The source of the Black Death in 14th-century central Eurasia

The geographic origin of the medieval Black Death (1346-1353 CE) has been a topic of continuous investigation due to the pandemic's extensive demographic impact and long-lasting consequences. To date, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk Kul of modern-day Kyrgyzstan. These sites are thought to have housed victims of a 14th-century epidemic, as tombstone inscriptions directly dated to 1338-1339 CE state “pestilence” as a cause of death for the buried individuals. Here, we report ancient DNA data from seven individuals unearthed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium, Yersinia pestis, in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the 14th century. Comparisons with present-day genetic diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early 14th-century source of the Second Plague Pandemic in central Eurasia.