Researchers already knew that living people from a vast area spanning the Philippines and New Guinea to China and Tibet have inherited 3% to 5% of their DNA from Denisovans. The leading scenario had suggested that as modern humans swept out of Africa, they first encountered Neanderthals and mated with them; hence, all people in Europe and Asia now have 1% to 3% of their DNA from Neanderthals. The ancestors of Asians then encountered Denisovans 50,000 years ago or so and acquired 3% to 5% of their DNA from them.
“Papuans carry DNA from at least two [other] Denisovan populations, called D1 and D2,” Cox said in his talk, which was filmed in advance and played at the meeting. When the team members analyzed the DNA with three statistical methods, they found that the two additional sources of Denisovan DNA came from populations so distantly related that they had diverged more than 283,000 years ago. And the D2 population is most distant from the Siberian Denisovans, splitting off roughly 363,000 years ago. That makes those two populations almost as distantly related to each other as they are to Neanderthals, Cox says. “We used to think of Denisovans as a single group,” notes Cox, who suggests as an aside that the D2 group might even need a new name.
The D1 DNA isn’t found in people outside New Guinea, and it’s found on large chunks of chromosome that haven’t been mixed over time, suggesting it entered the modern human genome from 15,000 to 30,000 years ago.
I consider the increasing details emerging to be strong evidence for the bigger picture.
An interesting question which occurs to me is why is the DNA contribution so small?
Possibilities:
The Homo sapiens slaughtered the vast majority of these subspecies when encountered.
Only very small populations remnants survived when they were encountered.
The appearance and features of those with this DNA were considered less attractive.
Those with higher portions of this DNA were less capable in some way.
Populations of these did coexist with humans for millennia with limited interbreeding but eventually declined or were wiped out, probably long before the beginning of human civilization.
…any other ideas? Any evidence to rule out some of these possibilities?
I think the answer is simple population genetics. The 3-5% number does not represent the only DNA shared with Denisovans, who as far as we know are just an interesting ancient human population. It represents the regions of the genome that remain identifiably intact over hundreds of thousands of years. Then there’s the D1 region, which is intact precisely because it was introduced much more recently. This region is identifiably Denisovan. The vast, vast majority of DNA in our genomes is not identifiably Denisovan, or Neanderthal, or modern human, because it’s just… human. In other words, it is probably an error to assume that the 95-97% of DNA not flagged as “Denisovan” is therefore “non-Denisovan.” It’s just human.
If you want to hear an actual expert on the topic, tag @glipsnort.
I’m not exactly an expert on this, but I did follow the Neanderthal work pretty closely for a while, and the Denisovan situation is similar. 3-5% is the best estimate of the fraction of each person’s DNA that comes from a Denisovan ancestor. It’s so small because the introgressed DNA was always only a small fraction of the DNA in the whole population. The child of one Denisovan and one anatomically modern H. sapiens would have had 50% Denisovan DNA. If the child and his/her offspring mated exclusively with moderns, that DNA would be diluted with each successive generation; how diluted depends on the size of the population. The fact that the Denisovan contribution is as high as 5% by itself suggests either that the introgression occurred multiple times or that it happened in a tiny population (on the order of ten people).
A separate question is how much of the Denisovan genome exists in some modern human. I don’t know what the number is for Denisovans, but for Neanderthals it’s much larger than a percent or two. Different researchers claim to have identified between a fifth and a third of the Neanderthal genome in modern humans. The total amount in modern humans has been estimated to be between 35% and 70%; the number is hard to pin down because lots of chunks can’t be distinguished between modern humans and Neanderthals. The fraction surviving would be even higher if it were not for purifying selection eliminating some of the Neanderthal DNA after introgression occurred.