Denisovan and Neanderthal DNA Uncovered in Caves without Skeletal Remains

New research led by the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) shows that Pleistocene cave sediments represent a rich source of ancient DNA that often includes traces of hominin DNA, even at sites where no hominin remains have been discovered.

Denisova Cave in the Altai Mountains of southern Siberia. Image credit: Alex Demin / CC BY-SA 4.0.

To date, DNA analysis from archaic hominins has greatly informed our understanding of evolution.

However, fossils from the Pleistocene epoch, often referred to as the Ice Age, have been scarce, impeding scientists’ understanding of ancient human movement in this epoch.

To investigate whether ancient DNA, especially of archaic humans, may be preserved in Pleistocene caves, MPI-EVA researcher Matthias Meyer and co-authors collected 85 samples from seven archaeological sites with known hominin occupation, varying in age between 14,000 and 550,000 years ago.

“We know that several components of sediments can bind DNA. We therefore decided to investigate whether hominin DNA may survive in sediments at archaeological sites known to have been occupied by ancient hominins,” said Dr. Meyer, who is the lead co-author of the paper reporting the results in the journal Science.

“Some samples were collected specifically for the purpose of this study: four from Les Cottés (France), five from Trou Al’Wesse (Belgium), one from El Sidrón (Spain), one from Vindija Cave (Croatia), three from Denisova Cave and 13 from Caune de l’Arago (France),” the authors said.

“The other samples, 49 from Denisova Cave and 9 from Chagyrskaya Cave, had been collected previously for luminescence dating. The latter two sites are located in the Altai Mountains, where remains of both Neanderthals and Denisovans have been uncovered.”

Ancient species detected in Late Pleistocene (LP) and Middle Pleistocene (MP) samples from seven sites: for each time period, the fraction of samples containing DNA fragments which could be assigned to a mammalian family and authenticated to be of ancient origin is indicated; the shaded symbols representing each family are not to scale. Image credit: Slon et al, doi: 10.1126/science.aam9695.

From the mammalian DNA identified in these samples, the team isolated mitochondrial DNA (mtDNA).

“From the preliminary results, we suspected that in most of our samples, DNA from other mammals was too abundant to detect small traces of human DNA. We then switched strategies and started targeting specifically DNA fragments of human origin,” said MPI-EVA researcher Viviane Slon, lead co-author of the study.

Eight samples contained Neanderthal mtDNA from either one or multiple individuals, while one sample contained Denisovan mtDNA.

Most of these samples originated from archaeological layers or sites where no hominin bones or teeth were previously found.

The results may help to establish DNA analyses of sediments as a useful archaeological procedure in the future.

“By retrieving hominin DNA from sediments, we can detect the presence of hominin groups at sites and in areas where this cannot be achieved with other methods,” said MPI-EVA researcher Dr. Svante Pääbo, co-author of the study.

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Viviane Slon et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science, published online April 27, 2017; doi: 10.1126/science.aam9695