Ancient plague mystery cracked after DNA found in 4,000-year-old animal remains

Long before the Black Death killed millions across Europe in the Middle Ages, an earlier, more elusive version of the plague spread across much of Eurasia.

For years, scientists were unsure how the ancient disease managed to spread so widely during the Bronze Age, which lasted from roughly 3300 to 1200 B.C., and stick around for nearly 2,000 years, especially since it wasn’t spread by fleas like later plagues. Now, researchers say a surprising clue may help explain it: a domesticated sheep that lived more than 4,000 years ago.

Researchers found DNA from the plague bacterium Yersinia pestis in the tooth of a Bronze Age sheep discovered in what is now southern Russia, according to a study recently published in the journal Cell. It is the first known evidence that the ancient plague infected animals, not just people, and offers a missing clue about how the disease spread.

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

And it was a lucky discovery, according to the researchers.

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

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The highly technical and time-consuming work requires researchers to separate tiny, damaged fragments of ancient DNA from contamination left by soil, microbes and even modern humans. The DNA they recover from ancient animals is often broken into tiny pieces sometimes just 50 “letters” long, compared to a full human DNA strand, which contains more than 3 billion of those letters.

Animal remains are especially tough to study because they are often poorly preserved compared to human remains that were carefully buried, the researchers noted.

The finding sheds light on how the plague likely spread through close contact between people, livestock and wild animals, as Bronze Age societies began keeping larger herds and traveling farther with horses. The Bronze Age saw more widespread use of bronze tools, large-scale animal herding and increased travel — conditions that may have made it easier for diseases to move between animals and humans.

When the plague returned in the Middle Ages during the 1300s, known as the Black Death, it killed an estimated one-third of Europe’s population.

“It had to be more than people moving,” Hermes said. “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.”

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Researchers believe sheep likely picked up the bacteria from another animal, like rodents or migratory birds, that carried it without getting sick and then passed it to humans. They say the findings highlight how many deadly diseases begin in animals and jump to humans, a risk that continues today as people move into new environments and interact more closely with wildlife and livestock.

“It’s important to have a greater respect for the forces of nature,” Hermes said.

The study is based on a single ancient sheep genome, which limits how much scientists can conclude, they noted, and more samples are needed to fully understand the spread.

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The researchers plan to study more ancient human and animal remains from the region to determine how widespread the plague was and which species may have played a role in spreading it. 

They also hope to identify the wild animal that originally carried the bacteria and better understand how human movement and livestock herding helped the disease travel across vast distances, insights that could help them better anticipate how animal-borne diseases continue to emerge.

The research was led by scientists at the Max Planck Institute for Infection Biology, with senior authors Felix M. Key of the Max Planck Institute for Infection Biology and Christina Warinner of Harvard University and the Max Planck Institute for Geoanthropology.

The research was supported by the Max Planck Society, which has also funded follow-up work in the region.