News from the Department of Genetics

A new study suggests that our ancestors’ close cohabitation with domesticated animals and large-scale migrations played a key role in the spread of infectious diseases.

The team, led by Professor Eske Willerslev at the Universities of Cambridge and Copenhagen, recovered ancient DNA from 214 known human pathogens in prehistoric humans from Eurasia.

They found that the earliest evidence of zoonotic diseases – illnesses transmitted from animals to humans, like COVID in recent times – dates back to around 6,500 years ago, with these diseases becoming more widespread approximately 5,000 years ago.

The study detected the world’s oldest genetic trace of the plague bacterium, Yersinia pestis, in a 5,500-year-old sample. The plague is estimated to have killed between one-quarter and one-half of Europe’s population during the Middle Ages.

In addition, the researchers found traces of many other diseases including:

Malaria (Plasmodium vivax) – 4,200 years ago

Leprosy (Mycobacterium leprae) – 1,400 years ago

Hepatitis B virus – 9,800 years ago

Diphtheria (Corynebacterium diphtheriae) – 11,100 years ago

This is the largest study to date on the history of infectious diseases and is published today in the journal Nature.

The researchers analysed DNA from over 1,300 prehistoric humans, some up to 37,000 years old. The ancient bones and teeth have provided a unique insight into the development of diseases caused by bacteria, viruses, and parasites.

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

He added: “These infections didn’t just cause illness – they may have contributed to population collapse, migration, and genetic adaptation.”

The significant increase in the incidence of zoonoses around 5,000 years ago coincides with a migration to north-western Europe from the Pontic Steppe – that is from parts of present-day Ukraine, south-western Russia and western Kazakhstan. The people embarking on this migration – and who to a large extent passed on the genetic profile found among people in north-western Europe today – belonged to the Yamnaya herders.

The findings could be significant for the development of vaccines and for understanding how diseases arise and mutate over time.

“If we understand what happened in the past, it can help us prepare for the future. Many of the newly emerging infectious diseases are predicted to originate from animals,” said Associate Professor Martin Sikora at the University of Copenhagen, and first author of the report.

Willerslev added: “Mutations that were successful in the past are likely to reappear. This knowledge is important for future vaccines, as it allows us to test whether current vaccines provide sufficient coverage or whether new ones need to be developed due to mutations.”

The sample material was primarily provided by museums in Europe and Asia. The samples were partly extracted from teeth, where the enamel acts as a lid that can protect the DNA against degradation as a result of the ravages of time. The rest of the DNA was primarily extracted from petrosa bones - the hardest bone in humans - located on the inside of the skull.

The research was funded by the Lundbeck Foundation.

Reference

Sikora, M. et al: ‘The spatiotemporal distribution of human pathogens in ancient Eurasia.’ Nature, July 2025. DOI: 10.1038/s41586-025-09192-8

Adapted from a press release by the University of Copenhagen.

Researchers have mapped the spread of infectious diseases in humans across millennia, to reveal how human-animal interactions permanently transformed our health today.

We’ve long suspected that the transition to farming and animal husbandry opened the door to a new era of disease – now DNA shows us that it happened at least 6,500 years agoEske WillerslevMarie Louise JørkovLate Neolithic skull from Madesø

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A team at Cambridge is helping to drive biological discovery through innovation in microscope technologies

Why are there so many different kinds of animals and plants on Earth? One of biology’s big questions is how new species arise and how nature’s incredible diversity came to be.

Cichlid fish from Lake Malawi in East Africa offer a clue. In this single lake, over 800 different species have evolved from a common ancestor in a fraction of the time it took for humans and chimpanzees to evolve from their common ancestor.

What’s even more remarkable is that the diversification of cichlids happened all in the same body of water. Some of these fish became large predators, others adapted to eat algae, sift through sand, or feed on plankton. Each species found its own ecological niche.

Now, researchers from the Universities of Cambridge and Antwerp have determined how this evolution may have happened so quickly. Their results are reported in the journal Science.

The researchers looked at the DNA of over 1,300 cichlids to see if there’s something special about their genes that might explain this rapid evolution. “We discovered that, in some species, large chunks of DNA on five chromosomes are flipped – a type of mutation called a chromosomal inversion,” said senior author Hennes Svardal from the University of Antwerp.

Normally, when animals reproduce, their DNA gets reshuffled in a process called recombination – mixing the genetic material from both parents. But this mixing is blocked within a chromosomal inversion. This means that gene combinations within the inversion are passed down intact without mixing, generation after generation, keeping useful adaptations together and speeding up evolution.

“It’s sort of like a toolbox where all the most useful tools are stuck together, preserving winning genetic combinations that help fish adapt to different environments,” said first author Moritz Blumer from Cambridge’s Department of Genetics.

These preserved sets of genes are sometimes called ‘supergenes. In Malawi cichlids, the supergenes seem to play several important roles. Although cichlid species can still interbreed, the inversions help keep species separate by preventing their genes from blending too much. This is especially useful in parts of the lake where fish live side by side – like in open sandy areas where there’s no physical separation between habitats.

The genes inside these supergenes often control traits that are key for survival and reproduction – such as vision, hearing, and behaviour. For example, fish living deep in the lake (down to 200 meters) need different visual abilities than those near the surface, require different food, and need to survive at higher pressures. Their supergenes help maintain those special adaptations.

“When different cichlid species interbred, entire inversions can be passed between them – bringing along key survival traits, like adaptations to specific environments, speeding up the process of evolution,” said Blumer.

The inversions also frequently act as sex chromosomes, helping determine whether a fish becomes male or female. Since sex chromosomes can influence how new species form, this opens new questions about how evolution works.

“While our study focused on cichlids, chromosomal inversions aren’t unique to them,” said co-senior author Professor Richard Durbin, from Cambridge’s Department of Genetics. “They’re also found in many other animals — including humans — and are increasingly seen as a key factor in evolution and biodiversity.”

“We have been studying the process of speciation for a long time,” said Svardal. “Now, by understanding how these supergenes evolve and spread, we’re getting closer to answering one of science’s big questions: how life on Earth becomes so rich and varied.”

Reference:
L. M. Blumer, V. Burskaia, I. Artiushin, J. Saha et al. ‘Introgression dynamics of sex- linked chromosomal inversions shape the Malawi cichlid radiation.’ Science (2025). DOI: 10.1126/science.adr9961

Researchers have found that chunks of ‘flipped’ DNA can help fish quickly adapt to new habitats and evolve into new species, acting as evolutionary ‘superchargers’.

banusevim via Getty ImagesDolphin cichlid (Cyrtocara moorii)

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