DNA from dirt
For the first time, nuclear DNA of Neanderthals was isolated from the soil of caves
Scientists for the first time extracted and deciphered the nuclear DNA of Neanderthals not from bones and teeth, but from the soil of caves where Neanderthals lived. The results of the work supported by a grant from the Russian Science Foundation (RNF) are published in the journal Science (Vernot et al., Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments).
Basically, the DNA of ancient people is obtained from bones and teeth, but such finds are very rare. This is due to the fact that in the Paleolithic there were no established burial customs and burials were done outside the sites, and, in addition, many ancient people simply did not return from hunting. In the case of bones and teeth, it is more often necessary to work with the genetic material of mitochondria, since the mitochondrial DNA in the cell contains much more than the DNA of the cell nucleus. But the information obtained from mitochondrial DNA is very limited: mitochondria are inherited from the mother, and not so many genes are encoded in them.
"Nuclear DNA is much more valuable, but its quantity is very limited: even with a bone fragment, it is not always possible to extract enough material. However, my colleagues and I have found a solution to this problem. Firstly, as a source of nuclear DNA, we used artifacts from excavations – stones, tools – in short, everything that could preserve the biological traces of ancient man. Secondly, we have applied a completely new approach to the processing of metagenomic material, that is, all the DNA from our samples. Gradually comparing the decoded sequences of nucleic acids with those available in the database and concentrating on fragments specific only to humans, we separated the material of Neanderthals from the material of animals, such as bears, with which we have a lot of similar genes. It is important to know that you are studying human DNA, and not some unknown species of hyena," says one of the authors of the work Andrey Krivoshapkin, Head of the RNF grant project, Doctor of Historical Sciences, Director of the Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences.
The scientists applied their approach to the Neanderthal artifacts from three caves: Chagyrskaya and Denisovskaya in the Altai Mountains in southern Siberia and the Spanish grotto in a place called Atapuerca. Siberian sites turned out to be relatively rich in bones of ancient people, so it was possible to compare the results for nuclear DNA from them and from cave deposits. As the analysis showed, the data from these two sources are consistent with each other, which means that even without skeletal fragments, it is really possible to obtain reliable results from precipitation.
Another interesting feature was found when constructing a kind of genetic "genealogies" based on sequentially decoded DNA of mitochondria (also isolated from the surface of artifacts). It turned out that two lines of Neanderthals lived in a Spanish cave, separated about 100 thousand years ago. One population replaced another, but it is unclear what caused it – the climate or some morphological changes. It is known that about 100 thousand years ago Neanderthals came to their "classic" appearance with a stocky build and a very protruding broad face. The transition took place in several stages, and perhaps the authors managed to detect the last stage.
"So far we cannot draw concrete conclusions about the evolutionary relationships of the inhabitants of these caves – new works will be directed at this. It is extremely important that we have proven the reliability of our approach. The study of the genetics and evolution of ancient people has always been complicated by the fact that there was not enough material from where DNA could be extracted. It is much easier to find artifacts than bones and teeth, and our technique will allow us to concentrate on the sequences of nucleic acids of a person, and not his animal neighbors. The results of this work mark the dawn of nuclear DNA analysis from the sediments of the sites. Undoubtedly, this will help shed light on many controversial and complex issues of human evolution," sums up Andrey Krivoshapkin.
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