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Ancient DNA Analysis Suggests Black Death Precursor Arose in Central Asia

Yersinia pestis bacteria

NEW YORK — The precursor bacterium to the Black Death likely arose in Central Asia, a new ancient DNA-based analysis has found.

The Black Death swept across Europe, the Middle East, and northern Africa between 1346 and 1353 where it is estimated to have killed about 60 percent of the population. It then settled into a 500-year-long pandemic known as the Second Plague Pandemic that lasted until the early 19th century. But where the Yersinia pestis strain that caused the pandemic arose has been unclear, with some studies pointing to western Eurasia or East Asia.

Archaeological studies uncovered cemeteries in what is now Kyrgyzstan with graves dating back to 1338 and 1339 — before the Black Death — that had markers indicating those buried had died of a pestilence. To further investigate, researchers from the Max Planck Institute for Evolutionary Anthropology and elsewhere collected DNA samples from remains in that cemetery.

As they reported in Nature this week, the researchers found some individuals buried there were infected with Y. pestis — one that appears to be a forerunner of the Black Death. Additional analyses of modern Y. pestis found that the ancient samples are most closely related to present-day plague found in animals near the Tian Shan mountains on the border of China, Kyrgyzstan, and Kazakhstan, further bolstering the idea that the Y. pestis strain ancestral to the Black Death arose there.

"These results, together with other analysis that we did for this paper, led us to conclude that the source location and the time when plague emerged before causing the Black Death was most likely in Central Asia, and that this emergence likely happened during the first half of the 14th century," first author Maria Spyrou, a postdoc at the University of Tübingen in Germany, said during a press briefing.

The researchers generated shotgun metagenomic data for seven individuals buried in northern Kyrgyzstan who died in 1338 or 1339 to find three of the individuals harbored pestis DNA. Additional whole-genome Y. pestis capture analyses generated 6.7-fold and 2.8-fold average Y. pestis genome coverage for two samples and a lower 0.13-fold coverage for a third sample. Still, this suggested to the researchers that the pestilence referred to on the grave makers was fueled by Y. pestis.

When the researchers then compared the two higher-coverage Y. pestis samples to other Y. pestis genomes, they found that the ancient samples found in the ancient cemeteries were highly similar to strains linked to the Black Death. The samples, the researchers noted, differed by two SNPs.

A further phylogenetic analysis indicated that these ancient samples are the most recent common ancestor of the strains associated with the Black Death, the emergence of which was a time of diversification for Y. pestis. Additionally, four of the five main lineages of Y. pestis appear to be descendants of these ancient cemetery samples.

At the same time, the researchers found these ancient samples were closely related to present-day plague isolated in the same region, found largely among marmots there, indicating genetic continuity of plague in the region and bolstering the notion that plague that gave rise to the Black Death and subsequent strains emerged there.

Additional archaeological and historical evidence indicated that these communities engaged in long-distance trade. For instance, grave goods like pearls, silks, and coins that were minted far away point to the region being a hub of long-distance trade, coauthor Philip Slavin from the University of Stirling noted during the press briefing.

Because of those ties, the researchers said it is likely that Y. pestis spread from what is now Kyrgyzstan to the Black Sea and into Europe along trade routes.

The findings also underscore the need to have a better understanding of what infectious diseases may be circulating in various animals and how they may then emerge. "To understand how those strains develop, how they get transmitted, how they mutate, how they evolve, but also how they disappear is, I think [it is] very, very important to consider both the evolutionary picture, but also the environmental and socioeconomic reality in which those strains originated," Slavin added. "And that would be, I think, a very major way forward to understand the phenomenon of emergent epidemic diseases."