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Traces of ancient DNA contained in old bones have spilled fascinating secrets about the past.
But extracting genetic material involves a certain amount of damage to the object in question, and many archaeologists have been reluctant to hand over their most precious finds to DNA labs.
Now, scientists have found a way to extract DNA in a non-invasive manner, applying the pioneering new technique to a pierced deer tooth likely worn as a pendant. The research, published in the journal Nature on Wednesday, revealed intriguing details about its ancient wearer and is the first time scientists have successfully isolated ancient human DNA from a Stone Age artifact.
Excavated from Denisova Cave in southern Siberia, the pendant was worn by a woman who lived between 19,000 and 25,000 years ago, according to the analysis of human genetic material preserved in the pendant. She belonged to a group known as Ancient North Eurasians, which have a genetic connection to the first Americans.
The new method will hopefully allow scientists to learn about the sex and genetic ancestry of the Stone Age makers, wearers and users of an array of bone tools and ornaments unearthed from digs around the world.
“It’s amazing. It means that we’ll be able to answer very simple questions such as what tasks males and females were doing at that point time,” said study coauthor Marie Soressi, a professor and chair of human origins at Faculty of Archaeology of Leiden University in the Netherlands. “We actually will have a direct line of evidence to tell us.”
The technique may also, for example, be able reveal whether a tool was used by a Neanderthal or our own Homo sapiens ancestors, she added.
Trial and error
Human DNA was likely preserved in the deer bone pendant because it is porous and therefore more likely to retain genetic material present in skin cells, sweat and other body fluids.
Typically, researchers would use a small drill to extract bone powder from an artifact or bone. Lead study author Elena Essel, a molecular biologist at the Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, described the newly developed technique as a “laboratory washing machine without the movement.”
The pendant was submerged in a sodium phosphate buffer solution while gradually increasing the temperature. This allowed the DNA to be released into the solution, where it was isolated, purified and sequenced using existing tools.
“If we want to stay in this image of the washing machine, it’s the wash water that was exciting for us,” Essel explained.
While bone tools and artifacts are rarer than stone ones, they are still much more common in the archaeological record than humans remains, opening up new avenues for research.
The pendant study, however, is essentially a proof of concept, and it’s not clear how easy it will be to extract ancient human DNA from other bone ornaments and tools.
The technique, at least as it stands, only worked on freshly excavated material and where archaeologists had taken steps to ensure that the artifact is “clean” — i.e. not contaminated with modern human DNA — by wearing gloves and a mask and making sure the object was sealed in a bag immediately after being unearthed.
The technique didn’t identify ancient DNA when applied to a set of bone tools from the French cave Quinçay excavated back in the 1970s to 1990s — when nobody had any idea that genetic material could be preserved for so long.
Nor was it possible to extract ancient DNA from three freshly excavated tooth pendants from Bacho Kiro Cave in Bulgaria, home to some of the earliest known modern humans in Europe, according to the study.
“Right now, it’s like this one sample. I would be really interested in learning more about how often we can can extract ancient human DNA and if it’s like a specific type of artifact that is more promising or if it works equally well for (bone) tools,” Essel said.
It’s not known why the deer tooth pendant contained such a large amount of the ancient woman’s DNA (about the same amount as a human tooth) — perhaps it was well-loved and worn close to the skin for an exceptionally long period of time, Essel said.
“How we think it works is that the longer there was close body contact, the higher the chances that a lot of DNA is in the material … but we have no idea if we’re talking about days or months or years or decades.”