The DNA of ancient humans can now be detected in samples of soil Sylvio Tupke/Max Planck Institute for Evolutionary Anthropology

We have an astonishing new way to study our early human ancestors: looking for their DNA in ancient sediments in places such as caves.

A team of researchers has found the DNA of Neanderthals and Denisovans in some of the sites where they are known to have lived.

“I think we show convincingly that these sequences are authentic,” says lead author Viviane Slon of the Max Planck Institute for Evolutionary Anthropology in Germany.


The approach can now be used to find out whether early humans were present even when no bones have been found – and what kind of humans they were. It might also help resolve the debate about when the Americas were first inhabited by people, for instance.

Universe in a gram of mud

Just about any sample of soil or water is full of DNA from all kinds of organisms. Sequencing this “environmental DNA” is an increasingly powerful tool for studying ecosystems.

For instance, biologists were recently able to identify several caves where “baby dragons”, or olms, live simply by analysing the water flowing out of them.

In sediments buried in cool caves and in permafrost, this environmental DNA can survive for up to 700,000 years. In 2003, a team led by Eske Willerslev, now at the University of Cambridge, was the first to show that it was possible to find ancient DNA from species like the woolly mammoth, in frozen mud in Siberian permafrost.

Now Slon’s team has shown that ancient human DNA can survive in sediments too. Her team sequenced all the DNA present in sediment samples from sites where hominins lived, such as Denisova cave in Russia. The biologists then used short pieces of modern human mitochondrial DNA to extract longer bits of DNA containing a matching sequence from the samples.

The team looked for DNA from the energy-generating mitochondria within our cells, because they each contain the same DNA and there are hundreds per cell, so it is the type most likely to survive.

The real thing

The team found ancient hominin mitochondrial DNA in samples from four of the seven sites they looked at. The DNA probably came from human excreta or from rotting soft tissue.

The discovered sequences had damage characteristic of ancient DNA and contained variants known to be unique to Neanderthals or Denisovans, so the team is sure they are the real thing, says Slon.

Ancient humans are just another mammal, points out Willerslev. Given that we can find the DNA of woolly rhinoceroses and cave bears in sediments, it’s not surprising that we can find ancient hominin DNA as well.

Slon’s team was even able to show that DNA from more than one individual was present in two of the samples.

The team now plans to look for DNA at some of the many hominin sites where no fossils have been found. “There are a lot of sites where there are stone tools, but it is unclear who made them,” says Slon.

Now we could start to get some answers. And if we can find enough ancient human DNA, it could even give us a better picture of how our ancestors moved around.

What could be an issue, says Willerslev, is establishing exactly how old ancient hominin DNA is. “Cave sediments are often highly disturbed,” he says, which makes it hard to accurately date them.

Journal reference: Science, DOI: 10.1126/science.aam9695

Read more: Rare ‘baby dragons’ discovered in five new caves thanks to DNA; DNA sequencing turns rivers into ecosystem surveillance systems; First Americans may have been Neanderthals 130,000 years ago