Around 5,000 years ago, the population in northern Europe collapsed, decimating Stone Age farming communities across the region. The cause of this calamity, called the Neolithic decline, has remained a matter of debate.

New research based on DNA obtained from human bones and teeth excavated from ancient burial tombs in Scandinavia – seven from an area in Sweden called Falbygden, one from coastal Sweden close to Gothenburg and one from Denmark – suggests disease, specifically the plague, may have driven the Neolithic decline.

The human remains came from a megalithic tomb type built of giant stones, called passage graves.

The remains of 108 people – 62 males, 45 females and one undetermined – were studied. Eighteen of them – 17% – were infected with plague at the time of death.

The researchers were able to chart the family tree of 38 people from Falbygden across six generations, spanning about 120 years. Twelve of them – 32% – were infected with plague. Genomic findings indicated that their community had experienced three distinct waves of an early form of plague.

The researchers reconstructed full genomes of the different strains of the plague-causing bacterium Yersinia pestis responsible for these waves. They determined that the last one may have been more virulent than the others and identified traits indicating the disease could have spread from person to person to cause an epidemic.

“We learned that the Neolithic plague is an ancestor to all later plague forms,” said University of Copenhagen geneticist Frederik Seersholm, lead author of the research published this week in the journal Nature.

A later form of this same pathogen caused the Justinian Plague of the 6th century AD and the 14th century Black Death that ravaged Europe, North Africa and the Middle East. Because the strains circulating during the Neolithic decline were much earlier versions, the plague may have produced different symptoms than witnessed in the epidemics millennia later.

The study demonstrated that the plague was abundant and widespread in the area examined.

“This high prevalence of plague indicates that plague epidemics played a substantial role in the Neolithic decline in this region,” University of Copenhagen geneticist and study co-author Martin Sikora said.

“Indeed, it seems plausible that the decline seen in other parts of Europe was also in some way affected by plague. We do already have evidence for plague in other megalithic sites in different parts of Northern Europe. And seeing how prevalent it was in Scandinavia, I would expect a similar picture to emerge once we study these other megaliths with the same resolution,” Sikora added.

The Neolithic, or New Stone Age, involved the adoption of farming and animal domestication in place of a roving hunter-gatherer lifestyle. The Neolithic decline population crash in Northern Europe occurred from about 3300 BC to 2900 BC. By that time, cities and sophisticated civilizations already had arisen in places like Egypt and Mesopotamia.

The populations of Scandinavia and Northwestern Europe ultimately disappeared entirely, only to be later replaced by people known as the Yamnaya who migrated from a steppe region spanning parts of present-day Ukraine. They are the ancestors of modern Northern Europeans.

“Up until now, multiple scenarios have been suggested that might explain the Neolithic decline: war or simple competition with steppe-related populations who became prevalent after the Neolithic decline; an agricultural crisis leading to widespread famine; and various diseases, including plague,” Seersholm said. “The challenge was that only a single plague genome had been identified before, and it was not known whether the disease was able to spread within a population of humans.”

The DNA evidence also offered insight into the social dynamics of these communities, showing men often had children with multiple women and that the women were brought in from neighbouring communities. The women appeared to be monogamous.

“Multiple reproductive partners could mean several wives. It could also mean men were allowed to find a new partner if they became widowers or they had mistresses,” Seersholm said.