New non-destructive DNA extraction method for Paleolithic artifacts from bones and teeth

Stone tools, bones, and teeth artifacts provide valuable clues about the behavior, culture, and subsistence strategies of early humans. However, due to the scarcity of burials and grave goods during the Paleolithic era, it has been challenging to associate these artifacts with specific individuals. Consequently, the ability to draw conclusions regarding social roles and division of labor during this period has been limited.

To gain a deeper understanding of Paleolithic societies by directly linking cultural objects to specific individuals, an interdisciplinary research team led by the Max Planck Institute for Evolutionary Anthropology in Leipzig has devised a new, non-destructive technique for extracting DNA from bones and teeth. The scientists focused their attention on skeletal elements, as they are more porous and thus more likely to retain DNA present in skin cells, sweat, and other bodily fluids, despite their relative rarity compared to stone tools.

A new DNA extraction method

To avoid damaging precious Paleolithic bone and tooth artifacts, the research team first prioritized preserving their surface structure, which contains important information about their production and use. According to Marie Soressi, an archaeologist from the University of Leiden who co-supervised the project with Max Planck geneticist Matthias Meyer, the integrity of the artifacts was a key consideration.

To develop a non-destructive method for DNA extraction, the team experimented with different chemicals and their effects on the surface structure of archaeological bone and tooth specimens. Lead author Elena Essel, who devised the method, likened it to a washing machine for ancient artifacts in their sterile laboratory. The team can extract DNA from the wash waters by washing the artifacts at temperatures of up to 90°C, while keeping the artifacts intact.

Early setbacks

The team’s initial test involved applying the DNA extraction method to a collection of artifacts from the Quinçay cave in France, which was excavated from the 1970s to the 1990s. While some of the extracted DNA came from the animals used to create the artifacts, most of it was modern human DNA from those who had handled the items during or after excavation. This posed a challenge in identifying ancient human DNA.

The pierced deer tooth discovered from Denisova Cave before DNA extraction. Credit: Max Planck Institute for Evolutionary Anthropology

To overcome this issue, the researchers shifted their focus to newly excavated materials collected using gloves, face masks, and clean plastic bags with attached sediment. They examined three tooth pendants from the Bacho Kiro Cave in Bulgaria, where the oldest securely dated modern humans in Europe were found. The samples showed significantly lower levels of modern DNA contamination, but the team was unable to identify any ancient human DNA in these specimens.

A pendant from Denisova Cave

The breakthrough came thanks to the efforts of archaeologists Maxim Kozlikin and Michael Shunkov, who were excavating the Denisova Cave in Russia. Unaware of the new DNA extraction method being developed in Leipzig, they carefully collected an Upper Paleolithic deer tooth pendant in 2019. The geneticists at the Max Planck Institute were able to isolate DNA not only from the wapiti deer, but also a significant amount of ancient human DNA.

Lead author Elena Essel describes the quantity of human DNA recovered from the pendant as exceptional, comparing it to sampling a human tooth. The team’s findings, which highlight the potential of their non-destructive DNA extraction method, have been published in the journal Nature.

The pierced deer tooth discovered from Denisova Cave after DNA extraction. Credit: Max Planck Institute for Evolutionary Anthropology
Excavation works in the South Chamber of Denisova Cave in 2019. Credit: Sergey Zelensky
The entrance to Denisova Cave. Credit: Richard G. Roberts
Top view of the pierced deer tooth discovered from Denisova Cave in southern Siberia. Credit: Max Planck Institute for Evolutionary Anthropology

Through the analysis of mitochondrial DNA, which is exclusively inherited from the mother, the researchers determined that most of the DNA extracted from the pendant likely originated from a single individual. By comparing the mitochondrial genomes of the wapiti deer and human DNA, they estimated the age of the pendant to be between 19,000 and 25,000 years, without the need for C14 dating.

In addition to mitochondrial DNA, the team was able to recover a significant portion of the nuclear genome of the individual who owned the pendant. Analysis of the X chromosomes indicated that the pendant was made, used, or worn by a woman who was genetically related to ancient individuals from Siberia.

Matthias Meyer, a Max Planck geneticist, noted the remarkable ability to isolate human DNA from an object handled 20,000 years ago. The team hopes to apply their non-destructive DNA extraction method to other bone and teeth artifacts from the Stone Age, in order to gain further insights into the genetic ancestry and sex of the individuals who made, used, or wore them.

Source: Max Planck Society

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