe. “I don’t think it is definitive, and in three to five years, people might think differently,” says Mark Achtman, a bacterial population geneticist at the University of Warwick in Coventry, UK.

Mega-settlement mystery

Europe’s first farming populations descended largely from Middle Eastern groups that trekked north and westward beginning 8,000–9,000 years ago. They kept livestock and lived in densely populated communities — ‘mega-settlements’ in eastern Europe comprised thousands of living structures and may have had tens of thousands of inhabitants.

But these settlements vanished entirely from the archaeological record around 5,400 years ago, followed by smaller Neolithic settlements in Northern and Western Europe. Their disappearance is something of a mystery.

Archaeologists have attributed the decline to various factors, such as over-exploitation of natural resources. Another suggestion is that technologically advanced groups migrated from the steppes of present-day Ukraine and Russia. Studies of ancient human genomes ^{2 , 3} have linked a dramatic shift in the genetics of Europe, beginning around 4,500 years ago, to the arrival of the steppe populations — mostly individuals associated with a culture dubbed the Yamnaya.

In 2015, Rasmussen’s team discovered ⁴ plague DNA sequences in individuals with steppe ancestry, and they and other scientists proposed that these groups seeded outbreaks of the disease in late Neolithic populations. But his team now wonders whether plague had swept through Europe before the arrival of steppe populations.

Emerging pathogen

The new strain come from two individuals found buried in a Neolithic settlement in western Sweden. Rasmussen’s team identified Y. pestis sequences in publicly available data from previous studies that examined the genetics of the region’s human inhabitants.

An evolutionary analysis found that the Swedish strain diverged from all other known plague strains around 5,700 years ago — hundreds of years before the steppe populations arrived in Western and central Europe. Rasmussen’s team suggests that plague first emerged in European mega-settlements — “the textbook example of where pathogens evolve”, he says — and then spread eventually to Sweden through trade networks, and not the migration of people with steppe ancestry.

“The earliest forms of plague spread before the steppe migrations and probably killed off a good chunk of Neolithic populations,” says Kristian Kristiansen, an archaeologist at the University of Gothenburg in Sweden and a co-author of the study. He predicts that burials from mega-settlements will harbour even more evolutionarily ancient strains of plague.

Scepticism

Barbara Bramanti, a molecular and physical anthropologist at the University of Oslo, says it’s exciting to find plague in Neolithic settlements — but not surprising. She says the hypothesis that plague emerged in mega-settlements is reasonable, given their unprecedented population density, but is not proven until plague DNA is actually found.

Achtman is glad to see two new plague genomes — especially from strains so deep in the bacterium’s evolutionary tree — but questions the conclusion. “The rest is speculation, but interesting speculation,” he says. “I like it and will recommend it to my students. But I don’t think it will be the last word.”

Johannes Krause, a palaeogeneticist at the Max Planck Institute for the Science of Human History in Jena, Germany, is more critical and says the suggestions are not backed up by data. “The authors speculate about the emergence in central Eastern Europe and dissemination by trade. They have no plague genomes from there,” he says.

In 2017, his team suggested ⁵ that plague entered Europe during the Neolithic and was then spread by individuals with steppe ancestry, on the basis of late Neolithic and early Bronze Age plague genomes. Nothing in the latest paper changes his view, he says.

It’s plausible that plague emerged in mega-settlements, says Philipp Stockhammer, an archaeologist at the Ludwig Maximilian University of Munich in Germany. But he doesn’t see how long-distance trading networks could have propelled its spread. “If you get the plague, you don’t go and travel a few hundred kilometres. You die.”