The plague has ravaged humanity for thousands of years, wiping out as much as half of Europe's population in the Black Death, and scientists have long puzzled over its origins and evolutionary history.
Researchers said Tuesday they had found its first known victim: a hunter-gatherer who lived 5,000 years ago in what is now Latvia, whose remains carried the Yersinia pestis bacteria that causes the disease.
"The analyses of the strain we identified shows that Y. pestis evolved earlier than thought," Ben Krause-Kyora, head of the aDNA Laboratory at the University of Kiel in Germany, told AFP.
Krause-Kyora and colleagues wrote in a paper in the journal Cell Reports the bacterial lineage emerged as far back as 7,000 years ago when it split from its predecessor, Yersinia pseudotuberculosis.
The new date pushes the previously held timeline back by 2,000 years.
The bacteria was missing key genes, such as one that enabled it to be spread via fleas -- meaning the ancient strain was both less contagious and deadly than the medieval version.
The hunter-gatherer was a man in his twenties called "RV 2039." He was one of two people whose skeletons were excavated in the late 19th century from a region called Rinnukalns in present-day Latvia.
The remains vanished until 2011 when they reappeared as part of the famed German anthropologist Rudolph Virchow's collection.
Following this rediscovery, two more burials were uncovered from the same site.
The plague finding "was really a surprise," said Krause-Kyora: the team was sequencing the teeth and bones of the four individuals to determine if they related to each other when they stumbled on the discovery.
Evidence of Y. pestis was found in RV 2039's bloodstream, and it likely killed him, though researchers think the disease course might have been slow.
He had a high level of bacteria in his blood at the time of death, and that has been linked to less aggressive infections in rodent studies.
The people around him were not infected, and he was buried carefully, meaning he was unlikely to have had a highly contagious respiratory version called pneumonic plague.
Researchers think instead he was infected by a single direct contact, such as a rodent bite, in keeping with other Neolithic findings.
"We see it in societies that are herders in the steppe, hunter-gatherers who are fishing, and in farmer communities -- totally different social settings but always spontaneous occurrence of Y. pestis cases," added Krause-Kyora.
The earliest plague strains that could be transmitted through fleas date from around 3,800 years ago, when "megacities" of 10,000 people began to form in the Middle East and the Mediterranean.
The growing population density likely triggered further adaptation of the bacteria.
Tracking the history of Y. pestis could also shed light on the ways in which human genomes evolved to keep up.
For example, around the same time as cities were forming in the Middle East and the Mediterranean, changes began to emerge in a set of human genes responsible for helping the immune system keep track of foreign pathogens.
"Therefore, we are very interested in future research into how these early infectious diseases influenced our present-day immune systems," said Krause-Kyora.