Consider a SNP where African populations are polymorphic (they have both alleles), but Eurasians are monomorphic (they only have one of the two alleles). Such a SNP may indicate one of three things:
- Ancestral modern humans possessed both alleles, but one of them was lost in the Out-of-Africa bottleneck.
- Ancestral modern humans possessed only one of the two alleles, and the second one appeared by mutation in Africans after the Out-of-Africa event.
- Ancestral modern humans possessed only one of the two alleles, and the second one appeared by introgression, from a second African population, after the Out-of-Africa event.
The third case involves a structured population: one sub-population ("Afrasians") is monomorphic and spawns Eurasians, while another ("Palaeoafricans") possesses the second allele.
When population structure breaks down, "Afrasians" and "Palaeoafricans" mix, but the Out-of-Africa event has already happened, so Eurasians, descended exclusively from "Afrasians" do not have the opportunity to possess the second allele. Africans, on the other hand, end up with both alleles at the SNP.
So, let's see how the PCA looks like when we consider such SNPs, which constitute ~14% of panel 4.
It is clear that the signal of differential Neandertal affinity is preserved for this class of SNPs. Eurasians are about 5.1% shifted towards Neandertals along the Neandertal-Yoruba axis, which is much stronger than in any of the experiments of the previous post.
The only reasonable explanation for this pattern is African population structure.
UPDATE (Aug 16):I have repeated the experiment including Papuans and Melanesians, and requiring SNPs to be monomorphic in both Papuans and Melanesians and polymorphic in Yoruba and Mandenka. The results can be seen below: