For forensics, personal items found at a crime scene are key because they may contain DNA that identifies the victim and even the killer. But it’s not easy to recover genetic material from 20,000 years ago, let alone something someone carried attached to their body. First, because most human creations, like clothing, have been lost to time. Second, because the artifacts that are preserved are so valuable that the most aggressive DNA extraction techniques cannot be used on them, because they could endanger them. But now, German scientists have discovered that genetic information can be recovered from a pendant belonging to the person who wore it simply by washing it.
The pendant in question was discovered by Russian archaeologists in one of the Denisova caves in Siberia. This is the region where the Denisovans lived, a species of hominid that must have coexisted with the ancestors of present-day humans and the Neanderthals (there are those who maintain that they were Neanderthals from the east). In 2019, a carved and pierced animal tooth was discovered in one of the caves. The researchers had before them an ornament probably made of a deer that, based on the stratum in which they found it, must have been worn by someone between 20,000 and 30,000 years ago, that is, when the Denisovans and Neanderthals had already disappeared in this part of the world. . But they could not investigate further and the thing stayed there, in another human creation for the collection. However, in 2021, researchers at the Max Planck Institute for Evolutionary Anthropology published a new method for extracting and isolating DNA from bones and teeth it doesn’t destroy them. On this occasion, the pendant almost matters less than the new technique for its genetic analysis.
Elena Essel, a Max Planck researcher, participated in the development of this technique. “For bone and tooth samples, it is usual to drill a small hole in the sample to collect the bone powder. This powder is then used for DNA extraction,” she explains. But when working with artifacts made from bones and teeth, “in many cases you can’t do destructive sampling, as it would ruin valuable information that the surface of these objects can provide,” she adds.
Essel indicates that the surface structure can give insight into how these objects were made and used. And he adds: “These insights are fundamental to our understanding of human subsistence strategies, behavior, and culture in the Pleistocene. Therefore, it is crucial to preserve the integrity of the artifacts during extraction. So we set out to develop a non-destructive DNA extraction technique, ”he completes.
Chemical solutions and gloves
After testing washing with various chemical solutions on different objects, they found that sodium phosphate extracted DNA without damaging them. Before testing it with the pendant, they used it to reanalyze a series of bone objects from thousands of years ago and recovered in the last century. They managed to extract a large amount of genetic remains, but all the DNA they identified was from the animal itself or from current humans: the samples were contaminated. So they tested it with other artifacts discovered in recent years, when archaeologists already work equipped as forensics, with gloves, hats and masks to prevent their hands, sweat or even their breath from contaminating something that has remained intact for millennia.
As Essel and his colleagues detail in the scientific magazine Nature, they used their new method with four bone pendants that had been carefully excavated trying to avoid contamination. “Compared to other solutions, phosphate does not dissolve the bone matrix to release the DNA into the solution,” explains Essel. What this compound does is lend its phosphate to the bone and by adding free phosphate, it allows them to “release the DNA from the bone matrix without involuting the bone itself”, concludes the German scientist.
Three of the pendants analyzed were from the Bacho Kiro cave in Bulgaria, and the other was from the Denisova cave. The first ones are relevant because in Bacho Kiro one of the oldest remains of Homo sapiens in Europe. The four samples were immersed in a sodium phosphate solution and washed at different temperatures. This allowed DNA to be obtained from all four. Two of the pendants from the Bulgarian cave were from some kind of extinct bear and the other from a bovid. As for the Denisovan pendant, it was made from the tooth of a wapiti, a kind of deer.
But the goal of the scientists was to find human DNA. They succeeded in one of the Bulgarian pendants, but in a proportion and concentration that prevented knowing much more. They had better luck with the Russian ornament: there was enough foreign genetic material that had slipped into the tooth. Both bones and teeth are porous and, more importantly, they contain hydroxyapatite. This compound, which for example is part of tooth enamel, is basically calcium. It is present in the bone matrix and absorbs foreign DNA as if it were its own. So cells from the hands that made it or from the neck that wore it (or even from their sweat) slipped into the pendant and all their genetic information has now been recovered.
From her genetic analysis, scientists have been able to infer that she was a sapiens woman, like modern humans, and not a Denisovan. She must have lived in that cave between 18,500 and 25,000 years ago. The dating between the animal and human DNA of the pendant, which differs by a few millennia, does not allow for further refinement. To do so, you would have to use the carbon-14 technique, which is very destructive. The woman’s genetics match that of other human remains found in Siberia, although when compared to current populations, she most closely resembles American Indians. This is logical, since the first modern humans to colonize America would leave shortly after from Siberia.
“20,000 years ago, a woman wore this pierced tooth and her sweat got into the pendant. 20,000 years later, we released the DNA of this ancient woman.”
Marie Soressi, archaeologist from Leiden University, the Netherlands
“It is related to a local population of the time and members of this population moved to North America,” says Marie Soressi, an archaeologist who is an expert in human evolution at the University of Leiden (Netherlands) and co-author of this research. For her, however, what is relevant about this work is that it is “the first extraction of ancient human DNA from a Stone Age object.” Soressi highlights the relevance of the method over the genetic analysis itself: “20,000 years ago, a woman in Siberia wore this drilled tooth and her sweat got into the pendant, the hydroxyapatite in the tooth bonded with her DNA and preserved it in the pendant. 20,000 years later, we freed the DNA of this ancient woman from her union with the hydroxyapatite of the deer’s tooth, raising the temperature and using a sodium phosphate liquid that has a very high capacity for attraction and binding with DNA molecules ” , she details.
There are many human remains from the Paleolithic and also many objects. The problem is linking them. Soressi explains: “We excavated sites with a large number of objects, stone tools, bone tools, faunal remains and, on occasions, personal ornaments… But the temporal resolution is very low: often tens of years, sometimes hundreds or even thousands of years collapsed into an archaeological layer. Applying the same time resolution to the present, we would confuse objects from medieval times with those from the 21st century. A question as simple as whether specific objects (for example, leather-working objects) were used by men or women cannot be answered. For the researcher, this new technique “opens up enormous opportunities to better reconstruct the role of individuals in the past according to their sex and ancestry.”
Professor Matthias Meyer, Essel’s colleague at the Max Planck Institute, highlights this recovery of human DNA from an object used by a person. “Currently, there are only indirect ways to link people to objects, for example, if human bones are found in the same archaeological layer,” he says. But this research can change everything: “Knowing that the objects themselves can preserve human DNA, we can now assign objects not just to groups of people but to specific individuals. With this we can know if the pendants and other adornments were worn by men, women or both”, he adds. They also expect the method to work with bone tools, and in cases where different groups, such as Neanderthals and modern humans, inhabited the same place, “we could determine which objects were used by which group,” he concludes.
The geneticist Carles Lalueza-Fox is one of the leading experts in ancient DNA and was a reviewer of this research before its publication. Regarding the scope of the method and the possibility of applying it to other remains from the past, he says: “Many methods are published that are not used later beyond their proponents, either because only positive results have been reported or because there are not many specimens where they can be applied. ”. But he does believe that it could be used on similar objects, “for example to determine if men and women used body ornaments, but the Denisova cave environment seems to be very special for the preservation of DNA; We’ll see if it can be applied to other sites and under what circumstances”, concludes the scientist from the Institute of Evolutionary Biology (UPF-CSIC).
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