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Ancient Woman’s DNA Recovered From a 20,000-Year-Old Pendant

A picture of an ancient pendant made from a deer's tooth.
Pierced deer tooth discovered from Denisova Cave in southern Siberia that yielded ancient human DNA. Credit: Max Planck Institute for Evolutionary Anthropology.
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A collaborative study led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, outlines a new technique for isolating DNA from ancient bones and teeth that is non-destructive. This method, published in Nature, has been successfully applied to recover a woman’s DNA from a 20,000-year-old deer tooth pendant.

Bottlenecks when recovering and isolating ancient DNA

Analyzing DNA that has been extracted from ancient specimens is helping scientists to better understand the genetic makeup of past populations, migration patterns and cultural exchanges in human history. Specimens such as bones, teeth or stone can offer useful insights into the methods and practices that early humans in the Paleolithic adopted to gather food and resources necessary for survival. However, directly linking these specimens to specific individuals has been challenging, as burials were uncommon in the Paleolithic, and individuals that were buried were rarely accompanied by their belongings.

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“Precise identification of the specific makers or users of these objects would require the recovery of human DNA directly from the objects themselves, analogous to modern-day forensic investigations,” the research team behind the new study write. “In theory, such analyses are most promising for artifacts made from animal bones or teeth, not only because they are porous and thereby conducive to the penetration of body fluids (for example, sweat, blood or saliva) but also because they contain hydroxyapatite, which is known to adsorb DNA and reduce its degradation by hydrolysis and nuclease activity.” Extracting DNA from ancient skeletal remains is not an easy feat, however; oftentimes it requires destructive sampling. 

Gradually releasing DNA trapped in ancient bones and teeth

In the current study, the scientists developed a novel method for enabling the gradual release of DNA trapped in bones and teeth – which is less destructive than current methods – to link cultural objects with specific people. “The surface structure of Paleolithic bone and tooth artifacts provide important information about their production and use. Therefore, preserving the integrity of the artifacts, including microstructures on their surface, was a top priority,” says archeologist Professor Marie Soressi from the University of Leiden. Soressi supervised the project alongside Max Planck geneticist Professor Matthias Meyer.

The researchers explored the effects of several chemicals on the surface structure of archeological bone and teeth samples, eventually discovering a non-destructive phosphate-based method for DNA extraction. Dr. Elena Essel, the study’s lead author and a molecular biologist in Meyer’s lab, likens the approach to a “washing machine for ancient artifacts”: "By washing the artifacts at temperatures of up to 90°C, we are able to extract DNA from the wash waters, while keeping the artifacts intact,” she explains.

Initial experiments testing the method on ancient artifacts encountered setbacks, including sample contamination from modern DNA and insufficient ancient DNA present in the sample for analysis. Then, in 2019, archeologists Maxim Kozlikin and Michael Shunkov excavated Denisova Cave in Russia, where they uncovered a Paleolithic deer tooth pendant. The team in Leipzig applied their novel method to the pendant, successfully isolating deer DNA and ancient human DNA. “The amount of human DNA we recovered from the pendant was extraordinary,” says Essel, “almost as if we had sampled a human tooth.”

The pendant was made, or worn, by a woman

Analysis of the pendant and the recovered DNA suggest the object is approximately 19–25,000 years old, and the DNA originated from a single individual. Based on the number of X chromosomes present in a portion of the nuclear genome that could be retrieved, the research team conclude that the pendant was worn, or made by, a woman. Her genetics suggest she was closely related to an ancient group of individuals located further east Siberia, known as the “Ancient North Eurasians”. Skeletal remains from this population have been recovered and analyzed previously, which enabled the genetic link to be established.

“Forensic scientists will not be surprised that human DNA can be isolated from an object that has been handled a lot,” says Meyer, “but it is amazing that this is still possible after 20,000 years.” The researchers are now eager to apply their novel approach to other Stone Age artifacts made from bone and teeth.

This article is a rework of a press release issued by the Max Planck Institute for Evolutionary Anthropology. Material has been edited for length and content.

Reference: Essel E, Zavala EI, Schulz-Kornas E, et al. Ancient human DNA recovered from a Palaeolithic pendant. Nature. 2023. doi: 10.1038/s41586-023-06035-2