Human teeth found in 700-year-old graves may reveal where the Black Death started

Ancient DNA indicates that the deadliest bubonic plague pandemic in history began in a Central Asian valley and spread along the famous Silk Road trade route

Russian archaeologists conduct excavations in a medieval cemetery between 1885 and 1892, in present-day Kyrgyzstan.
Russian archaeologists conduct excavations in a medieval cemetery between 1885 and 1892, in present-day Kyrgyzstan.A.S. Leybin, agosto de 1886

During a frenzy of archaeological activity in the waning years of the 19th century, a team of Russians excavated two medieval cemeteries near Lake Issyk-Kul (Kyrgyzstan). In the tombs they found small treasures of coins and ornaments brought from the farthest corners of Eurasia along the Silk Road that passed through the region. The archaeologists noted an unusually large number of tombstones from 1338 and 1339, a mystery that endured to this day. A collaborative study conducted by historians, archaeologists and geneticists recently published in Nature analyzed the teeth of people buried in the cemetery, and discovered the DNA of Yersinia pestis, the bacterium that caused the deadly pandemic of bubonic plague known as the Black Death, which ravaged Europe and Asia a decade later.

One of the tombstone inscriptions reads, “In the Year 1649 [AD1338 in the Gregorian calendar used in most of the world], the Year of the Tiger. This is the tomb of the believer Sanmaq. [He] died of pestilence.” The last word on the tombstone caused great confusion among historians of that time period. Pestilence could indeed refer to the plague, but the pandemic that killed between 50 and 200 million people did not officially break out until 1347, when it was first reported in Black Sea port cities, Constantinople, Marseilles and Barcelona. Much is known about the Black Death –what bacteria caused it, how fleas from infected rats passed it on to humans, that the same strain has caused outbreaks for the last 500 years, and that it came from somewhere in Central Asia. But the precise point of origin has been a topic of intense debate among historians until now.

German, British, and Russian scientists obtained permission from local authorities to remove 50 milligrams of enamel and dentin from the teeth of 30 bodies disinterred from the cemetery and preserved in the Russian Academy of Sciences’ Peter the Great Museum of Anthropology and Ethnography (Kuntskamera, St. Petersburg). They were able to extract DNA from seven of the samples, which confirmed that the people were residents of the area where they were buried. But the most important finding came later–three of the samples analyzed contained foreign genetic material. It was DNA from a strain of Y. pestis bacteria, and not just any ordinary strain.

“[This strain] is the predecessor of 80% of all the currently circulating strains, including the Black Death strain, and all the strains that came after it.”
Johannes Krause, Director of the Max Planck Institute for Evolutionary Anthropology

Johannes Krause, director of the Max Planck Institute for Evolutionary Anthropology (Germany) and senior author of the study published in Nature, unequivocally stated, “”[This strain] is the predecessor of 80% of all the currently circulating strains, including the Black Death strain, and all the strains that came after it.” To support their claim, Krause and his colleagues built the phylogenetic tree of Y. pestis with the genome of 250 specimens, 47 of them from historical outbreaks. They observed that a star-shaped explosion and diversification of bacterium strains occurred around the middle of the 14th century. One particular strain detected in bodies buried in the Chüy Valley (northern Kyrgyzstan and southern Kazakhstan), where Lake Issyk-Kul is located, triggered the pandemic known as the Black Death.

University of Tübingen researcher Maria Spyrou, the study’s lead author, wrote, “We found that the ancient strains from Kyrgyzstan are located exactly at the central node of this massive diversification event. In other words, we found the source strain of the Black Death and even know the exact date when it started [1338].” The Russian archaeologists who excavated the two medieval cemeteries near Lake Issyk-Kul suspected that something unusual happened that year. During the decade leading up to 1338, no more than 20 people were buried each year in the Kara-Djigach and Burana cemeteries. That number doubled in 1338, and reached 100 deaths the following year. The dots began to connect.

All the evidence indicates that the first documented cases of Black Death occurred in 1347 in the port cities of modern-day Turkey (which has recently changed its name to Türkiye). The following months saw outbreaks in ports further and further west, hitting Athens, Naples, Marseilles and Barcelona by the spring of 1348. Within two years, the pandemic had reached Scandinavian countries. It also swept through North Africa, the Arab countries, India and China. But the deadly pandemic must have started in or near the Chüy Valley, at the foot of the Tian Shan mountain range that sprawls across the Kazakhstan, Kyrgyzstan, and the People’s Republic of China border region.

“Both cemeteries were located in the heart of the Silk Road trade network, right next to the road.”
Philip Slavin, historian at the University of Stirling (UK)

Philip Slavin, a University of Stirling (UK) historian and co-author of the study, noted the key role played by trade routes in transmitting the plague and its inception in the region under study. “Both cemeteries were located in the heart of the Silk Road trade network, right next to the road,” he wrote in an email interview.

However, some historians disagree with the study’s conclusions, and one skeptic is a prominent expert in the field. Ole J. Benedictow is a Norwegian professor emeritus at the Institute of Archaeology, Conservation, and History at the University of Oslo (Norway). He published his best-known book in 2004: The Black Death 1346-1353: The Complete History (updated last year in a second edition). In an email, Benedictow summarizes the central thesis of his work. “There is substantial historical evidence that the Black Death originally broke out in the lower part of the Volga [River], most likely in the delta, where there is an active plague reservoir that is amply documented by a large body of historical data, and which still causes plague cases today.” Benedictow believes it all started where Russia’s Volga River empties into the Caspian Sea, far from the Chüy Valley.

When the Black Death broke out, most of the rodents in the area ruled by the khanate of the Golden Horde (one of the Mongol Empire successor states) carried the plague pathogen. Benedictow said, “This area [the khanate] extended from the western border of China to the eastern border of present-day Romania.” He accepts that the genetic structure of the plague strain found in the lower Volga reservoir could be similar to the strain identified in the two cemeteries, but does not believe the latter strain triggered the pandemic. “Issyk-Kul is situated in a rather remote part of a vast area that has a reservoir of wild rodent plagues. An area like this will experience continual episodes of plague infections in people who come into contact with diseased rodents. This must have been true for the population in Issyk-Kul. Whether there was any contact between Issyk-Kul and the lower Volga area is unknown, but I doubt it.”

Benedictow acknowledges that analyses of ancient DNA can significantly contribute to the study of the history of plagues. “It’s valuable to have a basic understanding of a pathogen’s origin and development.” But he diplomatically cautioned, “I hope that people who read this excellent study [published in Nature] will also realize that the genetic history of plague is of limited interest and importance in itself.” Benedictow says, “The most important aspect of plagues and Black Death epidemics is their impact on historical society. The significance of such events is derived from the actions of people at the time, and the plague’s efficiency in propagating throughout society resulting from human culture and technology.”

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