Extraction of ancient human DNA from artefacts

The Denisova cave in southern Siberia is now famous for the evidence that it has provided for Neanderthals and Denisovans and their interbreeding based on DNA recovered from their bones, even a tiny finger bone of the latter. Indeed we would not know of the former existence of Denisovans without such a clue. Scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, responsible for both breakthroughs, also pioneered the extraction of hominin DNA from soil in the cave. Now they have refined the intricate extraction of genetic material to such an extent that detailed hominin DNA sequences can be analysed from ornaments worn by ancient people, in much the same manner as applied in forensic studies of crime scenes (Essel, E. and 22 others 2023. Ancient human DNA recovered from a Palaeolithic pendant. Nature, early release 3 May 2023; DOI: 10.1038/s41586-023-06035-2).

Elk-tooth pendant found at Denisova cave, before cleaning and DNA extraction (top) and after the ‘washing’ procedure (bottom). Credit: Essel et al., Fig 1.

Russian archaeologists who continue to work at Denisova cave found a pierced pendant made from the tooth of a Siberian elk or wapiti during the 2019 field season. It was sent to Leipzig, where the palaeogenetics team had been trying to extract the DNA of whoever had worn personal artefacts found in French and Bulgarian caves. Their efforts had been unsuccessful, but such an object from Denisova clearly spurred them on. When someone wears next to the skin objects made of porous materials their sweat and the DNA that it carries seeps into the pores. If the materials decay very slowly, as do bone and especially teeth, genetic material can, in principle be extracted. But crushing up important ancient objects is not an option: for such rarities the extraction has to be non-destructive. It can only be done by ‘washing’ it in reagents that do not themselves break down DNA. Elena Essel and her many colleagues experimented with many ‘brews’ of reagents and repeated immersion at steadily rising temperature (up to 90°C). This releases genetic material in a stepwise fashion, allowing separation of contaminants in the host sediment from that which had penetrated into the tooth’s pores from whoever made the pendant and the wearer, and the animal from which it came

 Analysis of the recovered material yielded elk mtDNA, which was compared with that from four other ancient elks of known ages. This suggested that the elk had lived between 19 and 25 ka ago, thereby indirectly dating the time when the pendant was made and worn. A surprisingly large amount human DNA showed that the wearer was a female who was genetically allied with ancient anatomically modern humans who lived further east in Siberia at about that time.

Obviously this astonishing result opens up a wide vista for archaeology, though not from Palaeolithic burials, which are extremely rare. But artefacts of various kinds are much more common that actual human remains. Because the technique is non-destructive museums may be more willing to make objects in their collections available for analysis. Maybe the approach will be restricted to porous bone or tooth ornaments worn for long periods by individuals. Yet stone tools that were handled continually could be a more important target, depending on the rock from which they were made and its porosity.

See also: Lesté-Lasserre, C.. DNA from 25,000-year-old tooth pendant reveals woman who wore it. New Scientist, 3 May 2023.