Ancient DNA reveals well-kept secrets about the migrations, evolution and interbreeding of human populations, but also about the history of pathogens and animals. First article in a series on the bubbling paleogenomic science.
In January 2010, paleoanthropologist Bence Viola landed in Novosibirsk, Western Siberia, to better understand the origin of a mysterious phalanx. Russian colleagues had sent half of this fossilized bone, found in Denisova’s cave, to the German laboratory which he had just joined for a postdoctoral fellowship. Initial genetic analyzes suggested that this simple phalanx did not belong to a human like the others.
In the Siberian metropolis, Russian archaeologist Anatoly Derevyanko pulled an “absolutely huge” tooth from the same cave out of his shirt pocket and showed it to his visiting European colleagues. Mr. Viola, who is now a professor at the University of Toronto, was overwhelmed. “When I saw this tooth, he says, I knew immediately that it was not modern man, not Neanderthal: it was something completely different. »
A new human subspecies was discovered: the Denisovan. Exhaustive analyzes of the DNA of the 50,000-year-old phalanx would reveal that it is a subspecies close to Neanderthals which, without paleogenomics, would probably have remained in the shadows forever. And we would never have known that our own species, Homo sapiensmixed with the Denisovans and that several populations today bear the genetic mark.
Ancient DNA
“When we started analyzing ancient DNA from fossils, people thought it was just a fad, that it couldn’t tell us anything new,” says Viola. History has proved these detractors wrong: for the past dozen years, the number of scientific publications based on ancient DNA has grown exponentially. The most prestigious journals offer them a showcase like few other disciplines.
“The effectiveness of techniques has exploded over the past 20 years. This opened many, many doors for us, bioanthropologists and archaeologists, on specific questions that we were asking ourselves about populations and individuals”, underlines Isabelle Ribot, professor in the Department of Anthropology at the University of Montreal, who takes advantage of ancient DNA analysis to further his research.
A few large laboratories around the world are leading the paleogenomics ball. One of them is that of the geneticist Svante Pääbo, of the Max-Planck Institute for Evolutionary Anthropology, in Leipzig, with whom Bence Viola was working at the time of the identification of the Denisovans. Another ancient DNA master who has had enormous influence in this field of research is the geneticist David Reich at Harvard University.
Twelve years after the Denisovans were discovered, very few fossils are officially associated with these humans, who probably had the build of football players. In Denisova’s cave — also visited over the millennia by Homo sapiens and Homo neanderthalensis —, the specialists attributed only one phalanx, three teeth and a small bone fragment to the Denisovans. In 2019, a fossil from another site — the Xiahe mandible, found in Tibet — was first associated with the Denisovan subspecies.
Thanks to these finds, a certain profile of the Denisovan was taking shape. “We thought it was a species adapted to cold regions and high altitudes, because it had been found in the Himalayas and in Altai. [en Sibérie] “, notes the French anthropologist Fabrice Demeter, professor at the GeoGenetics Center of the Lundbeck Foundation, University of Copenhagen. However, paleogenomics would quickly cast doubt on this hypothesis.
Because as soon as the genome of Denisova’s man was deciphered, researchers compared it to that of modern humans. They found only a tiny trace of the Denisovan genome among Europeans. However, they discovered up to 5% Denisovan genetic material in certain populations of Southeast Asia and Oceania, such as the Aetas of the Philippines, the Papuans of Papua New Guinea and the aborigines of Australia. Did the Denisovans also live in the tropics, where they would have mixed with these populations?
A finding published this spring by a team including Demeter most likely answers that question.
Denisova in Laos
In 2018, Demeter and several colleagues were excavating Tam Pà Ling cave in Laos, where they had already found several ancient fossils. As usual, the specialists then prospected in the surrounding area in the hope of discovering new archaeological sites.
The geologists and speleologists of the team then found the entrance to a cave – “Cobra Cave” – where there was a fossiliferous breccia, that is to say sedimentary rock containing fossils. Teeth and bones, once belonging to humans and beasts living on the adjacent plain, were carried here millennia ago by heavy rains.
In such breaches, all the bones are fragmented, but the teeth — the hardest part of the skeleton — are usually intact. One of the teeth found in Cobra Cave aroused the curiosity of researchers. By meticulously comparing her form to those of Denisova, they concluded that she belonged to this subspecies. “It was really a moment of euphoria for the whole team,” says Mr. Demeter.
This summer, the team will analyze in the laboratory a few milligrams of the dentin – the part of the tooth that is under the enamel – of the sample to extract DNA. If this proves successful, the membership of this fossil to the Denisovan group will be established beyond any doubt, although the authors of the publication are already firmly convinced of this.
Thus, the Denisovans now appear as beings adapted to various climates. Many specialists believe that their territory, centered on China, was immense, and that the fossils found so far are only at the margins.
Fossils found in China are indeed “very good candidates” for Denisova, according to Viola. Western specialists are awaiting analysis from their Chinese colleagues to establish whether the Harbin skull — belonging to an ancient human nicknamed “Dragon Man” — is Denisovan. A mandible found by fishermen in the Taiwan Strait is also a fossil suspected to belong to the subspecies.
An encounter with Homo erectus?
And what about Denisova’s family tree? Paleogenomics tells us that Denisovans and Neanderthals diverged from common ancestors around 500,000 years ago. The Denisovans would have survived much later than their cousins: the interbreeding observed today in Southeast Asia would have occurred 50,000 to 20,000 years before our time, or even more recently. If these estimates hold true, the Denisovans would be the last surviving archaic humans.
Mysteries obviously persist about Denisova. Part of its genome (4%) comes from a mixture with an even older human population, whose identity is unknown for the moment. Professor Viola thinks it may beHomo erectus, arrived in East Asia almost two million years ago. That would mean that Denisova would have crossed his path—and shared his bed.
To see more clearly, it would be necessary to obtain more Denisovan DNA, but also to know how to decipher the genome of even older samples. This task is difficult: the passage of time breaks down the molecules storing genetic information.
There are also things that DNA can never tell us. What were the cultural habits of the Denisovans? What stone tools did they use? The discovery of a cave exclusively populated by this subspecies would help answer these questions. Like what genomics will never kill archeology.
“It’s always a work between disciplines, says Isabelle Ribot. You have to contextualize everything, find interesting research questions. Otherwise, what is the use of ancient DNA? »