Ancient DNA traces plague through hunter-gatherer families at Lake Baikal 5,500 years ago

Eighteen of 46 is 39 percent, and the 46 is the number of people whose remains could be tested at the four cemeteries, not the number of people living in those groups ^[4][5][2]. Cemetery detection rates measure who was buried and excavated, and how well DNA survived in a tooth. The University of Copenhagen release says the Baikal rate runs higher than what has been reported at some medieval plague burials ^[4]. The two figures are not directly comparable, though: those medieval graves were dug and sampled under different criteria.

The stronger part of the case is the patterning. The team combined the bacterial genomes with archaeology, genetic relatedness and radiocarbon dating ^[21], and the dates place many of the deaths close together, with siblings apparently dying together and other graves holding parents and children ^[7].

"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," said Ruairidh Macleod, the lead author. Macleod carried out the work as a PhD student at the University of Cambridge and is now a research fellow at Oxford ^[8][9].

That resolves a long-standing archaeological problem at the two largest sites ^[6]. "The unusually high number of children and the short timespan was a real puzzle that we've been trying to solve since the 1990s. Finding out that plague was the cause is extraordinary, but it makes so much sense," said Andrzej Weber, the University of Alberta archaeologist who leads the Baikal Archaeology Project ^[10][11].

The genomes also carry a superantigen, a toxin-producing genetic factor the team did not see in historic plague strains ^[12]. Superantigens can push the immune system into reacting with unusual intensity, and that reaction can produce severe inflammation ^[13]. "This finding changes our understanding of the earliest plague outbreaks: 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," said Martin Sikora, a senior author. Sikora is an associate professor at the University of Copenhagen ^[14][15]. The release documents the factor's presence in the ancient genomes. It reports no test of what the factor does in a living host.

Earlier work had found that ancient Yersinia pestis was missing some of the genetic features that later let bubonic plague move efficiently through fleas and rodents. Researchers took that to mean the earliest strains could not trigger severe outbreaks ^[18]. Eske Willerslev is a senior author and a professor at Copenhagen and Cambridge. "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," he said ^[16][17]. The material released with the paper does not say how the infection moved between families in small mobile groups. The authors conclude that some of the earliest known plague outbreaks may already have been as deadly as later historical epidemics, particularly for children ^[19].