CM – Nuclear DNA from sediments helps unlock ancient human history


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April 15, 2021

from the Max Planck Society

The area of ​​ancient DNA has revealed important aspects of the human evolutionary past, including relationships with Denisovans and Neanderthals. These studies relied on DNA from bones and teeth, which store DNA and protect it from the environment. However, such skeletal remains are extremely rare, making large parts of human history inaccessible for genetic analysis.

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In order to close these gaps, researchers at the Max Planck Institute for Evolutionary Anthropology developed new methods for the enrichment and analysis of human nuclear DNA from sediments, which are abundant in almost every archaeological site. To date, only mitochondrial DNA has been extracted from archaeological sediments, but this is of limited value for studying population relationships. The advent of nuclear DNA analysis of sediments opens up new opportunities to examine the deep human past.

When extracting ancient human DNA from the sediments, scientists had to be careful about the sizable amount of DNA from other mammals such as bears and Avoid hyenas. « There are many places in the human genome that are very similar to the DNA of a bear, for example, » said Benjamin Vernot, the study’s lead author. Researchers specifically targeted regions in the genome where they could be certain they would isolate only human DNA and developed methods to measure their success in removing non-human DNA. « We wanted to be sure that we weren’t accidentally looking at unknown species of hyena, » Vernot said.

The scientists used their techniques to examine more than 150 sediment samples from three caves. In two of these caves – Chagyrskaya and Denisova in the Altai Mountains in southern Siberia – previous studies had analyzed DNA from bones. This enabled the authors to compare the DNA from sediments with the DNA from bones. « The techniques we developed are very new and we wanted to be able to test them in places where we knew what to expect, » said Matthias Meyer, the study’s lead author. The researchers found that DNA from the sediments is most closely related to genomes obtained from the bones of these sites, which gives them confidence in the robustness of their methods.

During excavations at the third site, the Galería de las Estatuas in northern Spain, led by Juan Luís Arsuaga from the Universidad Complutense de Madrid, stone tools were discovered 70 to 115,000 years ago. However, only a single Neanderthal toe bone was found and it was too small to take DNA samples. « There was no way to study the genetics of the Neanderthals living in estatuas, » said Asier Gómez-Olivencia, a scientist on the Estatuas team at the Universidad del País Vasco / Euskal Herriko Unibertsitatea. The nuclear DNA extracted from the sediments revealed that not one but two Neanderthal populations had lived in the cave, with the original group being replaced by a later group about 100,000 years ago.

When the scientists investigated the sediment- Comparing DNA to other skeletal samples, they found a remarkable trend – there appeared to have been two « radiations » from Neanderthals, with the older Estatuas population coming from one radiation and the younger population from a second event. « We wondered if these radiations, along with population replacement in Estatuas, might be related to climate changes or changes in Neanderthal morphology during that period – although we need more data to be certain, » said Juan Luís Arsuaga.

Even in places where studies have previously analyzed DNA from bones, it is possible to gain new knowledge from the sediments. In the Chagyrskaya Cave, previous archaeological studies had shown that the inhabitants of the Neandertal belonged to a single population and lived there only for a short time. However, since previous work had only obtained a single genome from one of the bones found at the site, it could not be determined whether it was representative of the entire population living in the vicinity of the Chagyrskaya Cave. The sediment DNA was able to confirm this hypothesis. « We took sediment samples throughout the stratigraphy, all of which looked very similar to the DNA from the bone, even though the sediment DNA came from several people, » said Kseniya Kolobova of the Institute of Archeology and Ethnography of the Russian Academy of Sciences. the chief archaeologist in Chagyrskaya Cave.

« The beginning of nuclear DNA analysis of sediments massively expands the range of possibilities to work out the evolutionary history of ancient humans, » said Vernot. By freeing the ancient DNA field from the constraints of searching for human remains and increasing the number of potential study sites, « we can now study DNA from far more human populations and locations than previously thought possible « said Meyer.

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