Researchers Find DNA From Extinct Humans in Cave Sediments

The DNA was extracted from caves where no human remains were found, opening a new pathway for research into human evolution.

Scientists in Germany have recovered ancient human DNA from sediment, not bones or teeth, in a finding that could offer a new inroad into our own evolutionary history.

A team from the Max Planck Institute for Evolutionary Anthropology and led by geneticist Viviane Slon collected samples from seven archaeological sites in Europe and Asia, analyzing the sediment for traces of mammalian DNA. Looking at mitochondrial DNA, they found genetic evidence from 12 different families, including that of extinct species such as the wooly mammoth, the wooly rhinoceros, and the cave hyena.

When they searched for DNA fragments specific to hominins — a precursor of modern humans — they found what they were after: nine samples from four archaeological sites produced enough hominin DNA for further analysis. In eight of the samples, they found DNA from Neanderthals, and in one site in Russia they found DNA from a Denisovan, the Asian cousins of Neanderthals.

“It was a surprise,” said Slon. “We thought [hominin DNA] would be a very small minority in the samples, which was the case, and we were surprised by how well this worked.”

Most of the samples came from archaeological layers where no Neanderthal bones or teeth had been previously unearthed, further opening the field of evolutionary biology to include archaeological sites that have not yielded human remains.

“It is almost beyond comment that it’s exciting stuff,” said Robin Allaby, an evolutionary geneticist at the University of Warwick, responding to the study. “We have all been limited by the number of archaeological remains we can get at and this has the potential to release us from those constraints.”

The work of Slon and her team, which included soil samples spanning from 14,000 to 550,000 years ago, has been published in the journal Science. When preparing the study, researchers from Max Planck knew that certain components present in sediment had been known to bind DNA — other scientists have successfully fished plant DNA out of sediment samples, for example.

Using these studies as a reference, the team targeted archaeological sites known to have been occupied by ancient hominins. Specifically, they looked for mitochondrial DNA, which is abundant in cells. They targeted short sequences of human DNA, looking for chemical damage that is typical of ancient DNA in order to avoid confusion with more recent DNA present in the sample.

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There are, however, some limitations to the testing of DNA in sediment. While researchers have demonstrated that there is hominin DNA in the sediment, more data will be required to have a better understanding of how many individuals were present, accounting for the movement of DNA in the environment, and the age of these individuals, which cannot be determined from mitochondrial DNA.

Allaby emphasized the importance of further understanding how DNA is moving through the environment. What evolutionary scientists have long been interpreting as the breakdown of DNA over time, he said, may more likely be its diffusion through the environment.

It is a question that Slon is keenly aware of — her team found animal DNA in layers created when the animals were still alive, but not in later sediment layers when they would have been extinct. This, she said, indicates that DNA is not migrating beyond the corresponding sediment layers. Even so, the team is working to further refine their techniques, with hopes that they can get more detailed information about the individuals whose DNA they uncovered.

“It may be a while until they can get an entire genome out,” Allaby said. But he described the new technique as a “massive inroad” to our demographic past. “I think this could become standard practice,” he added.

For now, 32-year-old Slon is looking forward to her graduation. The study she led will form a good part of her doctoral thesis, which she is currently drafting.

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