Ancient plague genomes reveal the origins of the Black Death


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The origins of the Second Plague Pandemic have long been debated. One of the most popular theories has supported its source in East Asia, specifically in China. To the contrary, the only so-far available archaeological findings come from Central Asia, close to Lake Issyk Kul, in what is now Kyrgyzstan. These findings show that an epidemic devastated a local trading community in the years 1338 and 1339. Specifically, excavations that took place almost 140 years ago revealed tombstones indicating that individuals died in those years of an unknown epidemic or "pestilence."

In their study published in Nature, an international team of researchers analyzed ancient DNA from human remains as well as historical and archaeological data from two sites that were found to contain "pestilence" inscriptions. The team's first results were very encouraging, as DNA from the plague bacterium, Yersinia pestis, was identified in individuals with the year 1338 inscribed on their tombstones. "We could finally show that the epidemic mentioned on the tombstones was indeed caused by plague," says Phil Slavin, one of the senior authors of the study and historian at the University of Sterling, U.K.

The team now pieced together complete ancient plague genomes from the sites in Kyrgyzstan and investigated how they might relate with this Big Bang event. "We found that the ancient strains from Kyrgyzstan are positioned exactly at the node of this massive diversification event. In other words, we found the Black Death's source strain and we even know its exact date [meaning the year 1338]", says Maria Spyrou, lead author and researcher at the University of Tübingen.

"We found that modern strains most closely related to the ancient strain are today found in plague reservoirs around the Tian Shan mountains, so very close to where the ancient strain was found. This points to an origin of Black Death's ancestor in Central Asia," explains Johannes Krause, senior author of the study and director at the Max Planck Institute for Evolutionary Anthropology.

More information: Johannes Krause, The source of the Black Death in 14th-century central Eurasia, Nature (2022). DOI: 10.1038/s41586-022-04800-3. information: Nature

I have speculated for years that the host was always the marmot, which continues to harbor yestina pestis to the present day, and from which people of the steppe continue to get the plague.

"Although the dynamics that triggered the bacterium’s emergence in this region are unknown, previous studies showed that environmental factors, such as natural disasters and sudden changes in temperature and precipitation can have an impact on Y. pestis host ecologies and, as a result, can trigger outbreaks in human populations43,44,45,46. Although we have no evidence to infer such connections with the Kara-Djigach epidemic, we envision that our precise 1338–1339 date will serve as a reference point for future environmental, archaeological and historical research focusing on the events that caused a Y. pestis introduction into human populations and precipitated the second plague pandemic."

In another section they waffle as to whether the source of the spread was trade or warfare. I think it's quite clear that it was probably both. It spread from far, far in the east all the way to the Crimea. There, in the Mongols were laying siege to the Genovese colony of Caffa.

Now, the westerners have always maintained that as the Mongol soldiers started to sicken and die, their leader cut the heads off the bodies and catapulted them over the walls. Perhaps it might have been that prisoners were taken and brought inside.

It doesn't matter.

We know that the people inside Caffa began to die. People fled on a ship which sailed back west, with ports along the way. Each stop seeded another outbreak of the Black Death.

In 1345, the city of Caffa was razed by a vicious pandemic, in what would, centuries later, be recognized as the first use of biological warfare in history.After successfully repelling the first Mongol siege in 1343, Caffa certainly expected Jani Beg, the leader of Mongols, to strike again. But when he finally did, in 1345, he did not just come roaring with his Mongolian army, he came with something else, something more sinister: The Black Death."

"The Mongols benefitted immensely from the Genoese businesses in the bustling city as it earned them access to Italy’s largest commercial center while stimulating trade across its vast empire.

However, while many of the Mongols had been practicing Muslims from the 1200s, the Genoese merchants were Christians.

"These embers of hatred would burst into flames in 1343 in the city of Tana. After a fight between Genoese Christians and the local Muslims in Tana, one Muslim local was found dead.

Sensing the trouble that loomed like pregnant clouds over their heads, the Genoese fled to Caffa where they were granted protection.

"Not so long after their flight, the Mongols came after them. They demanded the city hand over of the culprits. It came as a shock to them when Caffa refused. Infuriated, Jani Beg chose to attack. So, in 1343, the Mongols laid siege to the city of Caffa.

Caffa did not turn out to be as feeble as the Mongols expected. Staring the Golden Hordes in the face, Caffa struck back in defense. Caffa had access to the sea and they made adequate use of this, bringing in supplies and reinforcements from Italy. The first siege ended after the Mongols retreated, suffering about 15,000 deaths and heavy damage to their siege equipment. Jani Beg took his army home, but his mind still raged."

"While the Mongols laid siege to the city of Caffa, they were struck by the plague. According to an account of the events of Crimea, the Tartars (Mongols) were suddenly struck by the pandemic. Falling on all sides as though they had been struck by thunder, with lumps on their joints and dark marks on their faces, they developed a putrid fever and were beyond help, neither from doctors nor their god."

"They put the corpses of their dead on their catapults and flung them over the defensive walls of Caffa.

The dwellers of Caffa watched as rotten bodies fell from the skies, crashing on their soil, spreading their putrid smell in all directions. The Christians could neither hide nor flee from the havoc that rained down upon them. They moved as many rotten bodies as they could, dumping them into the sea as quickly as they could. But by then, it was too late; the Black Death was already in Caffa.

The siege ended in 1347, after negotiations between the Mongols and the city, but by then the plague had begun its work."
Birth of the Black Plague: The Mongol Siege on Caffa (


from another forum (not anthrogenica):LOL:

Sample Name MT DNA haplogroup (final) Y-chromosome haplogroup
BSK001.A0101 HV2a2 NA
BSK002.A0101 T1a1b1 Q1a2a1c(Q-L334,Q-L330)
BSK003.A0101 B4c1a2 NA
BSK004.A0101 NA R1b1a2(R-PF6475,R-M269)
BSK005.A0101 NA NA
BSK006.A0101 NA NA
BSK007.A0101 NA NA
Rather as expected for Central Asians from the Medieval period.

Though it's 700 years ago, it left a lasting impact in Europe. In my own area, you can see the graves and the church records detailing the deaths.

Boccaccio's stories supposedly told by Florentines isolating during the plague of 1348 are one of the first if not the first use of the vernacular in Italy.

L'epidemia di peste del XIV secolo - (
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