On the trail of exciting DNA in sediments

On the trail of exciting DNA in sediments

Sampling from an impregnated sediment block for the analysis of old DNA. (Image: MPI for Evolutionary Anthropology)

How has the genetic material survived the millennia that has been discovered in the soil of archaeological sites in recent years? By examining sediment samples embedded in synthetic resin from numerous sites, researchers are now showing that the DNA is concentrated in microscopic bone and fecal particles. Considerable amounts of human or animal-rich genetic material can be obtained from microsamples from these “hotspots”, the scientists show, for example in the case of the Denisova Cave. The study shows that sediment samples prepared in synthetic resin decades ago are also suitable as test material.

For a long time, the focus was only on tangible finds – archaeologists and anthropologists, on the other hand, paid little attention to the soil material during excavations. But that has changed in recent years. Because it has been shown that important clues to former living beings may have survived in sediments: genetic remains. So far, they have been extracted from loose soil samples using certain analytical methods and then analyzed. “The extraction of ancient human and animal DNA from sediments offers exciting new opportunities to investigate the settlement history of humans and other organisms in places where skeletal remains are hardly or not at all,” says Matthias Meyer from the Max Planck Institute for Evolutionary Anthropology in Leipzig.

Specimens prepared in synthetic resin in focus

As part of their study, Meyer and his colleagues have now investigated the question of where exactly the old DNA is in the sediment. To do this, they examined blocks of sediment that they had previously taken from archaeological sites and soaked in plastic-like resin (polyester). In some cases this treatment has already been carried out in the last few decades for the preparation of sediments. By examining such samples, the researchers therefore also clarified to what extent this archive material, some of which has been stored for a long time, is still suitable for examining DNA residues. For the study, all test materials were cut into slices in the laboratory and then subjected to microscopic and genetic examinations. The international team also analyzed sediment blocks from the Denisova Cave in the Altai Mountains in south-central Siberia in this way. There, ancient DNA from Neanderthals, Denisovans and modern humans was previously detected in the sediment.

As the researchers explain, the use of the impregnated sediment blocks enabled targeted and detailed extraction of samples for DNA analysis from the fine structures. It turned out that the old DNA is not evenly distributed in the sediment. In contrast, it focuses on small “hotspots” – especially in microscopic bone and fecal particles. “This study takes us a big step further in understanding where and under what conditions old DNA is preserved in sediments,” sums up co-author Mike Morley of Flinders University in Adelaide. Concerning the samples from the Denisova Cave, it was found: “The high success rate in the recovery of ancient mammalian DNA from the sediments of the Denisova Cave is due to the abundance of micro-residues in the sediment matrix and not to DNA from fecal matter attached to mineral grains , Body fluids or decomposing cell tissue, ”says co-author Vera Aldeias from the University of Algarve in Portugal.

Potential for research

The researchers were also able to make it clear that samples that had been stored for a long time are also suitable for analysis: They succeeded in extracting DNA from a collection of sediment blocks that had been taken from archaeological sites in Africa, Asia, Europe and North America over the past four decades. “The fact that these blocks are an excellent source of old DNA, including that of hominins, despite the fact that they are often stored in plastic for decades, opens up access to a huge, previously unused reservoir of genetic information,” says Morley. “The study opens a new era in researching ancient DNA: samples stored in laboratories can now be re-examined”.

The scientists have also already been able to provide concrete results as part of their study: They succeeded in extracting considerable amounts of DNA from two male Neanderthals from samples from the Denisova Cave, which could be compared with known genetic information. In this way, they were able to prove that these individuals belonged to a population that was related to a Neanderthal man whose genome had previously been reconstructed from a bone fragment discovered in the cave. “The Neanderthal DNA contained in these small samples of sediment embedded in plastic was much more concentrated than what we normally find in loose sediment,” says first author Diyendo Massilani from the Max Planck Institute for Evolutionary Anthropology. “With the help of this technology, it could be possible in the future to extract the DNA of many different people from the past from just a small cube of solidified sediment,” says the scientist.

Source: Max Planck Institute for Evolutionary Anthropology, specialist article: PNAS, doi: 10.1073 / pnas.2113666118

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