Objects made of stone, bone or teeth provide important insights into the behaviour, way of life and culture of Stone Age people. So far, however, it has been difficult to assign these objects to specific people, because burials and grave goods were rare at this time. Researchers can only draw limited conclusions about how people lived back then, for example how their division of labor was organized and their social structure.
In order to link these objects directly to specific people and thus gain deeper insights into Stone Age societies, an international, interdisciplinary research team led by the Max Planck Institute for Evolutionary Anthropology in Leipzig has developed a new, non-destructive method for DNA isolation developed bones and teeth. Although these are less commonly found than stone tools, the scientists specifically focused on skeletal artefacts because they are more porous and therefore more likely to bind genetic material from skin cells, sweat and other bodily fluids.
A new method for DNA extraction
Before work could begin on real objects, the team first had to ensure that the valuable artifacts would not be damaged. »The surface structure of Stone Age art and utility objects made from bones and teeth provides important information about their manufacture and use. Therefore, it was a top priority for us to preserve these objects in their entirety, including the microstructures on their surface,” says Marie Soressi, an archaeologist at Leiden University who, together with Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Sciences Anthropologie, who led the project.
The team tested the influence of different chemicals on the surface structure of archaeological bone and tooth fragments and developed a non-destructive phosphate-based method for DNA extraction. “One could say that we have set up a washing machine for ancient artefacts in our clean room laboratory,” explains lead author Elena Essel from the Max Planck Institute for Evolutionary Anthropology, who developed the method. “If we wash the artifacts at temperatures of up to 90°C, we are able to extract DNA from the wash water while the artifacts remain completely intact.”
Early setbacks
The team first applied the new method to a series of finds from excavations in France’s Quinçay Cave between the 1970s and 1990s. Although in some cases it has been possible to identify the genetic makeup of the animals from whose bones or teeth the artifacts were made, the vast majority of the DNA isolated came from the people who had touched the objects during or after the excavation. This made it difficult to identify ancient human genomes.
In order to avoid the problem of contamination by modern humans, the researchers now focused on newly excavated objects. Equipped with gloves and face masks, the excavators packed their finds, which still had sediment on them, in clean plastic bags. Three animal tooth pendants from the Bacho Kiro Cave in Bulgaria, where the oldest securely dated modern humans in Europe were found, showed significantly less contamination with modern DNA; nevertheless, no ancient human genome could be detected in these samples.
A pendant from the Denisova Cave
Archaeologists Maxim Kozlikin and Michael Shunkov, who work in the famous Denisova Cave in Russia, finally made the breakthrough. At the time, they had no idea what new analytical method the Leipzig researchers were working on, but in 2019 they dug up a pendant made from a deer tooth from the Upper Palaeolithic, taking special precautions. From this find, the Leipzig researchers isolated not only the genome of the animal itself, an elk, but also large amounts of ancient human DNA. “The amount of human DNA that we were able to extract from the surface of the pendant was really extraordinary – almost as if we had sampled a human tooth,” says Elena Essel.
The researchers then analyzed mitochondrial DNA, the small part of the genome that is passed exclusively from mother to child. They concluded that most of this genome probably came from a single human. Using the elk and human mitochondrial genomes, they were able to estimate the pendant’s age at between 19,000 and 25,000 years, eliminating the need to sacrifice parts of the precious material for carbon-14 dating.
In addition to the mitochondrial genome, the researchers also reconstructed a significant part of the nuclear genome of the person to whom the pendant once belonged. Based on the number of X chromosomes, they determined that the pendant was made, used, or worn by a woman. They also found that this woman was genetically closely related to the so-called “Ancient North Eurasians” – people who lived in more eastern parts of Siberia at the same time and whose skeletal remains had been analyzed in previous studies. “Forensic scientists will not be surprised that human DNA can be isolated from an object that has been used a lot,” says Matthias Meyer, “but it is amazing that this is still possible after 20,000 years.”
The team now hopes to apply their method to many other Stone Age bone and tooth objects to learn more about the genetic ancestry and gender of the people who made, used or wore those objects.