Even Prehistoric Hunter-Gatherers Got the Plague

Plague is one of the deadliest infectious diseases in recorded history. The Justinian Plague ravaged the Mediterranean region and beyond from A.D. 541 to 750, and the 14th-century outbreak known as the Black Death killed nearly a third of Europe’s population.

Scientists now know that plague is caused by the bacterium Yersinia pestis, which spreads through animal-to-human transmission, including flea bites and contact with infected animals, as well as through human-to-human transmission via coughing and sneezing. But the origins of plague have remained a mystery.

The prevailing theory is that plague first emerged with the rise of agriculture during the Neolithic period. As humans transitioned from small, nomadic bands to the first densely populated settlements—shared with domesticated animals—it created ideal conditions for infectious diseases to spread.

But a June 17, 2026, paper published in Nature challenges the idea that plague required permanent human settlements to take hold. More than 5,500 years ago, a band of Siberian hunter-gatherers near Lake Baikal was stricken with a mysterious and deadly illness. By analyzing ancient DNA from their burial sites, researchers now believe the cause was plague.

The prehistoric Siberian burial sites represent the oldest known cases of plague and offer convincing evidence that infectious diseases plagued humans long before they settled in tightly packed communities.

“I think this really sheds light on the fact that major outbreaks of disease like this are universal throughout human history,” says Ruairidh Macleod, one of the paper’s lead authors and a research fellow at the University of Oxford.

In the 1980s, archaeologists in Russia's Lake Baikal region discovered the remains of 42 hunter-gatherers who died roughly 5,000 years ago and were carefully buried with ceremonial grave goods like clay vessels and arrowheads. Ancient burial sites like this aren’t uncommon in the region, but there was something different about these graves, says Macleod.

“Typically, in these hunter-gatherer cemetery sites, you'll find that they're reusing the same sites for hundreds of years at a time,” he says. “People keep coming back to the same place to bury their dead, and there's a real kind of continuity and tradition about that. But in this case, everybody seems to have died pretty much at the same time.”

Macleod and his fellow researchers—including scientists from Denmark, China, Canada and the United States—analyzed DNA extracted from the teeth of the Baikal skeletons and were surprised to find that nearly 40 percent of the deceased had been infected with plague.

“To put that in context, analysis from the East Smithfield Black Death Pit—which is a medieval plague pit in London—only returned a detection rate of about 20 percent, and you expect pretty much everybody there would have died of plague,” says Macleod. “These individuals are 5,500 years old, so getting a detection rate of 39 percent is pretty extraordinary.”

DNA analysis of the Baikal burial sites also revealed that each cemetery contained closely related individuals who died in two separate plague outbreaks, one about 5,520 years ago and another 400 to 600 years later. The disease was deadliest among children ages 8 to 11, who were often buried alongside their siblings. Two-thirds of the dead were younger than 15.

The bacteria that cause infectious diseases mutate and evolve just like all living things. The strains that survive are the varieties that find new ways to infect and spread. The plague that killed the prehistoric people of Lake Baikal was not the same strain of plague that struck Europe in the Middle Ages. The bubonic plague emerged 3,800 years ago when Yersinia pestis acquired a gene that allowed it to be transmitted through flea bites.

Scientists knew that earlier strains of plague existed, because isolated cases of plague have been found in infected individuals dating back thousands of years. The open question was whether these older varieties of plague were virulent enough to be fatal. The Baikal findings suggest they were.

The plague victims at Baikal were infected with a strain of pneumonic plague, a form of the disease that targets the respiratory system and is primarily spread through coughing. By sequencing the bacteria’s DNA, Macleod and his research team identified a gene associated with an extreme inflammatory response known as Kawasaki-like syndrome that is especially deadly in children.

In 1911, an epidemic of pneumonic plague known as the Manchurian Plague killed more than 60,000 people in northeastern China. The new Nature paper, however, cites the first direct archaeological evidence of a deadly plague outbreak in prehistoric times.

What’s amazing to Macleod is that DNA analysis indicates pneumonic plague didn’t diverge from the last common ancestor of all plague strains until 5,700 years ago. Just 200 years later, as the Baikal burials show, the disease had already spilled over from animal populations and was killing humans.

The new research also confirms that rodents play an outsized role in the transmission of plague. While flea-carrying rats were the primary vector of the bubonic plague, marmots—a large rodent native to parts of Asia—appear to have been the source of infection for the Lake Baikal victims.

Humans don’t need to be bitten by a marmot to catch the plague. It’s usually transmitted by eating undercooked marmot meat or while skinning marmots for their fur. Macleod thinks that the outbreaks in Baikal started with spillover from infected marmots, but spread through human-to-human contact. That’s why the burial sites contained so many close relatives, even though the cemeteries were separated by more than 20 miles.

“It's not the case that everybody ate from the same infected marmot one day and all died,” says Macleod. “We think that this is evidence of people passing it from one group to another.”

Because the Baikal plague outbreaks are the earliest ever identified, they lend support to the theory that Central Asian marmots were the original source of plague.

“There's a really deep evolutionary history between plague and marmots, and marmots are long believed to have been the natural host reservoir—the original host species in which plague kind of evolves,” says Macleod. “We see a lot of evidence for human interactions with marmots at Lake Baikal, including sites where people are collecting hundreds of marmot incisors and using them as grave goods.”

Macleod believes these 5,500-year-old findings remain relevant today because the world recently experienced another global pandemic that originated in a wild animal.

“I think it's about the risk of zoonotic disease outbreaks and understanding how severe that risk is,” says Macleod. “This was happening long before all of the international travel and high-density conditions that we have today, which makes us so much more susceptible.”