Ancient DNA Isn't Just History

I knew what DNA was. I knew what synthetic DNA was. I knew what mirror DNA was. I even knew what eDNA was. But I didn’t know about aDNA, or that the field of study for it is called genomic paleoepidemiology. A new study by one of the pioneers of the field illustrates its power.

Those cows are going to have some surprises for prehistoric humans. Credit: Microsoft Designers

The study was led by Eske Willerslev, who is both Professor of Ecology & Evolution, Department of Zoology at Cambridge University and Director/ Professor, Centre of Excellence in GeoGenetics at the University of Copenhagen. He studies ancient DNA, aka “aDNA.” The new study traces 37,000 years of human disease history by examining the DNA from 214 known human pathogens, coming from the remains of some 1,300 prehistoric humans.

Our recent experience with COVID-19 and, currently, with bird flu, should have made everyone aware that one of the dangers of living with large populations of animals (like livestock) creates opportunities for diseases to cross over from those animals to us, often with devastating effect. These are called zoonotic diseases, and they still kill millions of people each year.

 When humans transitioned from hunter/gatherers to a more pastoral lifestyle, and then to farming, the pathogens had their chance.

Humans are thought to have started domesticating animals around 11,000 years ago. “This is the time when you’re in close proximity to animals, and you get these jumps,” Dr. Willerslev told Carl Zimmer of The New York Times. “That was the expectation.” So the researchers were surprised to find that the earliest evidence of zoonotic diseases didn’t appear until around 6,500 years ago, and didn’t become widespread until about 5,000 years ago.

Not surprisingly, they found evidence of the plague bacterium, Yersinia pestis, in a 5,500-year-old sample. They also found traces of 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.   

Credit: Sikora, et. al.

In all, the researchers identified 5,486 DNA sequences that came from bacteria, viruses and parasites. Not bad for DNA from tens of thousands of years ago.

The authors note:

Although zoonotic cases probably existed before 6,500 years ago, the risk and extent of zoonotic transmission probably increased with the widespread adoption of husbandry practices and pastoralism. Today, zoonoses account for more than 60% of newly emerging infectious diseases.

“It’s not a new idea, but they’ve actually shown it with the data,” says Edward Holmes, a virologist at the University of Sydney, Australia. “The scale of the work is really pretty breathtaking. It’s a technical tour de force.”

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

The researchers speculate that populations in the Steppe region were among the first to tame horse and domesticate livestock at scale, and it was their migration west that caused the appearance of the zoonotic diseases in the wider population. Moreover, it seems likely that the Steppe populations had acquired better immunity for them, unlike the existing populations they encountered. That would have led to massive population losses and made the Steppe migration much easier.

Think of what happened to the indigenous populations of the Americas or Australia when European settlers first came to their shores, only this time it was the then-Europeans who were the victims, dying off in huge numbers. Those of “European” background may need to think further east for their actual heritage.

“It has played a really big role in genetically creating the world we know of today,” Dr. Willerslev told Mr. Zimmer.

This isn’t just of academic interest. Zoonotic diseases are still very much with us. “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.

Professor 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 study has several limitations. The samples are all from Eurasia. “Africa would of course be super exciting, but we don’t have enough data,” Dr. Sikora told Mr. Zimmer. The researchers were only able to identify pathogens present in high doses in the bloodstream. “I’m sure there’s more in there,” says Professor Sikora. Last but not least, it only looked at DNA-based pathogens, not ones that use RNA, such as the viruses that cause influenza or polio.

Nonetheless, as Hendrik Poinar, an expert on ancient DNA at McMaster University in Canada who was not involved in the study, told Mr. Zimmer: “The paper is large and sweeping and overall pretty cool.”

Pretty. Cool. Indeed.

The paper concludes:

Our findings demonstrate how the nascent field of genomic paleoepidemiology can create a map of the spatial and temporal distribution of diverse human pathogens over millennia. This map will develop as more ancient specimens are investigated, as will our abilities to match their distribution with genetic, archaeological and environmental data. Our current map shows clear evidence that lifestyle changes in the Holocene led to an epidemiological transition, resulting in a greater burden of zoonotic infectious diseases. This transition profoundly affected human health and history throughout the millennia and continues to do so today.

As Dr. Poinar told Mr. Zimmer: “It’s a great start, but we all have miles to go before we sleep.”

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 I’ve long been amazed at what archaeologists and paleontologists have been able to tell us about our past, based on a few fossils, bones, or artifacts. I’m even more impressed that we’re recovering ancient DNA and using it to tell us even more of the story about how we got here.

It should be sobering to us all that, as much as we worry about weapons and invasions, the biggest risk to a population remains infectious diseases, especially zoonotic ones. The “winner” is the one who happens to have the best immunity.