Genomics of cave soil
The study of the DNA of ancient people became possible without the remains themselves
Anna Kaznadzei, N+1
Biologists from the Institute of Evolutionary Anthropology of Leipzig and their Russian, European and Australian colleagues have found out that the DNA of Neanderthals and Denisov people can be successfully identified in samples taken from sedimentary rocks of archaeological locations. This method does not require, in fact, the ancient remains themselves, a small amount of mitochondrial DNA contained in such samples is enough. Article by Slon et al. Neandertal and Denisovan DNA from Pleistocene sediments is published in Science.
Mineral and organic components of samples taken from deep layers of geological deposits can store DNA fragments, which are quite successfully amenable to isolation and further analysis. Similar works have already been carried out for the study of ancient plants and animals. An important factor in the "antiquity" of the DNA under study is the replacement of some of its cytosines with thymines – this is due to the deamination reaction and serves as an indicator of the age of the molecule.
Scientists analyzed 85 samples from seven archaeological locations, including Denisov Cave and Chagyr Cave, located in the Altai Mountains. The age of the deposits ranged from 14 to over 550 thousand years and corresponded to the late or Middle Pleistocene. Some of the samples were collected specifically for this project, while others have been stored at room temperature for several years, which did not prevent the mitochondrial DNA contained in them from being successfully analyzed.
Mitochondrial DNA is contained in cells in a larger number of copies than nuclear DNA, so it is more convenient to work with it in cases when the number of nucleic acids in the samples is very small. Having isolated the DNA, the scientists compared it with 242 samples of mitochondrial DNA from different mammals by hybridization. More than two-thirds of the sequenced DNA could not be identified, however, among the rest, the presence of ancient nucleic acids corresponding to the DNA of elephant, hyena, polorog, ungulate, deer, canine and other animal species was shown. The study of genetic variations showed that the DNA of elephants mainly belonged to woolly mammoths extinct in the Holocene, the DNA of rhinoceroses – woolly rhinoceroses extinct in the late Pleistocene, the DNA of hyenoids – extinct cave hyenas or currently living spotted hyenas, and, finally, the DNA of bears found in the Croatian Vindija cave, belonged mainly to the extinct 25 thousand years ago the bear Ursus ingressus. The method successfully made it possible to separate ancient DNA from more modern, and the data on animal DNA corresponded to scientists' ideas about the species living in these territories in those time periods.
Identified mDNA fragments in different locations. LP is the late Pleistocene, MP is the Middle Pleistocene, numbers are the number of images from this location with identified ancient mammalian mDNA (here and below are figures from the article in Science).
At first, the DNA of hominids (a family of primates including humans and great apes) was found in only one location.
The animal DNA in the samples turned out to be too much, and the scientists repeated the experiment, now hybridizing DNA only with mDNA samples of known hominids. As a result, the presence of hominids was detected in 15 samples from four locations, and in nine of them there were enough fragments of mitochondrial DNA for further analysis. Comparing the sequences of these fragments with the known sequences of Neanderthals, Denisovan people and Heidelber man from the Spanish cave Sima de los Huesos, scientists were convinced that the DNA of eight samples correspond to Neanderthals by 87-98 percent (while the correspondence with modern man was 4-11 percent, and with Denisovan and Heidelber man – 0-2 percent each). These samples were taken from the Spanish location El Sidrón, the Belgian location Trou Al'WESSE, as well as Denisov Cave and Chagyr Cave. In the ninth sample, also taken from Denisov's cave, 84 percent of the DNA matched the Denisov man. Interestingly, hominid remains have not yet been found in the Pleistocene deposits of the Belgian location, although processed animal bones and other artifacts found in those places indicate that Neanderthals most likely really lived there. In Denisov Cave, Neanderthal DNA has also been identified, in particular, in samples from layers in which stone tools of the Middle Paleolithic were found, but the remains of Neanderthals themselves have not yet been found. In its Eastern Gallery, traces of DNA of Neanderthals and Denisovans were found in lower layers than the remains of ancient people themselves, which indicates the joint existence of these two species for a long time.
Found traces of hominins in Denisov's cave: green – Denisov people, red – Neanderthals; image of bones – remains, image of a shovel – rock samples. The lowest layers of the slice are the most ancient.
In the samples of the Middle Pleistocene of the Chagyr Cave and the French Caune de l'arago, the presence of hominid DNA could not be shown, which is not surprising, given their age – more than 300 thousand years. Scientists hope, however, that a larger-scale analysis with a large number of samples will allow us to study such ancient deposits, as well as to detect the presence of hominid DNA in those samples of the late Pleistocene, where it has not yet been possible to do this either. The phylogenetic trees constructed on the basis of the obtained data showed that the genetic variations of the studied DNA are within the normal range for the known mitochondrial genomes of Neanderthals and Denisovans. It was also possible to show in which DNA samples belonged to one individual, and in which – to different ones. Using the method of maximum truthfulness, scientists also managed to examine four additional samples from the Denisov cave and the Chagyr cave, and to detect the presence of DNA of ancient hominids in them, and DNA of two different individuals was found in one of the samples of the Denisov cave.
A phylogenetic tree built on the basis of mDNA samples from remains and from rocks in different locations. Red – Neanderthals, green – Denisov people, blue – Heidelberg man, purple – outgroup of modern people. The image of the bone is the remains, the image of the shovel is the rocks.
It is possible to obtain from 28 to 9142 fragments of mitochondrial DNA per milligram of human remains, and from 34 to 4490 fragments per milligram of rock (including, however, mDNA of all mammals). This is an amazing amount, and opens up many prospects for such research. In addition, additional studies have shown that DNA is usually distributed fairly evenly in the ancient rock layer and does not mix with lower or upper layers.
The study of ancient organisms is often difficult due to the small amount of archaeological and paleontological materials. For many techniques, one tooth lost by some Denisov man would be enough, but even such a find is very rare. The new figures and facts are encouraging – apparently, to study the DNA of ancient people, it will no longer be necessary to find their graves, remains or even body parts.
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28.04.2017