The earliest known plague outbreak happened in what is now Russia 5,500 years ago. Scientists found the evidence in ancient teeth.

About 5,500 years ago, several dozen hunter-gatherers died near Lake Baikal. DNA from the bacterium that causes plague survived in their teeth. Science journalist Ilya Kabanov, who runs the Telegram channel Laiflong Muki, explains how a study of ancient burial grounds became something of a detective story — and why the discovery changes our understanding of the history of epidemics.

An archaeological detective story: How researchers found hunters who died mysteriously near Lake Baikal — and picked up the trail of plague

About 5,500 years ago, small groups of hunter-gatherers roamed along the Angara River in the Lake Baikal region, an area rich in deer, moose, fish, and marmots. They did not build cities, farm, or keep domestic animals other than dogs. Still, scientists know quite a bit about their way of life from studies of burial grounds. These ancient Siberians used bows and arrows, for example. They also knew how to fire pottery.

The burial grounds along the Angara were far apart, sometimes as much as 340 kilometers (about 210 miles). Yet the people buried in them shared recent ancestors. Traveling along the riverbanks or by water probably helped them stay in contact. Their genomes also show almost no evidence of inbreeding, suggesting they usually found partners outside their close circle of relatives. Their burial practices varied: At one burial ground, bodies were usually laid parallel to the river; at others, perpendicular to it.

For archaeologists, including specialists at Irkutsk State University and the Russian Academy of Sciences’ Institute of Ethnology and Anthropology, burial grounds are a major source of information about the region’s hunter-gatherers. Bones, the positioning of bodies, grave goods, radiocarbon dates, and ancient DNA can reveal diets, family relationships, and sometimes the circumstances of death. In a recent paper in Nature, an international team led by Eske Willerslev, including researchers from Russia, examined the remains of 46 people from four burial sites: Ust-Ida-1, Shumilikha, Bratsky Kamen, and Serovo.

As is often the case with Willerslev’s studies — one of which Meduza covered in an article about why mammoths went extinct — the new research reads like the plot of a true-crime podcast. There is a crime scene with human remains. Many of the people died within a short period, and an unusually large number of the victims were children and adolescents. Some graves contain relatives. Yet the bones show no signs of violence.

To investigate the mystery, the archaeologists brought in geneticists, who examined the ancient people’s teeth. If an infection entered the bloodstream shortly before death, traces of it can survive in dental tissue. The researchers screened ancient DNA for pathogens and found Yersinia pestis, the bacterium that causes plague, in 18 of the 46 people. At Ust-Ida, the largest burial ground studied, they found traces of plague in a third of those buried there (11 of 31). They also recovered a well-preserved plague genome from Shumilikha and several less complete ones from Bratsky Kamen and Serovo.

The presence of plague DNA in a body does not, by itself, prove that plague caused the person’s death. Someone could have been infected but died of another disease. In this case, however, too many clues lined up: closely clustered burial dates, infected people buried together, family relationships among the dead, unusually high child mortality, and no other obvious cause of death. The paper’s authors concluded that the infections were part of a disease outbreak in small hunter-gatherer communities rather than isolated cases.

The researchers suggest that people in the first phase of the outbreak may have died within a few decades — possibly much sooner. The bacterial genomes recovered from them were very similar, most likely indicating that the infections occurred during a single phase of the outbreak.

The archaeological evidence fits the genetic findings. Ust-Ida has an unusually large number of shared graves, with no evidence that they were reopened later to add more bodies. This suggests the deaths occurred at nearly the same time.

Another clue is the age of those who died. At Ust-Ida and Bratsky Kamen, child mortality was especially high, peaking at roughly 7.5 to 11 years of age. This pattern is unusual for other burial grounds in the Lake Baikal region from that period.

One grave at Bratsky Kamen, for example, held three girls roughly 4 to 9 years old. Two were most likely related, possibly cousins; the third may have belonged to the same maternal line. The researchers found Yersinia pestis DNA in all three. The paper’s authors see this as evidence that the infection spread within a family.

There is a similar pattern at Ust-Ida-1. One grave held an aunt and nephew, both of whom tested positive for plague. In other cases examined by Willerslev’s team, brothers, sisters, and other close relatives were buried together or in neighboring graves. The researchers could not confidently identify the bacterium in all of them, but that is to be expected with ancient DNA: A negative result does not always mean there was no infection.

The authors found no other obvious causes of death. The bones showed no signs of injuries that could explain such high mortality. In one case, they found traces of brucellosis, but they believe that infection was not fatal. Together, the clues make a fairly strong case for plague.

“We have found the earliest evidence of mass mortality caused by plague,” Eske Willerslev said at a press conference, explaining the significance of the discovery. “Plague is an important part of human history and has been with our species for a long time. By studying its origins and evolution, we gain a better understanding of our own history.”

Different ‘diagnoses’: Why the ‘Baikal’ plague is not quite the same disease that killed millions in medieval Europe

The strain found near Lake Baikal lacked the ymt gene, which helps the bacterium survive in a flea’s digestive tract and allows it to spread efficiently through flea bites. A strain with this gene emerged later. That means the infection spread differently around Lake Baikal 5,500 years ago.

Where did the infection come from? Marmots are the prime “suspects.” Today, natural plague hotspots in Central and Northeast Asia are often associated with marmots and other rodents. People could have become infected after hunting these animals, butchering their carcasses, or eating their meat raw or undercooked. Contact with wild animals was an ordinary part of life for the region’s hunter-gatherers, so transmission from animals to humans seems plausible.

The precise route of transmission, however, remains unknown. After the first infection, the disease may have spread between people through respiratory droplets. Family relationships among the dead and shared graves also point to that possibility.

Scientists do not yet know why children were especially vulnerable. It may have had to do with differences in their immune responses. Or adults may have encountered a similar infection before and had some protection. There may also have been behavioral reasons. But there is no direct evidence for these explanations.

Historical significance: How plague in ancient hunter-gatherers challenges a theory about the origins of human infections

The new study is significant for the debate over the origins of epidemics. They are often explained by the shift to farming and herding: People began living closer together, keeping domestic animals, and establishing permanent settlements. These changes created opportunities for infections to spread. But the Baikal discovery shows that this hypothesis does not explain everything.

The people of Ust-Ida, Shumilikha, Bratsky Kamen, and Serovo were not farmers. Local groups remained hunter-gatherers. They had pottery, bows, stone tools, and elaborate burial traditions, but no domesticated plants or animals other than dogs. Yet plague was already present. A natural reservoir, contact with wild animals, and small groups of relatives were enough for an outbreak.

Hunter-gatherer societies are usually considered unlikely settings for early epidemics: They are mobile, live in small groups, and do not depend on a single resource. That makes the discovery near Lake Baikal all the more significant.

Speaking to journalists, Eske Willerslev said that as a child he had dreamed of becoming a hunter-gatherer and imagined it as a very romantic life. After this study, he said, he no longer wanted to. There is some truth in the joke: Hunter-gatherers’ lives were more complicated and dangerous than we tend to imagine.