Plague linked to mysterious disappearance of Europe’s first farmers

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The oldest known plague victims date back to about 5,000 years ago in Europe. But it has never been clear whether two cases, one in Latvia and one in Sweden, were isolated and sporadic or evidence of a wider outbreak.

A new study, based on ancient DNA found in 108 prehistoric individuals excavated from nine graves in Sweden and Denmark, suggests that an ancient form of the plague was widespread among Europe’s first farmers. This could explain why this population mysteriously died out over a period of 400 years.

“It’s pretty consistent across Northern Europe, France and Sweden, even though there are quite big differences in the archaeology, we still see the same pattern, they just disappear,” said Frederik Seersholm, a postdoctoral researcher at the Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen in Denmark and lead author of the study published Wednesday in the journal Nature.

This group, known as Neolithic farmers, migrated from the eastern Mediterranean, replacing small groups of hunter-gatherers and bringing agriculture and settled lifestyles to northwestern Europe for the first time some 6,000 to 7,000 years ago. Their legacy lives on in the continent’s many megalithic tombs and monuments, the most famous of which is Stonehenge.

Archaeologists are hotly debated about the cause of the population’s disappearance between 5,300 and 4,900 years ago. Some attribute their demise to an agricultural crisis caused by climate change, others suspect disease.

“Suddenly, there are no more people buried (at these monuments). And the people who were responsible for building these megaliths (are gone),” Seersholm said.

According to Seersholm, violence probably played no role in the next wave of newcomers, the so-called Yamnaya, who arrived after a period of archaeological record from the Eurasian steppe.

The study found that forms of the bacteria that causes plague were present in 1 in 6 ancient samples, suggesting that infection with the disease was not rare.

“These cases of plague date right into the period where we know the Neolithic decline was happening. So this is very strong circumstantial evidence that plague may have played a role in this population decline,” he said.

Genetic information about pathogens can be stored in human DNA, allowing scientists to travel through time and learn more about ancient diseases and how they evolved.

Yersinia pestis, the bacterium that causes plague, was the most prevalent of the six pathogens identified in the new study. The bacterium was present in 18 people, or 17% of the 108 people studied.

However, the study suggests that the true prevalence of the plague at the time may have been much higher, since ancient DNA can only be extracted from well-preserved human remains. (It’s also not possible to know for sure whether the people studied died from the plague — only that they were infected.)

Karl-Göran Sjögren

Archaeologists excavate a grave in Frälsegården, Sweden in 2001. DNA extracted from a number of bones showed the presence of the bacteria that causes the plague.

Still, the study authors said their findings did not necessarily point to a rapid and deadly plague epidemic. The bacteria were found in the remains of four of the six generations buried in some of the graves.

“I expected the plague to only be present in the last generation, which would be evidence that the plague kills them all, and that was it,” said Seersholm, who constructed family trees from the graves using the ancestry information in the ancient DNA.

“I also expected the plague to be exactly the same, that every single DNA base pair would be exactly the same, because that’s what you would expect if you saw a rapid outbreak of a disease, but that’s not what we found,” he said.

Instead, the team found evidence of three separate infection events, plus several variants of the bacteria that cause plague.

“The big question then is, how come the plague didn’t just kill everyone in the beginning? And that was confusing to us too, so we started looking at the genes to see if we could find some kind of explanation,” he said.

The team found instances where plague genes had been rearranged – lost, added or moved within the DNA sequences – which could potentially have affected the virulence of the pathogen over the course of a generation.

“It’s in a region of the genome where we know virulence is encoded, and (that’s) the reason our hypothesis is that it was more virulent (over the generations),” Seersholm said. “But this is, of course, this is very, very difficult to test, because you can’t just grow any old (bacterium).”

Given that the remains were carefully buried in a grave, Seersholm said it’s possible that the genetic data examined in the study captured the very beginnings of a plague epidemic. It’s also likely that the disease was less severe than the bubonic plague that caused the Black Death, the world’s most devastating plague epidemic that killed an estimated half of Europe’s population over the course of seven years during the Middle Ages.

Moreover, because the variants found in the samples lacked a gene that geneticists know is crucial for the bacteria to survive in a flea’s digestive tract, the resulting disease was unlikely to be identical to bubonic plague, which is spread by fleas carried by rodents, the study said. Bubonic plague still exists today, and symptoms include painful, swollen lymph nodes called buboes in the groin, armpit or neck, as well as fever, chills and cough.

The research suggests that the plague in Scandinavia at the time was probably transmitted from person to person, rather than sporadically from animals. However, it is not possible to know how deadly or chronic the disease was, said Mark Thomas, professor of evolutionary genetics at University College London.

However, Thomas, who was not involved in the latest research but was part of the team that first mapped the Neolithic decline, said he was less convinced that the plague was the main reason for the larger population decline. He said it happened at different times across Europe and was probably the result of a combination of factors, including poor farming practices that depleted the soil and widespread ill health.

“Neolithic people were very weak in terms of their general health. Their bones look bad,” Thomas said.

“There could have been a more general increase in pathogen burden,” he added. However, “from a DNA point of view,” Yersinia pestis is one of the diseases that is most visible to archaeological scientists and thus easier to identify and study.

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