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Say hello to X woman, your long-lost cousin

Scientists stunned as DNA analysis of bone fragment found in Russian cave reveals existence of a hitherto unknown ancestor

To the trained eye of the palaeontologist, the tiny fragment of fossilised bone can be identified as coming from the little finger of a child who lived about 40,000 years ago in the Altai mountains of southern Siberia. But in the hands of molecular biologists, the bone has revealed that it belonged to a new lineage of human being, an unknown "hominin" who, although human, was not a member of our own species, Homo sapiens.

The finger-bone was unearthed in 2008 from the floor of Denisova Cave, a rock shelter known to have been inhabited by ancient humans for several hundred thousand years. Now, after exhaustive tests on DNA extracted from the fragment, scientists can reveal that in Siberia at this time there lived a hitherto unknown type of human who was neither Homo sapiens nor Neanderthal, the only other human species living in the area at about this time.

It raises the intriguing possibility that in this part of central Asia about 40,000 years ago three species of human were living alongside one another, perhaps for thousands of years. Nothing is known of how they interacted or whether they interbred but it is clear that only one of the three species survived, anatomically modern humans.

Fossilised bone fragments of woolly mammoth and woolly rhino and ostrich shell, as well as a polished stone bracelet and bone tools, have also been unearthed at Denisova, a cave consisting of a central chamber and several short galleries overlooking the Anui River which runs through a steppe-like landscape.

Scientists have no other physical remains of this mysterious hominin who lived in the Denisova cave except the fragment of finger-bone. They do not know even whether it was male or female, but the size of the bone suggests that the little finger belonged to a child aged seven or eight, and carbon dating of the sediments surrounding it indicates that he or she lived between 30,000 and 48,000 years ago.

The scientists were able to identify a new lineage of hominin from DNA analysis alone by extracting the DNA of the mitochondria, tiny "organelles" inside the cells of the bone that house their own genetic material. Mitochondrial DNA is unlike the DNA found in the cell nucleus in that it is simpler and always inherited down the maternal line from the mother.

The scientists have nicknamed the fossil "X woman" to indicate that it was this maternally inherited mitochondrial DNA that has so explosively revealed the existence of another species of human who lived during the last Ice Age in these remote Siberian mountains.

When Johannes Krause, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, first analysed the genetic sequence of the mitochondrial DNA extracted from the fossilised bone be could not quite believe his own results, now published in the journal Nature.

"It really looked like something we'd never seen before," Dr Krause said. "It was a sequence that was similar in some ways to humans and yet it was still quite distinct from humans and Neanderthals. We did several analyses to make sure this DNA was authentic, that this DNA was really old, fossil DNA, and that it was not a modern contamination."

Scientists had already sequenced the complete mitochondrial DNA of Neanderthals and had found that they differed to modern humans by about 202 nucleotides, the sequence of "letters" making up the DNA code. Now they found that the Denisova individual differed from the mitochondrial DNA of modern humans by about 385 nucleotides.

"In a very general sense, from their mitochondrial DNA, we can say that they [X woman] was about twice as different from us as Neanderthals. So in their biology they were also probably more distant, but what that means in terms of their behaviour or how they looked, we have no clue," Dr Krause added. "So far, we know only of Neanderthals and Homo sapiens [in terms of their mitochondrial DNA]. Now we have another mitochondrial lineage."

After Dr Krause had checked his results he telephoned his colleague, Svante Pääbo, an authority on recovering ancient DNA from fossilised bone. "I thought it was absolutely amazing," Dr Pääbo said. "At first I didn't believe him. I thought he was pulling my leg." By calculating the time it must have taken for these genetic differences to arise, the scientists were able to calculate the age of the ancestor of X woman who had migrated into Asia from Africa.

They estimated that this ancestor must have migrated out of Africa about one million years ago, nearly a million years later than the earliest known human migration out of Africa, that of Homo erectus, and about half a million years earlier than the ancestral migration of the Neanderthals; H. sapiens migrated less than 100,000 years ago.

"The mitochondrial DNA of X woman was very different," Dr Pääbo said. "The common ancestor was a lot older, about twice as old as Neanderthal's ancestor. This makes this mitochondrial lineage different. It's not Homo erectus. It's some new creature that has not been on our radar screens so far.

"This mitochondrial DNA must come from an unknown migration out of Africa. Until we found this I was very much under the sway of the palaeontological view that we had a migration about two million years ago that gave Homo erectus and then the ancestors of the Neanderthals about half a million years ago and between that hardly anything coming out of Africa. But it is totally amazing to me that we clearly see something else coming out of Africa between these two time points," he added.

The scientists, including Michael Shunkov and Anatoli Derevianko, of the Siberian Branch of the Russian Academy of Sciences, are planning further investigations of the cave, as well as studies of the finger-bone to try to uncover more about the nature of this unknown branch of humans.

"There will be another excavation of the cave in the summer and it is possible that something else may be found," Dr Pääbo went on. "There may be something else there related to the X woman." But more importantly, the scientists hope to extract DNA from the cell nucleus. This nuclear DNA, if big enough fragments can be extracted and sequenced, will give the researchers more information on the relationship between X woman and the two other human species living in Siberia at this time.

It might even indicate whether there was any intermarriage between the three human lineages. Tests so far on Neanderthal DNA have ruled out interbreeding with Homo sapiens, but it is possible that the Denisova individual represents some kind of human hybrid between two other human species.

"If we are going to get a substantial part of the nuclear genome of this X woman we will be able to say if she or her ancestors interbred with the ancestors of people today," Dr Pääbo said. "At least we have one other lineage now in addition to Neanderthals to ask this question."

And one of the biggest mysteries of all is what happened during the period when these three human species lived close by one another? Did they fight, or did they live together in peace? "Of course something happened in that only we survived, and we can only speculate as to what that was," Dr Pääbo added. "I would share the view that we were somehow responsible but whether in a very direct way or by some kind of ecological competition, I don't know. We don't know what really happened."

But one clear implication of the Denisova find is that X woman and relatives must have been able to make clothes and control fire to protect them against the harsh Siberian winter, which probably would have been even harsher 40,000 years ago than it is today.