The field of ancient DNA has revealed important aspects of our evolutionary past, including our relationships with our distant cousins, Denisovans and Neanderthals. These studies relied on DNA from bones and teeth, which store DNA and protect it from the environment. But these skeletal remains are extremely rare, leaving large parts of human history inaccessible to genetic analysis.
To fill these gaps, researchers at the Max Planck Institute for Evolutionary Anthropology have developed new methods to enrich and analyze human nuclear DNA from sediments, which are abundant in almost all archaeological sites. So far, only mitochondrial DNA has been recovered from archaeological sediments, but this is of limited value for studying relationships between populations. The advent of nuclear DNA analyzes of sediments offers new opportunities to investigate the deep human past.
Sediments may contain genetic material from other mammals
When extracting ancient human DNA from the sediment, scientists had to be careful to avoid the sheer amount of DNA from other mammals, such as bears and hyenas. “There are a lot of places in the human genome that are very similar to the DNA of a bear, for example,” said Benjamin Vernot, the study’s first author. The researchers specifically targeted regions of the genome where they could be sure to isolate only human DNA, and they also devised 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.
Scientists applied their techniques to study more than 150 sediment samples from three caves. In two of them – the Chagyrskaya and Denisova Caves in the Altai Mountains of southern Siberia – previous studies had analyzed the DNA of the bones. The authors were therefore able to compare the DNA of the sediments to the DNA of the 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, lead author of the study. The researchers found that the DNA from the sediments was most closely related to the genomes extracted from the bones of these sites, giving them confidence in the robustness of their methods.
Nuclear DNA recovered from cave deposits in northern Spain
Excavations at the third site, Galería de las Estatuas in northern Spain, led by Juan Luís Arsuaga of the Universidad Complutense de Madrid, had unearthed stone tools spanning a period between 70 and 115 thousand years . But only one Neanderthal toe bone had been found, and it was too small for a DNA sample. “There was no way to study the genetics of the Neanderthals who lived in Estatuas,” said Asier Gómez-Olivencia, a scientist from the Estatuas team at the Universidad del País Vasco / Euskal Herriko Unibertsitatea. Nuclear DNA extracted from the sediments revealed that not one, but two populations of Neanderthals had lived in the cave, with the original group being replaced by a more recent group around 100,000 years ago.
When the scientists compared the DNA in the sediment to other skeletal samples, they noticed a striking pattern – there appeared to have been two Neanderthal ‘radiations’, the older population of Estatuas coming from radiation and the younger population of a second event. “We wondered if this radiation, along with the population replacement in Estatuas, could have been linked to climate change or Neanderthal morphological changes that occurred during this period – although we need more data to be sure.” , said Juan Luís Arsuaga.
New perspectives on the deep human past
Even for sites where studies have already analyzed bone DNA, it is possible to glean new information from the sediment. At Chagyrskaya Cave, previous archaeological studies had suggested that the Neanderthal occupants belonged to a single population and lived there for only a short time. But since previous work had only recovered a single genome from one of the bones found at the site, there was no way to tell if it was representative of the entire population that lived around. the Chagyrskaya cave. The DNA of the sediments was able to confirm this hypothesis. “We took samples of sediment from all over the stratigraphy, and they all looked like DNA from bone, even though the DNA in the sediment came from several individuals,” said Kseniya Kolobova of the Institute of Archeology. and ethnography of the Russian Academy of Sciences the principal archaeologist of the Chagyrskaya cave.
“The dawn of nuclear DNA analysis in sediments massively expands the range of options for unraveling the evolutionary history of ancient humans,” said Vernot. By freeing the ancient DNA domain from the constraints of searching for human remains and increasing the number of sites potentially suitable for investigation, “we can now study DNA from many more human populations and many more. places than previously thought, ”said Meyer.