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The Syriac engraving on the medieval tombstone was tantalizing: “This is the tomb of the believer Sanmaq. [He] died of pestilence.” Sanmaq, who was buried in 1338 near Lake Issyk Kul in what is now northern Kyrgyzstan, was one of many victims of the unnamed plague. By scrutinizing field notes and more photos from the Russian team that had excavated the graves in the 1880s, historian Philip Slavin found that at least 118 people from Sanmaq’s Central Asian trading community died in the epidemic.

Slavin was on the trail of the origin of the Black Death, which devastated Europe a decade after the Kyrgyzstan burials. But he knew the medieval diagnosis of “pestilence” encompassed many horrific diseases. “I was almost 100% certain it was the beginning of the Black Death,” says Slavin, a medieval historian at the University of Stirling. “But there was no way to prove it without DNA.”

Now, Slavin is senior author of a new study of ancient DNA from the “pestilence” victims showing they were indeed infected with the bacterium, Yersinia pestis, that caused the Black Death. The strain that killed them was ancestral to all the strains that rampaged across Europe a decade later and continued to kill for the next 500 years. The bacterium jumped from rodents to humans just before the Kyrgyzstan burials, perhaps after sudden changes in rainfall or temperature, the researchers propose this week in Nature.

“This is the place where it all started—the Wuhan of the Black Death,” says senior author and paleogeneticist Johannes Krause of the Max Planck Institute for Evolutionary Anthropology.

The finding confirms some other researchers’ hunches about Central Asia as a source for the Black Death strain, and pinpoints a precise time and place. “There’s not much doubt about it—[the region is] where you have lots of reservoirs of the plague,” says physical anthropologist Barbara Bramanti of the University of Ferrara.

In European historical accounts, the Black Death appears first in 1346 at ports on the Black Sea. Within a year it was in Europe, where scholars estimate it killed more than half of the population by 1353. In 1894, microbiologists identified Y. pestis as the cause. Ever since, they have debated where and when the deadly strain was born, considering China, Central Asia, India, and Genghis Khan’s armies marching from Mongolia.

A plague victim’s headstone discovered during the 1886 excavations at Kara-Djigach
A headstone of a “pestilence” victim buried near Lake Issyk KulA. S. Leybin

In 2020, a new analysis of more than 1300 modern and ancient genomes of Y. pestis narrowed the options. A team led by microbiologist Mark Achtman of the University of Warwick used a new software tool to sort all known strains of Y. pestis from humans and host animals into a family tree showing their evolution over 5500 years, starting with strains that were not closely related to the Black Death strain.

One branch of the tree underwent a “big bang” explosion of diversity at the time of the Black Death, creating a starlike pattern of four new lineages of Y. pestis whose descendant strains still persist in 40 species of rodents around the world. One of those lineages was the source of the Black Death and later outbreaks in Europe until the 18th century. The ancestral strain of this lineage was “literally the mother of them all,” Krause says.

Geneticists knew this mother strain did not arise in Europe, because the strains found in Black Death victims there differed by two mutations from the putative ancestral genome, says paleogeneticist Maria Spyrou of the University of Tübingen, who had been Krause’s postdoc. “We knew the European genomes were very close to origins of the Black Death, but not quite there,” she says. Several teams suspected the source was in Central Asia, where strains from rodents were the closest genetic match to the mother genome. But no one had DNA data on strains from human victims of the right time period.

Then Krause and Spyrou heard Slavin give a talk about the tombstones. When he reported that the people had died of “pestilence,” they each immediately thought, “We should do DNA!” Krause recalls.

Working with Slavin and Russian collaborators including Valeri Khartanovich of the Peter the Great Museum of Anthropology and Ethnography, where the Issyk Kul skulls were stored, Spyrou extracted DNA from the pulp of seven individuals’ teeth and found three were infected with Y. pestis. She was able to reconstruct a high-quality genome of the ancient strain that killed them.

That strain “fell exactly on the origin point of that big bang event” in the evolution of Y. pestis, Spyrou says. “That was incredibly exciting.”

Deadly spread

A new study pinpoints the first known cases of the plague that caused the Black Death, in people buried in 1338 near Lake Issyk Kul in today’s Kyrgyzstan. A decade later, bubonic plague had devastated Europe.

a map of Europe showing the spread of the bubonic plague
(Map) K. Franklin/Science; (Data) Ole J. Benedictow, The Complete History of the Black Death (2021)

The strain was closely related to ones found in rodents near Issyk Kul today. The authors suggest it spilled over to humans, perhaps from a marmot, which are abundant in the Tian Shan mountain region of northern Kyrgyzstan, southern Kazakhstan, and northwestern China. Sudden changes in rainfall or temperature could have led to surges in local rodent populations and the fleas or other insects they harbor. More rodents and their pests meant more opportunities to hop to a new host—humans—and adapt to it, says population biologist Nils Christian-Stenseth of the University of Oslo, who has shown a correlation between outbreaks of plague and warm, wet weather in Central Asia. He adds: “There are many good possibilities for plague reservoirs; you have the great gerbils, marmots, voles.”

The remaining mystery, he says, is how the Black Death traveled 3500 kilometers from Central Asia to the Black Sea, where historical accounts describe the Mongolian army hurling the bodies of plague victims into the besieged city of Caffa in Crimea in 1346 in an early form of biological warfare.

The meticulous archaeological records for each Kyrgyzstan grave offer hints, Slavin says. Many people were buried with pearls, coins, and other goods from the Indian Ocean, the Mediterranean, and Iran; some were apparently traders. As they traveled, their camel wagons may have harbored rats and fleas, long considered likely vectors for plague.

Another paper, in Nature Communications last month, suggests rats were perfectly positioned to help spread the Black Death. A team led by archaeologist David Orton of the University of York used the diversity of ancient DNA in rat bones to trace the ups and downs of black rat populations through history. In Europe, one population collapsed with the fall of the Roman Empire but was replaced by another in the 13th century, when growing cities offered new food and shelter for the rodents. Black rats and their fleas were everywhere at that time, Krause says, especially aboard ships traveling between the Black Sea and Mediterranean ports—the route the Black Death evidently followed.

Meanwhile, the Issyk Kul graveyard is giving names and identities to the first known victims of the Black Death. “To actually have Y. pestis from incredibly well dated burials is really exciting,” says bioarchaeologist Sharon De Witte of the University of South Carolina, Columbia. “We can clarify what other disease they were infected with and look at the biosocial factors that might have shaped risk of death in that first wave.”

As for Slavin, he’s still marveling at the discovery. “This was one of my dreams, to solve this outstanding puzzle.”

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