Science Notes: Sifting through the soil: surveying the future of DNA

For this month’s ‘Science Notes’, I started off writing about ‘sedaDNA’, a catch-all term for any ancient DNA – including from flora, fauna, fungi, and other microorganisms – which is extracted from archaeological sediments. It is a technique that is quickly becoming a standard procedure in many excavations but has only had a few passing mentions in recent CA articles (see CA 388 and 390). Then news broke of ancient human DNA being successfully, and non-invasively, extracted from a Palaeolithic bone pendant (RIGHT), and I had to completely rework this column! Both sedaDNA and this new extraction method from bone artefacts are set to revolutionise our understanding of the past, and they seemed a fitting subject for our 400th issue – where we are looking as much to the future of archaeology as to the past.

The last ten years have seen enormous leaps in our ability to extract and sequence ancient DNA from human remains, but in the last five there has also been a lot of exploration into how DNA is preserved in other parts of an archaeological site. Previously, the sediment in which archaeological finds were buried was seen as unimportant, something you had to dig through to get to the good stuff. This has been swiftly changing as we have come to realise all the information that remains trapped within the soil.

To find these hidden pockets of DNA, small samples of sediment – or in some cases whole, undisturbed blocks – are lifted from an archaeological site and then, in the lab, genetic analysis is carried out (and if a whole block were lifted, microscopy can also be done if the block is hardened with resin and thinly sliced). Through this ‘sedaDNA’ analysis, scientists are able to ‘locate’ the past presence of organisms by finding small sequences of their DNA still preserved in the sediment. In this way, we can recreate palaeoenvironments, seeing what organisms made up a particular ecosystem in the past.

More recently, the technique has also been used to identify the presence of humans and other hominins. One of the first projects to test this was at Denisova Cave in the Altai Mountains of Siberia – famous as the type site for the hominin group known as the Denisovans. There, an international team led by researchers from the Max Planck Institute for Evolutionary Anthropology has been able to recover both Denisovan and Neanderthal DNA in several different stratigraphic layers (many of which did not yield any physical remains), showing that they had both occupied the site repeatedly until at least 45,000 years ago, when modern human DNA was first detected in the sediments.

IMAGE: Max Planck Institute for Evolutionary Anthropology, artistic interpretation of the pendant by Myrthe Lucas IMAGE: Max Planck Institute for Evolutionary Anthropology, artistic interpretation of the pendant by Myrthe Lucas
IMAGE: Max Planck Institute for Evolutionary Anthropology, artistic interpretation of the pendant by Myrthe Lucas

Denisova Cave is also where the recently analysed bone pendant was discovered. To avoid contamination with modern DNA, it was carefully excavated to minimise any contact with humans, including everyone wearing gloves and masks once it had been located in the soil. Because bone is porous, it is able to ‘absorb’ the DNA of other organisms more than other materials might. After excavation, another international team (also led by researchers from the Max Planck Institute) incubated the pendant in a sodium phosphate buffer at varying temperatures, successfully extracting ancient DNA, both from the animal that the bone came from as well as from the human who had handled it thousands of years ago.

The DNA was then sequenced, revealing that the bone had come from a wapiti or elk (Cervus canadensis). As for the human DNA extracted, due to the level of degradation present the researchers determined that it was in fact from an ancient human and not a modern contaminant, and possibly came from the person who either made or wore this pendant, and would have had the most direct contact with it. This individual was found to be a female who was most closely related to a group of ancient North Eurasian individuals from further east in Siberia than Denisova Cave.

The team was also able to date the object by placing the sequenced DNA within the genetic trees of each species and seeing where in the timeline they fell. Thus, by combining the dates from both the elk and human genetic trees, they were able to narrowly date the pendant to between 19,000-25,000 years ago, while the radiocarbon dates from charcoal in the same layer only provided a date of c.40,000-20,000 years ago. This meant that the artefact did not need to be destructively sampled for dating.

These advancements in DNA extraction add a new dimension to our understanding of the past. While DNA cannot tell us everything about a society – which is much more complex than just our genetic material – it provides a level of knowledge that was previously impossible, including information on the movement of people and the possible role of the different sexes in a particular society. This is particularly relevant in prehistorical contexts, especially Palaeolithic ones, where previously archaeologists have had to rely on a small amount of data with wide dating margins. These new techniques allow us to fill in the gaps of how both sites and the objects within them may have been used, by whom, and when.