There is, however, what I think is a more important weakness of the paper. To substantiate the case for admixture, the authors compare West African Yorubans separately with Europeans and with East Asians.
Let's assume that they do in fact detect what is genuine archaic admixture, i.e., the introgression of chunks of DNA into regional humans from a species other than modern Homo sapiens. They can achieve this by detecting regions where Yoruban DNA sequence differs from European DNA sequence in a manner suggestive of a very ancient time depth.
But, is there a reason to ascribe these differences to Neandertal introgression?
Actually, there is not, as Europeans are derived from a specific East African population: they are not derived from Sub-Saharan Africans in general, or West Africans in particular. Indeed, this very paper finds evidence of archaic admixture in Africa itself!
Thus, what appears as a piece of Neandertal DNA in Europeans, could in fact be a piece of ancestral East African DNA which differs from Yoruba DNA because of population structure in Africa itself, for which there is more than enough evidence.
So, what this paper does, is tell us that a chunk of DNA in Europeans, and the corresponding chunk in Yorubans don't share ancestry within a conventional Out-of-Africa time frame. It does not, however, tell us that this is because of archaic introgression in Europeans. The culprit could equally well be long-term population structure in Africa, i.e., the presence of "modern" and "archaic" populations in Africa itself.
The way forward is to compare Europeans with Middle Eastern Caucasoids and East Africans. If the "archaic" European DNA is found across many of these populations, then the case for Neandertal introgression will weaken, and the hypothesis presented in this post (ancient African population structure) will be supported.
UPDATE (May 9): John Hawks has updated his blog entry in response to this post. He makes two points:
The East Asian and European comparisons come up with different genes showing evidence of putative introgression.What we don't know at this point is whether either (or both) of the European/East Asian introgression candidate genes are found in East Africa. If so, then the presence of different sets of genes in Europe and East Asia could be the result of random survivals of the diversity of the initial African population. Or, introgression happened in either Europe or East Asia, and one region preserves archaic DNA inherited from Africa and the other archaic DNA that introgressed in East Asia or Europe, which is why the two are different.
Furthermore, while Out-of-Africa is conventionally seen as one migration c. 40Kya which eventually spawned both Europeans and East Asians, there is Y-chromosomal evidence for a separate process linking Western Eurasia and East Africa (Y-chromosome haplogroup E). Thus, a later movement may have spread "archaic" East African genes into Western Eurasia but not in East Asia.
John's second point:
The entire point of the out-of-Africa replacement idea is to draw humans from an unstructured ancient population. Humans have to be inbred to explain the low genetic variation today. A long bottleneck in Africa is one explanation for this inbreedingWe do know that there was substantial variation in Africa at the time when modern Homo sapiens emerged. A long period of inbreeding in Africa would indeed create the fairly homogeneous species we discover when we look at most genes. This species would, however, during its population expansion -within Africa- come into contact with other previously isolated African populations, some of which would go extinct, while others might be absorbed, their genes persisting at low frequency in the expanding species.
This requires no great leap of faith. It parallels directly what happened in Africa in the last few thousand years, where previously isolated Pygmy and Khoi-San populations came into contact with expanding farmer-pastoralists, and contributing a little bit to the farmers' genomes.
Thus, the expanding African population that eventually spilled over into Eurasia, would indeed be quite inbred and homogeneous, but its gene pool would also contain traces of the smaller, less successful African populations it had absorbed. Because of their low frequency, these traces would be more susceptible to extinction in the series of bottlenecks that led to Europeans on one side and East Asians on the other, with different sets of archaic genes preserved in either region.
Molecular Biology and Evolution, doi:10.1093/molbev/msp096
Detecting ancient admixture and estimating demographic parameters in multiple human populations
Jeffrey D. Wall et al.
We analyze patterns of genetic variation in extant human polymorphism data from the NIEHS SNPs project to estimate human demographic parameters. We update our previous work by considering a larger data set (more genes and more populations), and by explicitly estimating the amount of putative admixture between modern humans and archaic human groups (e.g., Neandertals, Homo erectus, H. floresiensis). We find evidence for this ancient admixture in European, East Asian and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.