Human DNA Uncovered in Caves Without Bone Remains

Researchers plan their sediment sampling in the East Chamber of Denisova Cave, Russia. | IAET SB RAS / Sergei Zelensky

Scientists have recovered the first ancient human DNA from cave sediments lacking human skeletal remains. The highly sensitive screening technique they applied, reported in the 28 April issue of the journal Science, identified human genetic material from prehistoric sites where Neandertal presence has been proposed — based on the presence of stone tools, for example — but never demonstrated.

"There are many prehistoric sites where there are no human remains and where it is unclear who made the artifacts found there," said lead author Viviane Slon, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "Previously, we could not generate genetic data from the hominins who were present at such sites. Our ability to recover ancient hominin DNA from sediments opens the possibility to investigate the genetic affiliation of the occupants of such places. It could better inform patterns of migrations of ancient hominin groups over space and time."

To date, DNA analysis from archaic humans has greatly helped scientists understand the process of evolution. However, fossils from the Pleistocene (often referred to as the Ice Age) have been scarce, impeding scientists' understanding of ancient human movement in this epoch, which lasted from about 2,588,000 to 11,700 years ago.

Slon and her colleagues wanted to investigate whether hominin DNA could survive in sediments at archaeological sites even in the absence of bones. They collected 85 sediment samples from seven Pleistocene sites in Europe and Russia where ancient humans are known to have lived.

From the DNA identified in these samples (only a very small fraction of which was from mammals), the researchers isolated DNA fragments showing similarities to mammalian mitochondrial DNA, or mtDNA. Because mtDNA is present in numerous copies in most mammalian cells, it is a useful tool for distinguishing between mammalian groups.

Slon and her colleagues conducted intensive evaluation of the mtDNA found in the sediment and their work revealed Neandertal DNA in four caves. One of the caves, Denisova Cave, also yielded DNA from another extinct species of human called the Denisovans.

The results may help to establish DNA analyses of sediments as a useful archaeological procedure in the future. Though Slon and her colleagues identified DNA as old as Pleistocene-age specimens, their technique does have a maximum in terms of how far back in time it can probe.

"DNA degrades over time," said Slon. "Dinosaurs, for example, are too far back in time to allow for the recovery of their DNA. To date, the oldest DNA sequences recovered from bones are dated to around 700,000 years ago, and these were from a permafrost environment [where genetic material is better preserved]. DNA could potentially survive in sediments for this long as well."

Slon and her colleagues will continue their work, paving the way to further reconstructing human evolutionary history. "We are planning to expand the sampling of sediments to a larger set of archaeological sites, spanning a variety of geographical areas and time periods of interest for studying human evolution," she said.

[Credit for associated image: Johannes Krause, Max Planck Institute for Evolutionary Anthropology]