The plague may have wiped out most northern Europeans 5000 years ago

The Neolithic culture in Europe that produced megastructures such as Stonehenge went into a major decline around 5400 years ago. Now we have the best evidence yet that this was due to plague.

Sequencing of ancient DNA from 108 individuals who lived in northern Europe at this time has revealed that the plague bacterium Yersinia pestis was present in 18 of them when they died.

“We think that the plague did kill them,” says Frederik Seersholm at the University of Copenhagen in Denmark.

Around 5400 years ago, the population of Europe fell sharply, particularly in northern regions. Why this happened has long been a mystery.

Over the past decade, studies of ancient human DNA have revealed that local populations didn’t fully recover from the Neolithic decline. Instead, they were largely replaced by other people moving in from the Eurasian steppes. In Britain, by around 4000 years ago, for instance, less than 10 per cent of the population was derived from the people who built Stonehenge.

These studies of ancient humans also revealed several cases where the plague bacterium was present. This suggested a potential explanation – the plague might have wiped out Europe’s population, allowing the steppes people to move in with little opposition.

But not everyone agreed. Occasional sporadic plague cases are to be expected and aren’t evidence of a major pandemic, argued Ben Krause-Kyora at Kiel University in Germany in 2021. These early forms of Y. pestis were unlikely to cause a pandemic because their DNA shows they couldn’t survive in fleas, he and his colleagues wrote. Bites from infected fleas are the main way people contract bubonic plague, the form of the illness that killed people during the medieval Black Death.

So Seersholm and his colleagues set out to find more evidence of a plague pandemic. The 108 individuals whose DNA his team managed to sequence were buried in nine tombs in Sweden and Denmark. Most died between 5200 and 4900 years ago, and they represent several generations of four families.

There seem to have been three separate outbreaks of the plague over these generations. The last outbreak was caused by a strain with reshuffled genes that might have been much more dangerous.

“It’s present in a lot of individuals,” says Seersholm. “And it’s all the same version, which is exactly what you would expect if something spreads very quickly.”

The plague DNA was found mainly in teeth, which shows that the bacterium entered the blood and caused serious illness, and was probably the cause of death, he says. In some cases, closely related individuals were infected, implying person-to-person spread.

The team suggests this could be a result of Y. pestis infecting the lungs and spreading via droplets – a form of the illness known as pneumonic plague. Recent studies also indicate that human lice can cause bubonic plague, not just fleas, so it is possible that plague bacteria spread by this route.

“Of course, it’s worth noting that all of these individuals were buried properly,” says Seersholm, so society hadn’t broken down at this time. “If there was in fact an epidemic, we only see the very beginning of it.”

After about 4900 years ago, the megalithic tombs seem to have been abandoned for centuries. But 10 of the sequenced individuals were buried in them much later, most between 4100 and 3000 years ago. These individuals were of steppes origin, unrelated to those who built the tombs.

“It is 100 per cent complete replacement,” says Seersholm. “Five thousand years ago, these Neolithic people disappear. And now we show that plague was widespread and abundant at exactly the same time.”

The researchers aren’t claiming their findings are definitive, but they do bolster the case that plague caused the Neolithic decline, says Seersholm.

“I would say that we’ve definitely shown that it had the potential to spread within humans, and that it had the potential to kill an entire family, for example.”

Krause-Kyora accepts that the findings show the plague was highly prevalent in this particular place and time. “Our previous explanation needs to be revised somewhat, and we can’t just talk about isolated cases,” he says.

But there is no evidence of high prevalence in other regions, he says. And he thinks the normal burials show there was no deadly epidemic. “The results could even suggest that the Yersinia infection was more of a chronic disease over a long period of time.”

Seersholm and his team will now look for more evidence elsewhere in Europe. But the only way to know for sure how deadly the reshuffled strain was would be to bring it back to life, he says, and that is far too risky to attempt.

“I think that this paper will convince many colleagues who were skeptical about our previous work,” says Nicolás Rascovan at the Pasteur Institute in Paris, whose team proposed in 2018 that the plague was responsible for the Neolithic decline after finding it in two individuals from the period.