Scientists discover ancient DNA in the soil of caves

A team of researchers and scientists have discovered a way to detect where our human ancestors lived, even when no bone or skeletal remains are present, by analysing ancient DNA found in sediments. The discovery could help complete the map of ancient human occupations and show us where species may have overlapped and interacted.

Beth Shapiro, an evolutionary biologist at the University of California said:

"If one must rely on finding bones, one will always have incomplete data. By isolating DNA directly from sediments, we can dramatically expand what we know about where people were, when they got there, and how long they stayed."

The team of researchers looked at seven areas in Belgium, Croatia, France, Russia and Spain, covering a timespan from 14,000 to 550,000 years ago.

Scientists have known that DNA can survive in ancient sediments for years, but there was no way to distinguish ancient human sequences from modern ones that can contaminate samples as they are handled. New techniques for filtering out such contamination have since been developed, which encouraged Matthias Meyer, a Max Planck geneticist, to try and extract human DNA from sediments in once-occupied caves.

Meyer and Viviane Slon from Max Planck Institute for Evolutionary Anthropology said they were overwhelmed after the team first sequenced the DNA from the sediments found in the caves.

Meyer states:

"It’s on the order of trillions of DNA fragments in a sample the size of a teaspoon."

Only a small fraction of those DNA fragments might belong to ancient humans. The pair were initially worried that the human DNA would be too scarce that even their careful techniques would fail to find it. However, Meyer and Slon detected Neanderthal DNA in sediment from four of the seven cave sites. They also discovered Denisovan DNA from sediment in the Denisova cave, the Siberian site containing the only known Denisovan bones.

Both the Neanderthal and Denisovan DNA was extracted from layers where no bones had been found, pushing back the period of human occupation by tens of thousands of years.

In addition to discovering hominin DNA, the researchers also identified genetic data from extinct mammals, including the woolly mammoth, woolly rhino, cave bears, and cave hyenas.

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