One can be forgiven for thinking that the first modern humans who ventured out of Africa stumbled into a vibrant bar scene. DNA from just a single cave in Siberia revealed that it had been occupied by two archaic human groups that had interbred with the newly arrived modern humans. This included both the Neanderthals, whom we knew about previously, and the Denisovans, who we didn't even know existed and still know little about other than their DNA sequences. The DNA also revealed that one of the Denisovans had a Neanderthal ancestor a few hundred generations back in his past.
But in almost all of these cases, the ancestry seems to have come from a single exchange of chromosomes many generations prior. There was little indication that the interbreeding was frequent.
Now, the same cave has yielded a bone fragment that indicates the interbreeding may have been common. DNA sequencing revealed that the bone fragment's original owner had a mom that was Neanderthal and a father who was Denisovan. The fact that we have so few DNA samples from this time and that one is the immediate product of intermating gives us a strong hint that we should expect more examples in the future.
What is this?
The Denisova Cave sits within Russia near its borders with China, Kazakhstan, and Mongolia. It appears to have conditions that favor the preservation of ancient DNA, as bones from the site have yielded high-quality genomes from both Neanderthals and Denisovans. It does not seem to have favored the preservation of skeletons themselves, as most material has been fragmentary; all we know about the appearance of Denisovans comes from a molar and a small finger bone, though dating indicates they occupied the cave more than 30,000 years after the Neanderthal.
Because of the fragmentary nature of many of the bones, the team exploring the cave has been slowly going through them, determining which ones are human by looking at the collagen that comprises much of the bone. An ID of human caused them to focus more on a fragment called Denisova 11, which originated in a long bone (like an arm or leg bone) of an individual who was at least in their teens. Beyond that, there was nothing even distinctive enough to determine what part of the body the fragment originated in, much less which group of humans its owner belonged to, although carbon dating placed it at a time when Denisovans were known to occupy the cave.
To find out more, the researchers sequenced its mitochondrial DNA. Since this is only passed on via the egg, it tells you about an organism's mother. In this case, the mitochondrial DNA was clearly Neanderthal, which was somewhat surprising, given the date on the bone. In any case, this was enough for the researchers to decide to sequence the genome of Denisova 11. It was completed so that the average base was sequenced 2.6 times, meaning that there are still a lot of gaps and uncertainties in the genome. Still, it was enough to perform some detailed analyses.
The first thing that was clear was that Denisova 11 was a she; X-chromosome sequences showed up as often as ones from any other chromosome, suggesting she had a pair of them. The other was that the researchers' excavation techniques were very good, as contamination with the DNA from those who did the excavating couldn't account for more than 1.7 percent of the total sequences. Beyond that, most of the results were unexpected.
Because we now have several Neanderthal and Denisovan genomes, we have some sense of how they consistently differ from each other and from the genomes of modern humans. Running Denisova 11 through an analysis of these differences showed she was a nearly even mix. Instead of being mostly Neanderthal, as you would expect from the mitochondrial DNA, only 39 percent of the DNA fragments were clearly Neanderthal. Another 42 percent, by contrast, were Denisovan, meaning she was nearly an even mix of the two groups of archaic humans.
The authors checked other samples they sequenced at the same time for signs of contamination and also looked at whether there might be a software glitch, but the results held up. There are two ways to explain that. One is that she's an immediate product of a mating between these two different people. The second is that she's part of a population of hybrids, where her parents both carried mixes of Neanderthal and Denisovan DNA.
To figure out which was happening, the researchers looked at each individual site where Neanderthals and Denisovans differ. If Denisova 11 were the product of a mixed population, you'd expect a fair number of these sites to be either all Neanderthal or all Denisovan, since the genomes should be pretty randomly mixed. If she were the immediate product of a mating between individuals from distinct groups, you would expect many of these sites to have one Neanderthal and one Denisovan version. (You wouldn't expect them all to be like that, because we don't know the full diversity of either Neanderthals or Denisovans at this point.)
The results clearly favored her being a 50-50 mix. "We conclude that Denisova 11 did not originate from a population carrying equal proportions of Neanderthal and Denisovan ancestry," the researchers conclude. "Rather, she was the offspring of a Neanderthal mother, who contributed her [mitochondrial] DNA, and a Denisovan father." The differences were also spread evenly throughout her genome, as you'd expect if each half of every chromosome pair came from a different group of ancestors.
A more detailed look at her ancestry showed there were at least five small regions where both chromosomes seem to have had a Neanderthal ancestry, suggesting that Denisova 11's father came from a population that had already interbred with Neanderthals in the distant past. And her mother seems to be most closely related to a Neanderthal skeleton found in Croatia, rather than a descendent of the Neanderthals that occupied the same cave tens of thousands of years earlier.
Mixing and yet distinct
The authors argue that, despite the indications left in modern genomes, Denisova 11 strongly suggests that interbreeding was common whenever two different groups overlapped. After all, we don't have a lot of genomes from archaic humans, and we've already found one that's the direct product of interbreeding between two groups.
So why is there the difference between this expectation and what we've seen in other genomes, which suggests the two groups seem to be largely distinct lineages? For one, we don't really know how often different populations overlapped. Based on where modern populations have higher levels of Denisovan DNA, we can infer that Denisovans inhabited East Asia, but the details on where and when simply aren't known. The full extent of Neanderthals' range is also poorly constrained.
All of which means that interbreeding could have been limited by the fact that the populations simply didn't meet up that often. "This, as well as possibly reduced fitness of individuals of mixed ancestry, may explain why Neanderthals and Denisovans remained genetically distinct," the authors conclude.
By contrast, modern humans seem to have displaced archaic ones fairly rapidly, suggesting there was a limited time window in which interbreeding could have taken place. Still, the clear signs of interbreeding and apparent past willingness to live together may indicate that the modern humans absorbed earlier populations rather than completely displacing them.
But there's also a little nugget in the paper that suggests this won't be the last time the Denisovan Cave revolutionizes our understanding of our ancestry. The only skeletons mentioned in the paper are Denisova 3 and Denisova 11, but the paper notes that there have been "over 2,000 undiagnosed bone fragments excavated in Denisova Cave." That means there are probably a lot more potential sources of DNA we still haven't looked at yet.