Picture yourself in south-central Siberia many thousands of years ago.
You stand in the mouth of a cave on an elevated slope, giving you a clear view of the woods and valley below and of any animals that happen to be moving along the Anui (Anuy) River at your forefront. The cave behind you is quite comfortable, with three rooms and a natural opening that serves as a chimney. Sound cozy -- at least for a band of hunters?
During the 18th century the cave was reportedly the home of a hermit. His Anglicized name was Denis -- hence the cave's name: Denisova. But long before Denis, the cave had housed at least three different types of peoples. One group was earlier members of our own species, Homo sapiens. Another was our famous relatives, the Neanderthals. And third was the very tantalizing but little-known group: the Denisovans.
The cave has been excavated down through some 22 layers of sediments so far, and those seem to date back to between 125,000 and 180,000 years ago. The cave contains many stone tools and art objects from Neanderthals and ancient humans. But of greatest interest are two human-like teeth (molars) and a tiny finger-bone fragment, which did not belong to any known human ancestral group. They were not from our species, and they were not Neanderthals. So who were these unknown individuals? Paleoanthropologists decided to recruit some geneticists and see what they could do.
The premier laboratory for the study of ancient DNA is the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. It is operated by a transplanted Swedish scientist, Svante Paabo -- world-famous for the work he and his students have done on a variety of extinct organisms but especially those apparently related to humans, including the Neanderthals. The Leipzig group played major roles in sequencing the complete genetic makeup (genome) of Neanderthals, though their work has been complemented by work at other laboratories.
But researchers of ancient DNA have traditionally been hampered by the fact that re-building genomes required the use of double-stranded DNA (the famous double helix), and ancient DNA is often degraded beyond that. The breakthrough for better work came as the brainstorm of a post-doctorate researcher in Paabo's lab, Matthias Meyer. Meyer conceived a method for using single-stranded DNA that worked marvelously. So we now have a virtually complete genome of the Denisovan female to whom the pinky bone belonged. Indeed, we know her genome as well as those of individual modern humans, and better (for now) than that of the Neanderthals.
It had been evident already that direct human ancestors had traded some genes with Neanderthals many millennia ago. About one to four percent of modern human DNA (of non-Africans) seems to have come from Neanderthals. But it now becomes evident that the Denisovans also traded some genes with early humans, particularly with peoples ancestral to modern Melanesians. A "trace" of Denisovan DNA is found also among the Han and Dai peoples of China. Overall, however, the Denisovans are a bit closer genetically to Neanderthals than to us.
But the Paabo team has identified specific genes that differ between us and the Denisovans. Eight such genes operate in our nervous system. One is a gene implicated in some forms of autism. Another is FoxP2, much studied these days because it is critical for speech. And 34 genes of difference have to do with disease resistance.
Her DNA indicates that the Denisovan female lived between 50,000 and 80,000 years ago, and had brown eyes, hair and skin. But what did she look like beyond that? That question passes the ball back to the fossil-hunting paleontologists!
• Duane Jeffery is an emeritus professor of biology at Brigham Young University.