SIBERIAN SURPRISE: DNA retrieved from a fossil found in Denisova Cave, located in the Altai Mountains, belongs to a previously unknown form of human. The excavation field camp is visible in this view from above the cave. Image: Johannes Krause
For much of the past five million to seven million years over which humans have been evolving, multiple species of our forebears co-existed. But eventually the other lineages went extinct, leaving only our own, Homo sapiens, to rule Earth. Scientists long thought that by 40,000 years ago H. sapiens shared the planet with only one other human species, or hominin: the Neandertals. In recent years, however, evidence of a more happening hominin scene at that time has emerged. Indications that H. erectus might have persisted on the Indonesian island of Java until 25,000 years ago have surfaced. And then there's H. floresiensis—the mini human species commonly referred to as the hobbits—which lived on Flores, another island in the Indonesian archipelago, as recently as 17,000 years ago.
Now researchers writing in the journal Nature report that they have found a fifth kind of hominin that may have overlapped with these species. (Scientific American is part of Nature Publishing Group.) But unlike all the other known members of the human family, which investigators have described on the basis of the morphological characteristics of their bones, the new hominin has been identified solely on the basis of its DNA.
Johannes Krause and Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and their colleagues obtained the DNA from a fossilized pinky finger bone found at Denisova Cave in the Altai Mountains of southern Siberia. The species was impossible to determine from the shape and size of the bone—it simply did not contain any diagnostic morphological traits. But there were good reasons to believe it came from a Neandertal or an early modern human. For one, the bone was recovered from a stratigraphic layer of the cave dated to between 50,000 and 30,000 years ago that contained artifacts belonging to the so-called Middle Paleolithic and Upper Paleolithic industries associated with these two groups. For another, Neandertals and modern humans were the only hominins known to have lived in this region during that time period. But the DNA the team extracted from the Denisova pinky bone turned out to be markedly different from DNA sequences previously obtained from early modern humans and Neandertals.
The researchers focused on a type of DNA known as mitochondrial DNA (mtDNA). Mitochondria are the power plants of the cell, and they have their own DNA that is separate from that housed in the cell nucleus and is passed down from mother to offspring. Because each cell has thousands of mitochondria, but only a single nucleus, mitochondrial DNA is much more abundant than nuclear DNA and is therefore more likely than the latter to be preserved in fossilized bone. To date, scientists have sequenced the mitochondrial genomes of both Neandertal and early modern human individuals, and the sequences for the two groups are quite distinctive.
Comparing the order of the genetic "letters"—or base-pairs, as they are termed—making up the Denisova mtDNA with the sequences of modern day humans and an early modern human, Krause and his collaborators found that the Denisova mtDNA differed from humans today in nearly twice as many letter positions as Neandertal mtDNAs do. Further analysis indicated that the most recent common mtDNA ancestor of the Denisova individual, Neandertals and modern humans dates to around a million years ago (making it twice as old as the most recent common mtDNA ancestor of Neandertals and moderns). This divergence date, the team says, indicates that the Denisova mtDNA is distinct from that of the H. erectus population that left Africa 1.9 million years ago, and also from that of the Neandertal ancestor H. heidelbergensis, which branched off from the lineage leading to modern humans around 466,000 years ago. As such, the researchers contend the Denisova mtDNA reveals a previously unrecognized migration out of Africa by a hitherto unknown group of hominins. (The team is holding off on giving the creature a formal name for now, but informally they refer to it as X-woman.)