A Draft Sequence of the Neandertal Genome
Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture.
They describe the results of a shotgun sequencing of several Neanderthal genomes, which provide strong evidence for introgression of Neanderthal DNA into the human lineage from interbreeding. From the overview:
... Substantial controversy surrounds the question of whether Neandertals interbred with modern humans. To address this question, Green et al. tested whether Neandertals are more closely related to some present-day humans than to others.* Because modern humans are believed to have originated in Africa, if Neandertals diverged from modern humans before present-day populations began to differentiate, one would expect Neandertal sequences to match sequences from non-Africans and Africans to the same extent. Unexpectedly, the researchers found that Neandertals share more genetic variants with present-day non-Africans than with Africans. These results can be explained if gene flow occurred from Neandertals into the ancestors of non-Africans.
The observation that the Neandertal genome appears as closely related to the genome of a Chinese and a Papua New Guinean individual as to the genome of a French individual is particularly surprising as there is, to date, no fossil evidence that Neandertals existed in East Asia or Papua New Guinea. Green et al. thus suggest that gene flow between Neandertals and modern humans occurred prior to the divergence of European and Asian populations. Based on comparative genomic data, as well as a mathematical model of gene flow, the authors further estimate that between 1 and 4% of the genomes of people in Eurasia may be derived from Neandertals.
... Using this comparative approach, Green et al. came up with a list of 20 candidate regions that may have been affected by positive selection in ancestral modern humans. Five of these regions contain no protein-coding genes and may thus include structural or regulatory elements. Among the remaining 15 regions, the team identified genes involved in metabolism and cognitive and cranial development, which suggests that aspects of these processes may have been functionally important for the evolution of modern humans. [This is evidence for human evolution due to selection in the time since humans diverged from Neandertals about 300ky ago.]
The presence of Neanderthal DNA in some but not all modern human populations implies divergent evolution between groups. Needless to say, this is one of the biggest scientific results in human evolutionary history in some time.
... The team measured the genetic proximity of Neandertals to pairs of modern humans from different continents, first using single-nucleotide polymorphisms (SNPs), or sites in the genome where a single nucleotide differs between individuals. When they compared a Neandertal with a European and an Asian, they found that the Neandertal always shared the same amount of derived (or more recently evolved) SNPs with each of them. But when they compared a Neandertal with an African and a European, or with an African and an Asian, the Neandertal always shared more SNPs with the European or Asian than with the African. "We've shown that Neandertals are significantly more closely related to non-Africans than Africans on average," says Reich.
Even though they looked at just two Africans for this part of the study, those two have a particularly ancient, diverse heritage, so they are a good proxy for much of the genetic diversity in Africa. But sequencing additional Africans would be a good idea, says Reich.
For now, it seems Neandertals interbred with the ancestors of Europeans and Asians, but not with the ancestors of Africans. At first, "we were baffled that this affinity with Neandertals was not only in Europe and West Asia [where it was most expected], but also in Papua New Guinea" where Neandertals never set foot, says Pääbo.
See earlier post for more background.
Also see John Hawks for in-depth analysis, including the following. In earlier work (see also here), Hawks, Wang, Cochran, Harpending and Moyzis argued that the rate of human evolution has sped up in the last 10ky or so. If their estimates are correct, the amount of change in the last 10ky may be greater than what occurred over most of the 300ky since modern humans diverged from Neanderthals.
... Green and colleagues did a similar exercise, except they went looking for "selective sweeps" in the ancestors of today's' humans. These are regions of the genome that have an unusually low amount of incomplete lineage sorting with Neandertals, and therefore represent shallow genealogies for all living people. They identify 212 regions that seem to be new selected genes present in humans and not in Neandertals. This number is probably fairly close to the real number of selected changes in the ancestry of modern humans, because it includes non-coding changes that might have been selected.
Again, that's really a small number. We have roughly 200,000-300,000 years for these to have occurred on the human lineage -- after the inferred population divergence with Neandertals, but early enough that one of these selected genes could reach fixation in the expanding and dispersing human population. That makes roughly one selected substitution per 1000 years.
Which is more or less the rate that we infer by comparing humans and chimpanzees. What this means is simple: The origin of modern humans was nothing special, in adaptive terms. To the extent that we can see adaptive genetic changes, they happened at the basic long-term rate that they happened during the rest of our evolution.
Now from my perspective, this means something even more interesting. In our earlier work, we inferred a recent acceleration of human evolution from living human populations. That is a measure of the number of new selected mutations that have arisen very recently, within the last 40,000 years. And most of those happened within the past 10,000 years.
In that short time period, more than a couple thousand selected changes arose in the different human populations we surveyed. We demonstrated that this was a genuine acceleration, because it is much higher than the rate that could have occurred across human evolution, from the human-chimpanzee ancestor.
What we now know is that this is a genuine acceleration compared to the evolution of modern humans, within the last couple hundred thousand years.
Our recent evolution, after the dispersal of human populations across the world, was much faster than the evolution of Late Pleistocene populations. In adaptive terms, it is really true -- we're more different from early "modern" humans today, than they were from Neandertals. Possibly many times more different.