Today, a paper by David Reich and colleagues presents the nuclear genome of the Denisova pinky bone [1]. This is the second “whole genome” of an apparently extinct population of Pleistocene humans. This genome is nearly as distinct from Neanderthals as the draft Neanderthal genome is from living people.

Between the draft Denisova genome, the draft Neanderthal genome, and the genomes of living people, we now have a record of three human populations that share origins relatively early in the Pleistocene.The paper presents some population modeling that attempts to estimate the divergence times and levels of gene flow among these populations. I think as a first effort these models answer some questions definitively, but leave substantial room for elaboration and improvement. There are many clear mysteries, most notably whether any known fossil samples can be attributed to the population represented by the Denisova sequence.

The most significant finding in the paper is the demonstration that some living humans trace significant fraction of their ancestry to the population represented by the Denisova genome. As in the case of Neanderthals, different human populations show significantly different levels of similarity to the Denisova sequence. For Neanderthals, the similarities indicated between one and four percent Neanderthal ancestry for living people outside of Africa. In the case of the Denisova sequence, the greatest similarities are with living people in Melanesia – in this paper, represented by genome samples from Papua New Guinea and Bougainville. The similarities are consistent with approximately 4% contribution of a Denisova-like population to the ancestry of these living Melanesians.

The paper estimates that together, the Denisova and Neanderthal-derived genes account for 8% of the ancestry of these living people.

The prior DNA studies from Neanderthals showed they were quite similar - the Denisova individual is very different. That suggests that more genetic variety existed among the very ancient relatives of humans than we had known before. These groups may well have been at least as diverse as modern humans. That is an argument I have suggested before, and I am happy to see this indication.

Third, the scientists argue that they have established a weak tie between the Denisova DNA sample and contemporary Melanesian Islanders - around 4%. This is particularly intriguing to me (I am a specialist in Melanesian genetics), but such a low shared percentage hardly proves an important ancestral tie between Denisovans and contemporary Island Melanesians - the tie they've shown between Neanderthals and Eurasians is also weak, I should add. It suggests to me that other very ancient populations yet unstudied or unknown may have played more important roles in our ancestry. So it opens up a very interesting prospect for further work, if the right samples can be found.

Last year this group reported that humans outside Africa all have 1 to 4% Neanderthal DNA. In this paper they tighten up their estimate a bit to 2.5-3%. No trace of Neanderthal DNA yet in any African population. In this paper they look at the human data that are available and show that Melanesians are about 6% Denisovans and no one else has any Denisovan DNA. (They don't have data about Australians: I expect they will be about the same as Melanesians.)

The 'out of Africa' hypothesis has dominated our thinking about human origins for the last 20 or 30 years, in large part I think because it conformed so well to the ideology of human differences being "only skin deep" and meaningless for medicine and for social sciences and for politics. Our textbooks are just saturated with long winded explanations about the irrelevance of race to anything else, and the idea pervades our universities like Marxism did in universities in the former Soviet Union. The new data show that there are likely rather profound and important differences among human groups and that we have to face up to them.