Ancient Plague Mystery Solved with DNA from 4,000-Year-Old Animal Remains

Long before the notorious Black Death devastated Europe in the Middle Ages, an earlier, more mysterious form of plague swept across Eurasia. Scientists have long puzzled over how this ancient disease managed to spread so extensively during the Bronze Age and persist for nearly two millennia, especially since it lacked the flea vectors associated with later plague outbreaks.

A groundbreaking discovery may now provide the missing piece to this historical puzzle: a domesticated sheep that lived more than 4,000 years ago.

Researchers have identified DNA from the plague bacterium Yersinia pestis in the tooth of a Bronze Age sheep discovered in southern Russia, according to a study recently published in the journal Cell. This represents the first documented evidence that the ancient plague infected animals, not just humans, potentially explaining how the disease maintained its widespread presence for so long.

“It was alarm bells for my team,” said study co-author Taylor Hermes, a University of Arkansas archaeologist specializing in ancient livestock and disease transmission. “This was the first time we had recovered the genome from Yersinia pestis in a non-human sample.”

The finding was particularly fortuitous given the significant challenges involved in extracting useful genetic material from ancient animal remains. Unlike carefully preserved human burials, animal remains are often poorly conserved, making DNA analysis exceptionally difficult.

“When we test livestock DNA in ancient samples, we get a complex genetic soup of contamination,” Hermes explained. “This is a large barrier… but it also gives us an opportunity to look for pathogens that infected herds and their handlers.”

The research required painstaking separation of minuscule, damaged fragments of ancient DNA from contamination left by soil, microbes, and modern human handling. The ancient animal DNA fragments recovered are often just 50 genetic “letters” long, compared to the more than 3 billion letters in a complete human DNA strand.

This discovery sheds crucial light on the plague’s transmission dynamics during the Bronze Age, which lasted from approximately 3300 to 1200 B.C. The period was characterized by significant societal changes including the widespread use of bronze tools, large-scale animal herding, and increased mobility—conditions that likely facilitated disease spread between animals and humans.

The researchers believe sheep probably contracted the bacteria from another animal reservoir, such as rodents or migratory birds, that carried the pathogen without becoming ill themselves, before passing it to humans. This finding highlights how many deadly diseases originate in animals before jumping to human populations, a zoonotic transmission pattern that continues to pose significant public health challenges today.

“It had to be more than people moving,” Hermes noted. “Our plague sheep gave us a breakthrough. We now see it as a dynamic between people, livestock and some still unidentified ‘natural reservoir’ for it.”

The discovery was made at Arkaim, a fortified Bronze Age settlement in the Southern Ural Mountains of present-day Russia near the Kazakhstan border. While offering valuable insights, the researchers acknowledge the limitations of basing conclusions on a single ancient sheep genome and emphasize the need for additional samples to develop a more comprehensive understanding of the disease’s spread.

When the plague returned in Europe during the 1300s as the Black Death, it killed an estimated one-third of the continent’s population. Unlike the Bronze Age version, this later outbreak was primarily spread by fleas.

The research team, led by scientists at the Max Planck Institute for Infection Biology, with senior authors Felix M. Key and Christina Warinner of Harvard University and the Max Planck Institute for Geoanthropology, plans to study more ancient human and animal remains from the region. Their goal is to determine how widespread the plague was and identify which species played key roles in its transmission.

“It’s important to have a greater respect for the forces of nature,” Hermes cautioned, noting that the findings underscore the ongoing risks as humans continue to encroach upon new environments and interact more closely with wildlife and livestock.

The research, supported by the Max Planck Society, could ultimately help scientists better anticipate and respond to emerging animal-borne diseases—a concern that remains critically relevant in today’s interconnected world.