Mud DNA means we can detect ancient humans even without fossils

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.

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.

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.