Ancient teeth from Siberia rewrite the plague's timeline, revealing outbreaks 5,500 years ago

A cemetery's grim mystery

For years, the Ust'-Ida cemetery on the banks of the Angara River baffled archaeologists. An unusual number of children and adolescents lay in the graves, with no signs of violence or skeletal trauma to explain their deaths. When researchers turned to ancient DNA, the answer was startling: Yersinia pestis, the bacterium that caused the Black Death.

We focused on a specific site called Ust'-Ida, which presented a very unusual mortality profile. There was a notable excess of deceased children and adolescents and no clear explanation for it.

The team analysed dental pulp from 46 individuals buried across four hunter-gatherer cemeteries near Lake Baikal and found plague DNA in 18 of them, a 39% positivity rate, higher than some medieval plague pits. The findings were published Wednesday in the journal Nature.

A timeline pushed back

Until now, the oldest unambiguous evidence of a plague outbreak dated to about 5,300 years ago. The new genomes, recovered from teeth radiocarbon-dated to roughly 5,500 years before present, push that milestone back by at least two centuries. The data point to two distinct phases of lethal outbreaks among the region's nomadic fishing, hunting and gathering communities.

We found the oldest plague genome identified so far.

The discovery challenges the conventional view that mass disease outbreaks emerged only after humans settled into crowded agricultural societies. The hunter-gatherers of the Angara valley were living in small, mobile groups, yet the plague still tore through them.

Transmission from marmots to families

The hunter-gatherers likely contracted the bacterium by butchering or eating raw marmots, large ground squirrels that serve as the primary animal reservoir in the area. Person-to-person transmission then followed via coughing and sneezing, spreading the infection within families. Three young girls, two of them likely cousins, were buried side by side. An aunt and nephew shared one grave, while her niece was found in a separate nearby burial.

People were around to bury the dead who knew who these people were when they were alive. And that's a really human element to all of the scientific work.

Children were hit hardest. At two of the cemeteries, at least two-thirds of the dead were under 15, and many of the plague victims were aged 8 to 11. Researchers suspect that older individuals may have gained partial immunity from prior exposure, leaving the young exceptionally vulnerable.

An ancient pathogen with modern virulence

The strain recovered from Siberia lacked the genetic adaptations that later allowed bubonic plague to spread efficiently via fleas. Yet it proved highly lethal none the less. The bacterial genomes revealed a suite of virulence factors that, even without flea-borne transmission, could cause high mortality during person-to-person outbreaks.

Even before the bacterium developed efficient flea transmission, these ancient strains appear to have possessed a potent combination of virulence factors that could make the infection highly lethal.

The finding complicates an idealized picture of hunter-gatherer life, one free of the infectious diseases that later plagued dense settlements. Mass outbreaks, it now appears, were part of the human experience long before agriculture.

Myself, I had this very romantic notion... if we could just go back to that time, we'd be in a much better state. You get a result like this, and it just rocks the boat. You're happy you're born when you are, you know?

The research, led by teams in Copenhagen, Oxford, Cambridge and Alberta, suggests that plague originated among Central Asian hunter-gatherers and that devastating outbreaks were frequent, rewriting a chapter of human prehistory.