Some 20,000 years ago, a woman living in Siberia put on a pendant fashioned from a deer tooth. She wore it for a long time, perhaps until she died or lost the artifact. Now, thousands of years later, that pendant has been found and scientists have extracted the DNA of the woman who wore it, using an innovative method that promises to answer many questions about ancient peoples and their way of life.
In recent years, researchers have been perfecting the art of extracting ancient DNA of animals and humans, first from teeth and bones directly, and, more recently, obtaining it from the soil of caves once inhabited by prehistoric hominins. These efforts have led to major discoveries on human evolution, on the migrations of ancient populations and the origins of modern groups.
The new method, publicized Wednesday in Nature, offers direct insight into the identity of people who made or handled artifacts thousands of years ago, says the international team led by researchers from the Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany.
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She wore elk tooth
The team successfully extracted DNA from a pendant excavated at Denisova Cave, a major prehistoric site in the Altai Mountains of Siberia, by submerging the artifact in a chemical solution and then gradually increasing the temperature. Strands of genetic material, which was then sequenced, were slowly released into the solution without the pendant being damaged at all, report Elena Essel, Matthias Meyer, Marie Soressi and colleagues.
“The fact that it is a non-destructive method is key here because we don’t want to destroy these objects, as there is so much more information in them,” says Essel, a molecular biologist who is the first author on the Nature paper.
The analysis of the pendant from Denisova Cave returned DNA belonging to an elk, whose tooth had been used to make the artifact, and to a human female, presumably the maker or wearer of the ornament. Both genomes were dated to 19,000-25,000 years ago using the molecular clock, a dating method based on the known rate at which DNA mutates. This also allows researchers to date an ancient artifact without the need to use other methods, like radiocarbon dating, which can be more destructive, Essel tells Haaretz.
The analysis showed that the pendant’s owner was closely related to a group of North Eurasian individuals who lived around the same time but were previously detected only further east in Siberia. It is only the third genome of this population that has been recovered, Essel adds.
Given the amount of time that has elapsed and the fact that only a partial genome was recovered, it would be impossible to tell whether the woman has living relatives today, she says. We also don’t know how long she held the pendant or whether she lost it or was buried with it – there were no human remains found close to the object.
A cave of wonders
Denisova Cave was inhabited by different hominins over a quarter of a million years and has proven to be a veritable treasure trove for archaeologists. The site is best known for giving its name to an entire species of hominins, the Denisovans, who were unknown until they were identified in 2010 through DNA analysis of a handful of human remains found in the cave. Later excavations also unearthed the 90,000-year-old remains of a teenage girl who was a Neanderthal-Denisovan hybrid, proving there had been close contact between the two hominin groups.
The pendant analyzed in the new study, dated to around 20,000 years ago, came from the more recent layers of the cave and a time when the only remaining hominin in the region (and in the rest of the world) was Homo sapiens.
Beyond what it can tell us about this little-known Siberian population, the analysis is an exciting proof-of-concept for this new method of DNA extraction, says Viviane Slon, a paleogeneticist from Tel Aviv University.
One problem faced by researchers who study our evolution and dispersal is that human remains are fairly rare and different hominins often made the same tools, so it can be difficult to identify the inhabitants of a particular site or region from artifacts alone, says Slon.
The ability to extract DNA from prehistoric artifacts is “an amazing application for all those cases where we don’t know who made what,” notes Slon, who was not part of the latest study but was behind many of the scientific findings from Denisova, including the Neanderthal-Denisovan hybrid.
The method can also give insight into cultural norms, gender differences and division of labor in ancient populations, Essel says. For example, we could learn whether certain tools were used more by men or women or whether one sex preferred ornaments from a specific animal. The analysis could also tell us whether a certain heirloom was passed on through multiple generations, if, for example, the DNA of a father and son were detected, she says.
There are still limitations to the new method. It likely works best for artifacts made with teeth and bones, porous materials that allow the DNA of the owner to seep in through sweat, blood or saliva over time. Future studies will attempt to recover human genetic material also from stone tools, which were ubiquitous in prehistoric times, Essel says.
There is little doubt that the DNA Essel and colleagues detected came from the artifact itself – which absorbed it over time through contact with its user – rather than from the soil in which it was buried. The team did test the sediments in which the tooth was encased and did find some human genetic material. But the amount of DNA obtained from the tooth itself was much higher than what was in the surrounding sediments, and the genomes also belonged to different people, Essel avers.
There was not enough DNA in the sediments to run a full analysis but the team was able to determine that the genetic material in the soil belonged to a different haplogroup – that is, a completely different population – than the one in the pendant.
While the researchers can clearly distinguish between genetic material found in the object itself and in the surrounding environment, one major hurdle for this new method remains contamination of artifacts from the DNA of the archaeologists who discover and study them, she adds. Attempts by the team to analyze prehistoric tools that were unearthed in the 1970s in France failed because any ancient DNA signal was “drowned out” by the much larger amount of modern genetic material left by researchers over recent years.
The study of the pendant from Denisova was likely successful because it was excavated in controlled conditions, by archaeologists using gloves and facemasks, Essel says.
“We are looking for a way to wash off the contaminated material from previously excavated artifacts but we don’t know if we will find a solution,” she says. “So, for now, if we want answers to all those interesting questions, archaeologists should slip on their protective gear as soon as they see something interesting coming out of the soil.”