Ancient DNA reveals 37,000 years of hidden human infections

Using ancient DNA recovered from prehistoric bones and teeth, scientists have built a 37,000‑year timeline of human infections, stretching from the icy mammoth camps of Siberia to medieval graveyards in Denmark.

The new genetic map shows how early microbes began shaping human history. The scientists sequenced remains from 1,313 individuals and found genetic traces of 214 different pathogens. These range from hepatitis B viruses to the bacterium that causes plague.

The scale of the study provides an opportunity for researchers to test ideas about how culture, climate, and migration changed disease pressure over time.

Skeletons hold disease secrets

The study was led by evolutionary geneticist Eske Willerslev of the University of Copenhagen and the University of Cambridge.

“We’ve long suspected the transition to farming and animal husbandry opened the door to a new era of disease,” Willerslev said. “Now DNA shows us it happened at least 6,500 years ago.”

His team sifted through more than 400 billion sequencing reads and used chemical damage patterns to confirm which fragments truly came from ancient microbes.

The analysis uncovered infections in roughly three‑quarters of the skeletons, indicating that illness was a constant companion rather than a rare ordeal. The oldest sample, dating back about 37,000 years, contained mostly oral bacteria still common today.

The results revealed that blood-borne infections didn’t show up until people began settling down, storing grain, and living closely with sheep, goats, and cattle.

Farming sparked new infections

Livestock pens and crowded villages arrived in Eurasia around 8,000 years ago, and the genomic record registers an immediate uptick in disease.

A clear inflection point appears at 6,500 years ago, the moment when zoonotic pathogens, the kind that jump from animals to humans, first show up consistently.

One notorious example is Yersinia pestis, the plague bacterium, whose oldest genetic trace dates back to about 5,500 years ago in western Russia.

This pushes the timeline of plague back two millennia and shows the microbe shadowing early farmers long before recorded pandemics.

Waves of new infections

A second surge of infection follows the migration of steppe pastoralist groups roughly 5,000 years ago, when horse‑drawn wagons carried people, livestock, and microbes across the continent.

Skeletons from that period revealed plague, relapsing‑fever spirochetes, and the parasites that cause vivax malaria.

Such waves of infection probably devastated local communities, clearing ecological space for newcomers and turning pathogens into unlikely allies of conquest.

Ancient immune‑gene data hint at strong selection beginning in the Bronze Age – a genetic fingerprint of relentless pressure from emerging pathogens.

Human infections from animals

The catalog reveals that cowpox relatives, leptospirosis bacteria, and meat-borne yersiniosis showed up soon after pigs, sheep, and goats were domesticated.

This finding aligns with estimates that around 60 percent of emerging infections come from animals. Close contact clearly reshaped the disease landscape.

The researchers also found skeletons that harbored two or more bugs at once, and these co-infections can worsen outcomes. An ancient Viking‑Age skull carried both hepatitis B and plague DNA, demonstrating how mixed infections may have driven sudden mortality spikes.

Curiously, no clear evidence of tuberculosis surfaced, probably because its bacteria rarely circulate in high numbers in healthy blood. But as the team notes, absence of proof doesn’t mean ancient lungs were safe – only that some microbes leave fewer traces in the molecular record.

What ancient infections teach doctors

“Mutations that were successful in the past are likely to reappear,” said lead author Martin Sikora. She noted that the ancient genomes can help scientists anticipate future mutations. 

Vaccine makers already test candidate antigens against panels of modern strains – a practice encouraged by the World Health Organization – and prehistoric DNA provides a deeper benchmark. Comparing lineages over millennia highlights which protein targets stay stable and which drift.

Old plague sequences, for instance, are missing the ymt gene that helps modern strains survive in fleas. This points to the key step that turned a local infection into a global pandemic threat.

Similar evolutionary tipping points could lurk in viruses still endemic in bats or rodents. Public‑health planners can combine the new database with climate and land‑use models to gauge spillover risk.

Pathogens rewrote human genes

The skeletal archive captures natural selection in action. It shows that human alleles linked to inflammatory responses became more common after farming took hold.

The same alleles, still common today, now raise the risk of autoimmune disorders in industrialized nations.

Immunologists argue that this trade‑off is the cost of survival: genes that helped ancestors fight livestock‑borne bugs can misfire in cleaner modern environments. Ancient DNA provides the infection history that scientists need to test that idea.

“Infectious diseases have left lasting impressions on human genomes, as selective pressures from pathogens have continuously shaped human genetic variation,” wrote the researchers.

“Where and when different human pathogens first emerged, how and why they spread, and how they affected human populations are important but largely unresolved questions.”

The study is published in the journal Nature.

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