The skull of a prehistoric hunter-gatherer, discovered in a European archaeological site, contains genetic evidence that the Black Death’s ancestor killed entire communities 5,000 years earlier than previously believed, according to a study published today in Nature. DNA analysis of the remains, dated to roughly 3,000 BCE, confirms the presence of Yersinia pestis, the bacterium responsible for the plague, shattering assumptions that early strains were benign.
Researchers from the University of Tübingen, who led the study, sequenced the genome of the pathogen found in the skull and compared it to modern strains. “This isn’t just an older version of the plague—it’s the same bacterium, but with a far deadlier impact on Neolithic populations,” said Johannes Krause, director of the Max Planck Institute for the Science of Human History and a co-author of the study. The findings suggest that the plague’s virulence evolved much earlier than historical records indicated, with the earliest known outbreaks occurring in Bronze Age Europe.
Why does this challenge long-held assumptions about the plague’s origins?
The discovery contradicts a prevailing theory that Y. pestis initially caused mild, localized infections before mutating into the lethal strain that devastated medieval Europe. Instead, the genetic data shows that the bacterium was already capable of causing mass fatalities in prehistoric times. “The idea that early plague was a minor ailment is simply not supported by the evidence,” said Krause. The skull, excavated from a burial site in what is now Germany, belonged to an individual who died during an outbreak that likely wiped out nearby settlements.
Archaeologists have long speculated that the plague may have played a role in the decline of Neolithic communities, but this is the first direct genetic confirmation. The study also reveals that the bacterium had already developed resistance mechanisms, including a gene linked to antibiotic resistance in modern strains—a finding that raises questions about how early humans may have combated infections before the advent of medicine.
How does this change our understanding of prehistoric pandemics?
Historically, the Black Death—responsible for killing an estimated 75–200 million people in the 14th century—was thought to have emerged from Central Asia around the 1300s. However, the new research pushes the timeline back by at least 3,500 years. “This isn’t just about the plague’s age—it’s about recognizing that pandemics aren’t a modern phenomenon,” said Hendrik Poinar, an evolutionary geneticist at McMaster University who was not involved in the study. “They’ve been shaping human history for millennia.”
The study also highlights how genetic analysis is rewriting the narrative of ancient diseases. Previous research had identified Y. pestis in samples dating back to the Bronze Age, but those cases were often isolated and not linked to widespread mortality. The German skull, however, shows clear signs of systemic infection, including bone lesions consistent with septicemic plague—the most lethal form of the disease.
What are the implications for modern plague research?
Public health officials caution that the findings do not suggest a resurgence of the plague, which remains treatable with antibiotics. However, the study underscores the importance of monitoring antibiotic-resistant strains. “The fact that this ancient bacterium had resistance genes is a reminder that we need to stay vigilant,” said Maria Van Kerkhove, technical lead for COVID-19 at the World Health Organization. The WHO has previously noted that Y. pestis has evolved multiple times, with modern strains showing varying levels of resistance to treatments.
Meanwhile, archaeologists are now prioritizing the search for additional prehistoric plague victims. “This is just the beginning,” said Krause. “We’re likely to find more evidence that the plague was a recurring threat long before it became infamous in the Middle Ages.” The study’s authors are calling for expanded genetic screening of ancient remains to map the full history of the bacterium’s spread.
No immediate next steps have been announced by the WHO or archaeological institutions, but researchers say the findings will inform future studies on disease evolution and human migration patterns.
