Ancient DNA points to plague outbreak in Siberia 5,500 years ago
Researchers say teeth from Lake Baikal burials preserve the oldest sequenced Yersinia pestis strain and evidence of a lethal outbreak.
By Maya Lindqvist · Senior Technology Correspondent
3 min read
Plague killed people in hunter-gatherer communities near Russia’s Lake Baikal about 5,500 years ago, according to a new ancient-DNA study. The finding matters because it pushes the earliest known plague outbreak into mobile foraging groups, before the disease appears in Neolithic farming communities.
Ruairidh Macleod of the University of Oxford and colleagues reported in Nature that they found DNA from Yersinia pestis, the bacterium that causes plague, in teeth from people buried at four cemeteries along the Angara River in southeastern Siberia. The team also sequenced what it describes as the oldest Y. pestis genome yet recovered.
Evidence from teeth and graves
The researchers examined dental-root samples from 46 ancient people. Teeth can preserve traces of pathogens that were circulating in the bloodstream at death, and the team used shotgun sequencing to screen for microbial DNA without knowing in advance which organisms might be present.
At Ust’-Ida I, one of the cemeteries, 11 of 31 tested people carried Y. pestis DNA, according to Macleod and his colleagues. Macleod said in a press conference that the detection pattern is consistent with plague having killed most or all of the people buried there, comparing it with results from a known plague mass grave at Smithfield in London.
Archaeologists with the Baikal Archaeology Project had already noted signs of an unusual mortality event at Ust’-Ida I, including many child burials, a cluster of radiocarbon dates and no evidence of violent deaths. The new DNA results give a likely cause, the researchers said.
A challenge to older assumptions
The study contests a common model in which major infectious disease outbreaks became a major human threat after farming, denser settlement and closer contact with domestic animals. Macleod and his co-authors wrote that the Lake Baikal evidence shows plague outbreaks among prehistoric hunter-gatherers centuries before known infections in Neolithic farmers.
Macleod said the result was unexpected because small, mobile groups have often been seen as poor conditions for an epidemic that could devastate a community. The Angara River groups lived by hunting, fishing and foraging, but the researchers said they appear to have maintained social and family links across long distances.
The same plague strain appeared at Ust’-Ida I and at Shumilikha, another cemetery 37 kilometers away, according to the study. The researchers said that pattern fits a shared outbreak across connected communities.
How the outbreak may have spread
The ancient strain lacked some genes associated with later bubonic plague, including traits tied to flea-borne transmission and bubo formation, according to the researchers. They argue that person-to-person respiratory spread, similar to pneumonic plague, is a plausible explanation for the rapid deaths among related people.
The team also points to marmots as a possible starting point. Macleod and colleagues said marmots remain plague reservoirs in the region, and long-standing hunting of marmots around Lake Baikal could have brought people into contact with infected animals through skinning or eating undercooked meat.
Family relationships reconstructed from human DNA suggest the disease moved through kin networks. The researchers described co-buried relatives with Y. pestis in their remains, including a boy and his aunt, and said such patterns are consistent with human transmission during a short, deadly outbreak.
Children appear to have been hit especially hard. The study found a marked concentration of deaths among children aged 7 to 11, while adults over 20 had the lowest death rate. Oxford immunologist Astrid Iversen said the ancient bacterium carried a gene for a superantigenic toxin, which can trigger a harmful immune overreaction, and that children are more vulnerable because their immune systems are still developing.
University of Copenhagen evolutionary geneticist Eske Willerslev said the genome may help researchers understand which combinations of mutations can persist in pathogens. Although the ancient strain differs from plague bacteria circulating today, the team argues that its genome offers evidence about how dangerous pathogen traits can emerge and endure.
This story draws on original reporting from Ars Technica.