Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
To cut a long story short…
The authors suggest that non-Africans having about 1-4% Neanderthal ancestry is the most likely explanation for the variation in the DNA they have found. It’s not an absolute. A much less likely but not impossible scenarios is that the variation is due to population structure in Africa prior to the OOA, which may relate with the earlier separation of the ancestors of modern Africans and non-Africans inside Africa, although John Hawkes thinks this is so unlikely he was surprised they gave it space on the paper.
But, considering the number of genes in non Africans that have a time depth that is considerably older than the OOA movement (over 1 million years on one in one study by Hammer et al), and I think there is now decent evidence for Neanderthal ancestry in non-Africans.
I have some issues with the paper. Modern humans were in the near East about 120k ago, keeping company with Neanderthals for many millennia, but the interbreeding date comes out at 80,000 to 50,000 years. What were they doing with the rest of the time?
Such a scenario is compatible with the archaeological record, which shows that modern humans appeared in the Middle East before 100,000 years ago whereas the Neandertals existed in the same region after this time, probably until 50,000 years ago.
And they observe that modern Europeans don’t seem to have a higher amount of Neanderthal ancestry than anyone else. But then they add:
This possibility can be addressed by the determination of genome sequences from pre agricultural early modern humans in Europe (85). It is also possible that if the expansion of modern humans occurred differently in Europe than in the Middle East, for example by already large populations interacting with Neandertals, then there may be little or no trace of any gene flow in present-day Europeans even if interbreeding occurred.
Which is what I suspect is more likely. I’d also like to address the apparent lack of modern human ancestry in the Neanderthals: well a quick look at the dates of the remains sampled; not younger than 38,000 BP. Which is prior to the date modern humans started to move into that part of Europe. Possibly a future investigation of later dated remains would show some AMH ancestry in them, as their appearance suugests they may be hybrids. I think the Lagar Velho specimen would be a possible source, although it would be a pity to damage the specimen, possibly the Gorham’s Cave bones could yield relevant information.