Prehistoric DNA Detected in Caves Reveals Secrets of Neanderthal History

Innovation allows researchers to extract hominin genetic material from sediments, and reveals that Neanderthals may have come close to extinction twice before their disappearance

Ariel David
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A view of Chagyrskaya cave in Siberia
A view of Chagyrskaya cave in SiberiaCredit: Fabrizio Mafessoni
Ariel David

A new method to extract the DNA of prehistoric hominins from the soil of caves they inhabited has revealed that Neanderthals may have bounced back from the brink of extinction at least twice before their final disappearance some 40,000 years ago.

In a study published Thursday in Science, an international team of researchers details how they recovered fragments of Neanderthal genetic material dated to between 200,000 and 50,000 years ago from cave sediments in Spain and Russia.

The data indicate there were two radical replacements of the Neanderthal population throughout Eurasia, once 135,000 years ago and again 100,000 years ago. This may be indicative of environmental pressures, possibly caused by cooling climate, that temporarily decimated local hominin groups, says Benjamin Vernot, a population geneticist from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Both times, it seems that when conditions improved a surviving lineage of Neanderthals managed to repopulate the continent, says Vernot, who is the lead author on the study.

This dramatic finding on the history of our close evolutionary cousins comes not from the discovery of new skeletons or other archaeological remains – but from mere soil. The team sequenced Neanderthal DNA from sediments at Galeria de las Estatuas, a cave in Northern Spain, as well as from the Siberian sites of Denisova and Chagyrskaya.

Of these sites, Denisova Cave is perhaps the best known as it has already been the stage for a major coup in prehistoric genetics. About a decade ago, scientists sequenced the DNA of a single finger bone that had been found there and identified it as belonging to a previously unknown hominin, which they dubbed the Denisovan.

Denisova Cave, which at different times housed both Neanderthals and Denisovans (as well as a at least one hybrid individual) has now made a new contribution to our understanding of human evolution.

Flirting with extinction

The DNA extracted there and at the other two caves shows that Neanderthal populations were replaced twice by groups of the same hominin lineage but with much less genetic diversity, says Matthias Meyer, a molecular biologist from Max Planck who led the new study.

To put it in modern terms, the level of genetic difference between the older and the more recent populations was similar to what we find between humans in Africa and Europe today, Meyer says. Except of course that Africans and Europeans are contemporaneous populations, while the Neanderthal groups that replaced one another lived thousands of years apart.

The cause of these two “radiations” – as the experts call them – in the Neanderthal genetic tree are not yet clear. It is unlikely that they were caused by one group of Neanderthals sweeping into a new region and wiping out the original population, says Vernot.

What the genetic data suggest is that at some point a large part of the Neanderthals in Eurasia died off, he tells Haaretz. “Only a small group survived, who knows where, and then when conditions improved they spread out again and repopulated Eurasia, but they now display much less genetic diversity, and this is reflected in the data,” he says.

Inside Denisova cave in SiberiaCredit: Fabrizio Mafessoni

We can only speculate as to the cause of these early brushes with extinction, but the Science paper suggests they may be linked to changes in climate and environmental conditions triggered by the last glacial period, which began around 100,000 years ago.

Most probably, modern Homo sapiens had no involvement in this postulated crisis, as back then we were still largely confined to our evolutionary cradle in Africa, even though we had already started making early forays into the Middle East and, possibly, Europe.

Humans may have indeed had a hand in the final extinction of Neanderthals around 40,000 years ago, though the extent and nature of our role are still hotly debated. And don’t forget that a bit of Neanderthal DNA survives in each one of us, as we managed to interbreed with them before their disappearance.

Whatever the cause of their ultimate demise, the newly published research shows there is still much we don’t know about the distant history of the Neanderthals and other hominin groups. Special attention should also be paid to the method that was used in the study, which promises to be a revolutionary tool in the exploration of our evolutionary roots.

No bones

Until now, archaeologists have relied on finding human remains to reconstruct the various branches of the hominin family tree. But most prehistoric sites yield few or no human remains, and even fewer bones in which DNA is preserved and can be extracted, says Vivian Slon, a paleogeneticist from Tel Aviv University who was also a lead researcher on the study published in Science.

