An investigation in which the CSIC participates has been able to find human remains where there were not even bones. One of the sites studied has been the El Sidrón cave, in Asturias.

Inside the El Sidrón cave, in Asturias.

Anyone who has seen any chapter of the series CSI, or for that matter any police film, knows that today gloves and a stocking on the head are not enough to get away with a crime unpunished. Sherlock Holmes’ magnifying glass has given way to DNA technologies, and a tiny biological trace left by a criminal at the scene of the crime is as revealing evidence as a photograph of the offender red-handed. What we could not suspect until today is that the power of this technology could betray the presence of someone who passed through a place not days or weeks ago, but tens of thousands of years ago.

This is what an international team of researchers led by Matthias Meyer, an evolutionary geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has achieved. In this case, the settings are several caves in Europe and Siberia where long ago some of our extinct relatives inhabited such as Neanderthals. The relevance of the finding is that for the first time it has been possible to detect such an ancient human presence through DNA without the need for bones, but directly in the rock sediment that over the years was deposited on the settlements.

A state-of-the-art magnifying glass

In the late 20th century, the development of DNA technologies allowed researchers to begin salvaging useful samples of fossil remains. These new State-of-the-art archeophorens loupes have been sophisticated in recent years to previously unthinkable extremes: in 2016 parts of the genome of individuals that left their bone remains in the Sima de los Huesos de Atapuerca 430,000 years ago could be identified.

However, you don’t always find ancient human bones or teeth from which to extract a DNA sample. In many of the sites The presence of those inhabitants is only known by the tools they left there, or by the vestiges of their feasts. In 2003, the researcher at the University of Copenhagen (Denmark) Eske Willerslev managed for the first time to extract DNA from animals and plants without the need for fossils, directly from frozen Siberian soils up to 400,000 years old, and from cave sediments from a few hundreds of years.

But identifying ancient human DNA poses a special difficulty. Since it is humans who collect and manipulate the remains of the caves, until a few years ago it was difficult to differentiate ancient DNA from modern contamination. Today archaeologists and paleontologists no longer enter the sites with hats and whips, but with divers similar to those used by the forensic police at crime scenes.

With this background, the authors of the new study, published in the journal Science, they decided to give the attempt to recover DNA from the soil a chance. “As achievements are achieved, other possibilities are being tested,” Antonio Rosas, a researcher at the National Museum of Natural Sciences of the CSIC and co-author of the study, in which Marco de la Rasilla, from the University of Oviedo, and Carles Lalueza-Fox, from the Institute of Evolutionary Biology of the CSIC and the Pompeu Fabra University. Specifically, scientists collected soil samples from seven caves that had a human presence between 14,000 and 550,000 years ago, in France, Russia, Belgium, Croatia and Spain; in the latter case, the Asturian cave of El Sidrón, an important Neanderthal settlement from which DNA has previously been obtained from bones.

Neanderthals and Denisovans

For all samples, the researchers tried to fish for mitochondrial DNA, which is not found in the nucleus of the cellBut in the tiny power plants called mitochondria. The advantage of this DNA, which is inherited from the mother, is that there are multiple copies in each cell, unlike the chromosomes in the nucleus. The study authors focused on the recovery of mammalian mitochondrial DNA.

It was precisely the soil of El Sidrón that yielded Neanderthal mitochondrial DNA on the first attempt. The peculiarity of the Asturian cave is that no animal remains have been found there, only human remains. Concerning that perhaps in other sites the abundance of DNA from other animals was hiding the human, the researchers used only human-specific genetic hooks, and there the rest turned up. In total, they have recovered human DNA from five caves, and in several of them also from animals such as mammoths, cave bears and woolly rhinos.

A special case is the Denisova cave, in Russia. This enclave It is famous for having previously found a small fragment of bone from a finger and some teeth that genetic techniques assigned to an unknown human species. The so-called Denisovans, related to Neanderthals, are still largely a mystery and are not formally recognized as a species, as their anatomical features have not yet been defined. But the new job confirms detection of DNA from both Neanderthals and Denisovans, and it is precisely there where the oldest DNA in the study has been recovered, from the Middle Pleistocene, at least 130,000 years ago.

But what is the origin of that DNA, and how can it be preserved for so long? According to Rosas, when bones have been found in the same place, that DNA dispersed in the soil could remain there after the decomposition of the soft tissues of the same individuals. However, when no bones have been found but DNA has been found in the soil, as in the case of the Belgian cave of Trou Al’Wesse, or if there are bones in the site but in different layers to the sampled soils, there are other possibilities: “Let’s imagine for example a childbirth, with the placenta; imagine a hemorrhage from a hunting wound or a defecation; all that contains DNA ”, says the researcher.

Regarding the preservation of these genetic traces, Rosas points out that it is due to the properties of clays, a type of sediment frequent in caves. “They act as preservatives, since the DNA chains are captured within the clay network; then you have to take them off ”. The CSIC researcher adds that the possibility of obtaining DNA from other types of soils has yet to be explored, including open-air fields.

But according to Rosas, in this field of research technical barriers are breaking down one after another at a surprising rate. “Now they are doing things that ten years ago would have seemed impossible, almost science fiction.” Today’s date, the record for the oldest human DNA that has been recovered and sequenced is that of the Sima de los Huesos, dating back 430,000 years. But regarding whether we will see this mark fall, and if we will one day get to know the DNA of, for example, our African ancestors who lived more than a million years ago, Rosas has no doubt: “I am convinced of it.”