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Ancient Human DNA Isolated From 20K-Year-Old Deer Tooth Pendant Sheds Light on Owner

Ancient deer tooth

NEW YORK — An international team of researchers has developed a new technique for isolating DNA from bones and teeth that has led them to recover ancient human DNA from a Paleolithic deer tooth pendant that was either made or worn by a woman.

"Combining such genetic and cultural analyses of a Pleistocene artifact could help uncover possible task specialization by individuals of a particular biological sex or genetic ancestry," said Elena Essel, a molecular biologist at the Max Planck Institute for Evolutionary Anthropology, in an email. She is the lead and co-corresponding author of a study published in Nature on Wednesday describing the work.

Essel and colleagues noted that artifacts such as the deer pendant, which are made from animal bones or teeth, are porous and allow easy penetration of body fluids such as sweat, blood, or saliva, making them a treasure trove of DNA information. Such artifacts also contain a mineral called hydroxyapatite that is known to adsorb DNA and reduce its degradation by hydrolysis and nuclease activity.

A big advantage of their new DNA extraction technique is that it doesn't require physical destruction of the artifacts.

"Conservation is a primary concern because of the scarcity of bone and tooth artifacts at Pleistocene sites, especially of pendants and other ornaments that were extensively handled or worn in close body contact," wrote Essel, who spearheaded the research along with Matthias Meyer, also from Max Planck, and Marie Soressi of Leiden University.

The researchers applied their method, based on a series of incubations in sodium phosphate buffer at different temperatures, to a number of ancient bone and tooth objects that were excavated at different times, followed by mammalian mitochondrial DNA enrichment and sequencing. 

They found that objects from earlier excavations that had been handled with bare hands were extensively contaminated with modern human DNA. However, the deer tooth pendant, found in Denisova Cave, Russia, in 2019 and handled with gloves and facial masks, allowed them to recover both ancient human and elk DNA.

By conducting phylogenetic analysis on the extracted deer and human mitochondrial DNA, they estimated the age of the pendant at approximately 19,000 to 25,000 years.

Further analysis of the nuclear human DNA also revealed that the pendant once belonged to a female, who the researchers presumed was either the maker or wearer of the pendant. It also showed that the woman had strong genetic links to a group of ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia.

Essel said that developing the new DNA isolation technique wasn't easy and involved trial and error.

"One could say we have created a washing machine for ancient artifacts within our clean laboratory," she said in a statement. "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." In the future, the technique could be used to extract DNA from other bone and tooth samples from the Stone Age.

According to Essel, her team is also interested in studying the microbial content of the extracted DNA and might start by looking for bacteria known to be present in sweat or saliva. "Maybe the DNA of microbes can tell us more about where the DNA originates from," she said.