For example, at the Spanish site that was part of the study, hundreds of stone tools have emerged from the cave, which was occupied from some 110,000 to 70,000 years ago, but only a single Neanderthal foot bone was found.

And that’s still considered lucky. Since the same shapes of stone tools were often used by different hominin groups, there are many sites where, in the absence of skeletal remains, researchers can only guess at the identity of the inhabitants.

Even when human remains are found at a cave, and they yield genetic information, they tend to represent just a few points in time in the occupational history of the site, which can sometimes span tens of thousands of years, Slon notes.

“There are only about 18 Neanderthal bones that have had DNA extracted from them,” Vernot notes. “This is supposed to represent a population that spanned across Eurasia and lived for hundreds of thousands of years?”

By extracting DNA from sediments, scientists can collect reams of additional data and reconstruct the changing genetic profiles of a cave’s inhabitants layer by layer.

“The strength of this new method is that it allows us to do genetic analysis even when there are no bones,” Slon tells Haaretz. “This means opening hundreds or thousands of archaeological sites to genetic studies.”

A view of Chagyrskaya cave in SiberiaCredit: Fabrizio Mafessoni

Go fish, for DNA

Back in 2017, Slon was the lead researcher on a team that pioneered this method by extracting mitochondrial DNA from the sediments of that paleontological cornucopia that is Denisova Cave. Mitochondrial DNA (or mtDNA) is found in the mitochondria, the organelles that power our cells. It is easier to identify, partly because we have many more copies of it per cell than our nuclear DNA. However, mtDNA gives us also less information about our genetic past since it is inherited from the mother’s side (with very rare exceptions) and it has a much shorter sequence than our genome – some 16,000 base pairs versus three billion.

That’s why the newly-published genetic research successfully attempted to identify nuclear DNA, rather than mtDNA, from the sediments of the three caves that were part of the study.

The way human DNA that can be hundreds of thousands of years old is extracted from sediments is quite ingenious. Geneticists only need a few milligrams of soil to start the process, Meyer explains. First they use chemicals to extract all the DNA present in the sample. Then they face the problem that most of that genetic material belongs to bacteria that naturally live in the soil. Even the small percentage of mammalian DNA derives mostly from cave bears, hyenas and other prehistoric fauna.

Since we share most of our DNA with other mammals, it can be difficult to identify human genetic material, so to fish it out from this tangled mass of genetic residue the researchers must literally go on a fishing expedition.

We know that there are about 1.6 million locations in the genome that are unique to humans and their evolutionary relatives (not a lot, considering the three billion base pairs in our genome). Geneticists can thus construct artificial nucleotide sequences, or “probes,” that mimic these locations: If any of these probes binds to the ancient genetic material to reform DNA’s signature double helix, lo-and-behold, we can be certain that we’ve hooked on to some human DNA.

The microscopic catch can then be compared to known genomes of humans and other hominins to trace population changes and the evolution of the species over time, just as the team did with the Neanderthal DNA they fished out.

Hyena poo and ghost hominins

At this point you may be wondering how all this human DNA ended up in the sediments of prehistoric caves. The short answer is we don’t know, Sloan says. However, there are probably several sources involved, she notes, from the decomposed remains of dead people buried in the cave to all the bodily fluids that live humans routinely spread around: spit, blood, feces and so on.

“In some cases it could even be that a hyena ate a human and pooped out some bone fragments in the cave,” Meyer speculates. Whatever the source of the DNA, its extraction from cave sediments opens up new and exciting avenues for research.

By this method, for example, it should be also possible to identify so-called “ghost hominins,” Slon and Meyer say. These are hominins that have left traces in our DNA (because our distant ancestors had sex with them) but whose remains have not yet been found in the fossil record.

“We really have no good idea of who was around in the late Pleistocene, especially in Central and East Asia,” Meyer notes. “We’ve known about the Denisovans only for the last 10 years, and who knows who else we will find.”