It's a busy time in our attempts to study our species' pre-modern history. Just two weeks ago, researchers reported the sequence of the oldest bones to yield human DNA. Now, the same research group is back with an entire genome, obtained from a bone found in Siberia's Denisova cave. This genome comes from a Neanderthal, but all the data reveals a lot about all the interconnections among the pre-modern human groups that were wandering around Eurasia tens of thousands of years ago. The analysis came with a tantalizing hint that one of those groups had interbred with a species separated from modern humans by over a million years—perhaps Homo erectus.
The Denisova cave is famous for having yielded the bones that helped us identify the Denisovans, a group of archaic humans that inhabited Asia at the same time as the Neanderthals. Although we haven't found enough bones to know much about what the Denisovans looked like, DNA analysis has revealed that they are most closely related to Neanderthals and that they interbred with modern humans that went on to populate East Asia, the Americas, and the Pacific.
The new results spring from a toe bone found in the same cave, this one from a layer that is estimated to be tens of thousands of years earlier. DNA sequencing revealed the bone to be from a Neanderthal, a different group of pre-modern humans that is most closely related to the Denisovans. The DNA was in excellent condition and had a minimal (about one percent) contamination with sequences from modern humans. The team generated a high-quality genome using samples from this bone.
The sequence that resulted tells us a lot about Neanderthals. For one, it shows that other populations we've obtained DNA from (samples found in the Caucasus and Croatia) were closely related but distinct, indicating that the Neanderthals were already well established by the time this individual died. Those populations were apparently quite small, however, since there's not a lot of genetic diversity among them. In the case of the specific individual in the Denisovan cave, the lack of diversity was quite severe. Rather than carrying two distinct sets of chromosomes, large stretches of the two chromosomes were identical, indicating that they were inherited from a single individual in the recent past.
The extent of this identity suggests that the parents of this individual were half-siblings, although other combinations (uncle-niece, aunt-nephew) would also produce a similar pattern.
But the more significant results come from what this new sequence tells us about the other groups of humans present at the time, including modern humans. To begin with, it confirms the rough timing of the split between the ancestors of modern humans and the ancestors of Neanderthals and Denisovans, which took place about 550,000-600,000 years ago. The Neanderthals and Denisovans became a distinct population about 400,000 years ago.
The sequence also provides a clearer estimate of the amount of Neanderthal DNA that shows up in modern human populations: 1.5 to 2.1 percent. And it confirms that it got there via interbreeding, since the Neanderthal sequence looks most similar to the sample obtained from the Caucasus remains. Had it been inherited through a structured ancestral population in Africa, it should look like it was equally distant from all three of the Neanderthal genomes. The other thing that's apparent is that modern Asian and American populations have a bit more Neanderthal DNA than others, suggesting that a low amount of interbreeding continued as our ancestors moved east.
Our ancestors weren't the only ones who couldn't resist getting a piece of the Neanderthals. At least a half percent of the Denisovan genome also came from them as well.
But perhaps the most unexpected finding comes from a comparison with the Denisovan genome. Modern humans in Africa never overlapped geographically with Neanderthals or Denisovans and thus contain none of their DNA. Therefore, any shared DNA they have should be inherited from a common ancestor, and the African's should be equally distant from the Neanderthals and Denisovans. Yet they're not. The Denisovans have some sequences that are much more distant than you'd expect.
After considering and rejecting a couple of alternative explanations for this, the paper settles on a rather radical explanation: Denisovans themselves interbred with a population that had been separated from their common ancestor with modern humans for about a million years. This, as the authors note, suggests that the DNA's source was Homo erectus. In fact, they suggest that the Denisovan's entire mitochondrial genome might have come from this interbreeding event, since it's much more distant from the Neanderthals' than the rest of the genome is.
Of course, that explanation is even harder to square with the findings from the ancient bones in Spain, which had a similar sequence but came from skeletons that looked somewhat like Neanderthals. Unless, of course, the Spanish population also interbred with Homo erectus (or whatever this is) at some point.
In any case, the results add yet another layer onto the increasingly complicated Out-of-Africa model of the origin of modern humans. We still arose in Africa and migrated out into Eurasia. But once we got there, we interbred with a previous wave of African expatriates and incorporated a small bit of their genetic legacy into our own. And one part of that previous wave may have even incorporated a tiny piece of a species that hadn't seen Africa for a very long time.