Yersinia pestis (200× magnification), the bacterium that causes plague. Credit: CDC/Larry Stauffer, Oregon State Public Health Laboratory
In 1347, plague first entered the Mediterranean via trade ships from the territories of the Golden Horde in the Black Sea. The disease then disseminated across Europe, the Middle East and northern Africa, claiming up to 60 percent of the population in a large-scale outbreak known as the Black Death.
This first wave further extended into a 500-year-long pandemic, the so-called Second Plague Pandemic, which lasted until the early 19th century. The origins of this second plague have long been debated.
In a new study, an international team of researchers analyzed ancient DNA (aDNA) from human remains as well as historical and archaeological data from cemeteries to piece together the timeline of havoc Yersinia pestis wreaked.
The researchers investigated two cemeteries in Central Asia—near Lake Issyk-Kul of modern-day Kyrgyzstan. These cemeteries showed a disproportionally high number of burials dating between 1338 and 1339, with some inscriptions stating that the cause of death was due to an unspecified pestilence.
The team was able to extract aDNA from seven individuals, with three showing evidence of ancient Y.pestis DNA. Using just the two with the highest genomic coverage, the team compared SNP (single-nucleotide polymorphism) profiles to see if they represented distinct bacterial strains—which they did not. The researchers found that the two genomes were identical.
The next step was comparing the cemetery genomes with historical Y. pestis chromosomal genomes. Researchers have previously shown the Black Death to be associated with a star-like emergence of four major lineages—branches 1, 2, 3 and 4—with published Second Pandemic genomes liked to branch 1.
Comparative SNP analysis revealed the cemetery genomes to be ancestral to all published 14th-century genomes, leading researchers to conclude they are the direct ancestor of branches 1 to 4.
“We found that the ancient strains from Kyrgyzstan are positioned exactly at the node of [the Black Death’s] massive diversification event. In other words, we found the Black Death’s source strain and, thanks to the tombstones, we even know its exact date—the year 1338,” said Maria Spyrou, lead author and researcher at the University of Tübingen.
Working with the cemetery genomes as the common ancestor, Spyrou and her team constructed a timeline spanning the first half of the 14th century for the emergence of branches 1 to 4. They then compared that with a modern dataset of Y. pestis.
According to the study, published in Nature, 64 percent (130 out of 203 genomes) of modern Y. pestis strains belonged to branches 1 to 4.
“[This] reflects the high worldwide frequency known for these lineages,” explain the researchers in their paper. “We estimate that branches 1 to 4 represent approximately 40 percent of the overall phylogenetic diversity within present-day Y. pestis based on our full dataset.”
The closeness of the modern strains to the ancient strains also gave the researchers as to the geographical origins of the bacteria.
“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,” explains Johannes Krause, senior author of the study and director at the Max Planck Institute for Evolutionary Anthropology. “This points to an origin of Black Death’s ancestor in Central Asia.”
The international team says their study demonstrates how investigations of well-defined archaeological contexts, and close collaborations among historians, archaeologists and geneticists can successfully resolve mysteries of the past with “unprecedented precision.”