John Hawks writes that different "Neandertal"-derived haplotypes are found in Europe and China. He attributes this to genetic drift after a population of modern humans admixed with Neandertals in West Asia.
As you all know, I've voiced significant reservations about the interpretation of the Neandertal genome data as evidence for Neandertal admixture in Eurasians. So, I decided to pull up an old experiment I had as a draft for ages because it is quite pertinent to the issue.
East Africa is a possible source of information about the issue of "Neandertal" admixture. The populations of the region are complex: they are thought to preserve features of very old Africans, perhaps the earliest Homo sapiens but they have also been affected by gene flow from Sub-Saharan Africa and West Asia.
If Neandertal admixture occurred in West Asia, then we would not expect East Africans to possess any of it, as Neandertals did not exist in East Africa. At most we would expect them to possess as much of it as could be explained by back-migration from West Asia.
So, I took the Maasai (MKK) sample from HapMap (r3 b36) and calculated allele frequencies for all SNPs in common with it and the 13 genomic regions of Neandertal admixture from Reich et al. (2010), first described by Green et al. (2010) and available here (xls).
There are 190 SNPs in that file, and 46 of them are in the HapMap data. Fortunately, this includes 9 SNPs on chromosome 5 (from rs17617368 to rs16898552) which cover all the length of a 70kbp region attributed to Neandertal admixture (from 28986511 to 29056374).
The interesting thing about this region is that 3/45 Asians possess the "Neandertal" alleles while Africans and Europeans (AFR and CEU) do not. So, it is an example of "Neandertal" genes that survived in Asians but not Europeans.
Here is a table of the minor ("Neandertal") allele frequencies on the MKK sample of 156 individuals:
Maasai seem to have some "Neandertal" genes in common with East Asians that are not shared by Europeans.
Admixture of Maasai with East Asians seems unlikely. Thus, there are three possibilities:
- A recent back-migration of West Asians who possess these alleles
- A really old back-migration of undifferentiated "Neandertal"-admixed West Asians in which these alleles had not yet been lost by drift
- Origin of these alleles in the common ancestors of East Africans and Eurasians rather than introgression from Neandertals
So, I will tentatively exclude the possibility that recent Caucasoid back-migrations brought these alleles to East Africa.
This leaves open two possibilities: that (i) these aren't Neandertal genes at all and were part of the ancestral gene pool of East Africans and Eurasians, or that (ii) they were brought back to Africa by a major early back-migration of undifferentiated Eurasians.
To conclude the post:
- It's not as simple as Africans vs. non-Africans.
- Sample more diverse African groups for "Neandertal" genes. Both Green et al. (2010) and Reich et al. (2010) claim that African groups do not differ from each other with respect to Eurasian archaic hominins, which is what you'd expect for admixture that took place in Eurasia. But, they haven't sampled broadly in Africa to make that claim convincingly.