Plague did not arrive with medieval cities and rats. It was already decimating small populations in Siberia thousands of years before farming communities even existed, according to research published in Nature.
An international team sequenced genetic material from human remains found at four hunter-gatherer cemeteries near Lake Baikal in East Siberia. The work identified ancient strains of plague that were circulating among these prehistoric communities, upending the assumption that early forms of the disease were too weak to cause serious outbreaks.
Researchers detected DNA from Yersinia pestis, the bacterium responsible for plague, in 18 of the 46 individuals examined. Nearly 40 percent carried the infection, a detection rate that exceeds some medieval burial sites.
"Whether the earliest forms of plague were mild or virulent has been a matter of debate, but our findings demonstrate that these ancient strains were already highly lethal," said Eske Willerslev, senior author and professor at the University of Copenhagen and University of Cambridge.
A Deadly Pattern Hidden for Decades
For years, archaeologists had puzzled over an unusual pattern in these cemeteries: an abnormally high concentration of children and young teenagers among the dead. The burials clustered within remarkably short time windows. Radiocarbon dating showed that in some cases, siblings or parents and children died and were buried together in rapid succession.
"The unusually high number of children and the short timespan was a real puzzle that we've been trying to solve since the 1990s," said Andrzej Weber, an archaeologist at the University of Alberta and principal investigator of the Baikal Archaeology Project. "Finding out that plague was the cause is extraordinary, but it makes so much sense."
Ruairidh Macleod, lead author and now a research fellow at the University of Oxford, worked through these details as a PhD student. "Based on the plague DNA, the genetic relationships between the victims, the archaeological analysis and the radiocarbon dating, we've built a really clear, complete picture of what happened during these outbreaks," he said.
The findings challenge decades of scientific assumption. Earlier research suggested that ancient plague strains lacked genetic features needed for efficient transmission through fleas and rodents, leading many experts to conclude that these early versions could not trigger large or deadly epidemics.
The new evidence shows otherwise.
A Hidden Toxin Weapon
Researchers identified a distinctive superantigen in the ancient plague strains, a genetic factor that produces toxins and has not been found in later historic plague forms. Superantigens trigger powerful immune reactions and are linked to severe inflammatory responses, potentially making infections far more dangerous.
"This finding changes our understanding of the earliest plague outbreaks," said Martin Sikora, senior author and associate professor at the University of Copenhagen. "Even before the bacterium evolved efficient flea-borne transmission, these ancient strains appear to have carried a potent combination of virulence factors that could make infection highly lethal."
The ancient plague strains were capable of causing devastating mortality in small communities despite lacking the flea-borne transmission mechanisms associated with bubonic plague epidemics that would later ravage Europe. The impact was particularly severe on children.
Archaeological evidence suggests the hunter-gatherers in the study had close contact with marmots, large burrowing rodents that still harbor plague today. Researchers believe the disease jumped directly from infected animals to humans in these prehistoric groups, setting off the outbreaks that killed entire families in Siberia.
The work also supports the theory that plague first emerged in Central or North-East Asia before spreading across Eurasia through wild rodent populations over centuries and millennia.
Author Jessica Williams: "Plague has always been deadlier and older than we thought, and these ancient Siberian communities paid the price thousands of years before anyone knew what hit them."
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