By sequencing the nuclear genome of an ancient finger bone, researchers have confirmed the discovery of a new type of human that lived in the Altai Mountains in southern Siberia more than 30,000 years ago. This long-lost group of people, which researchers are calling "Denisovans" after the Denisova cave in which the bone was found, lived at roughly the same time modern humans and Neandertals were in the region, and it appears to be more closely related to Neandertals than us. Although these Denisovans went extinct, they were widespread enough in Asia to interbreed with modern humans before they disappeared, leaving behind a ghostly legacy in the genomes of Melanesians.
After archaeologists discovered the bone in 2008, scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, isolated remarkably well-preserved DNA—comparable to DNA frozen in permafrost. In a study  reported earlier this year in Nature, the team sequenced the finger's mitochondrial DNA (mtDNA), which suggested that the digit did not belong to a Neandertal or a modern human. The mtDNA, which is passed down only from the mother and represents a small fraction of the total genome, didn't provide enough data to draw firm conclusions about the identity of the finger's owner, however.
In the new study, the Max Planck team sequenced 70% of the nuclear genome, which comes from DNA on 23 pairs of chromosomes. The researchers then compared this sequence with the genomes of Neandertals and modern humans and confirmed that the girl was neither human nor Neandertal. Her DNA was more like that of Neandertals than that of modern humans, suggesting that Neandertals and Denisovans are sister groups that shared a common ancestor after they split from the ancestors of modern humans, says evolutionary geneticist and lead author Svante Pääbo. But they were not Neandertals, because their DNA diverged from that of Neandertals about 640,000 years ago and because the large molar was too primitive to belong to a Neandertal, according to team member David Reich, a population geneticist at Harvard Medical School in Boston.
The researchers also compared different parts of the Denisovan genome with the same segments of DNA in 53 populations of present-day humans. The data revealed that the Denisovans shared certain mutations with Melanesians from Papua New Guinea and Bougainville Island, mutations that are not found in Neandertals or other modern populations. Melanesians appear to have inherited between 4% and 6% of their DNA from these extinct Denisovans, the team reports  online today in Nature.
The best scenario to fit this data is that after Neandertals and Denisovans split, the Neandertals interbred with modern humans just after they left Africa but before they spread into Europe and Asia in the past 80,000 years. Later, Denisovans living in eastern Asia encountered a group of modern humans heading east from Africa toward Melanesia and interbred with them. As a result, Melanesians now carry DNA from both encounters with Neandertals and Denisovans, which means that as much as 8% of their DNA comes from archaic populations, says Reich. The team is already trying to identify the function of those mutations.
Paleoanthropologists are also taking a new look at old fossils in Asia, trying to figure out which ones might be the Denisovans—if any. Along with the discovery in 2004 of the diminutive Homo floresiensis—a.k.a. the hobbit—that lived on the island of Flores as recently as 13,000 years ago, there are now at least three other types of humans who were alive at the same time as modern humans were taking over the world. Clearly, this means “the story [of the origins of modern humans] has undoubtedly got a lot more complicated,” says paleoanthropologist Chris Stringer of the Natural History Museum, London.