D-statistics reveal contrast between Yoruba and San in "Neandertal ancestry"

I have been exploring the HGDP version released by Patterson et al. (2012) in order to see whether patterns  of "archaic Eurasian" admixture could be detected in living Africans. In a previous experiment, I looked into a surprising link between Denisovans and Africans. Now, I want to investigate possible differences in Neandertal ancestry within Africa itself. An ASHG 2012 abstract suggests that both Neandertal and Denisovan ancestry may be relevant to the African story.

Previous research has concluded that living African groups do not appear to have substantial differences in their apportionment of archaic Eurasian ancestry. This has led to the reasonable idea that the signal of Neandertal admixture in non-Africans was driven by the encounter of Out-of-Africans with a Neandertal population in Asia, perhaps in the Near East, during their early steps outside Africa, involving a single or limited episodes of admixture, although more complex models may be needed as of late.

I have long suspected that part of this signal is due to population structure in Africa itself, and the possibility of archaic admixture in that continent, a hypothesis that is feasible a priori due to the geographical and ecological diversity of Africa and its large surface area, and which has also found support on the basis of recent palaeoanthropological and genetic research. In my opinion, the well-known abundance of polymorphism in Africans vis a vis non-Africans is not only due to the Out-of-Africa bottleneck, but may also be due to an addition of polymorphism via admixture with divergent native African hominin groups.

Advancing a good case for this admixture is rendered difficult by two factors:

1. The inability of methods relying on linkage disequilibrium to operate on old admixture events, due to the exponential decay of LD over time, which renders archaic-introgressed segments pitifully small at long time scales.
2. The high temperatures prevalent in sub-Saharan Africa which render DNA preservation problematic, although, to be honest, I have not even seen many attempts to test this hypothesis on whatever prehistoric skeletal remains there do exist from the region.

Why do African groups appear so little different in terms of possible "Neandertal admixture"? I conjecture that the answer lies in the idea that archaic African admixture will tend to even out the signal of Neandertal admixture. To use a geographical analogy, there is little distance difference (in relative terms) between Tokyo and Beijing from the vantage point of New York, but quite a lot from the vantage point or Hong Kong. Tests of archaic admixture rely on relative allele sharing between individuals or populations; consequently, the signal may be muddied by the occurrence of archaic admixture in Africans which -to use our geographical analogy- transposes them from Hong Kong to New York.

Now, consider the Z scores of the D-statistic of the form D(African1, African2, Neander, Outgroup) calculated using different panels and Outgroup being Chimp, Gorilla, or Orang. The raw numbers can be found in this spreadsheet.

Look at the Pearson correlations between the different panels:

While the Z-scores in most of the panels are strongly correlated with each other, the San panel #4 is strongly anti-correlated. An inspection of the raw numbers show why this is the case. For example:

Surprisingly, the San appear more Neandertal-admixed than the Yoruba using all Eurasian and the Yoruba ascertainment, and less so, using the San ascertainment!

A possible explanation for this pattern involves Eurasian back-migration into Africa combined with differential archaic African admixture.

The San may possess Eurasian ancestry consistent with the positive D(San, Yoruba, Neander, Chimp) statistics for all panels except their own; the negative statistics for their own panel is due to their archaic African ancestry which makes them less like Neandertals.

I conjecture that different archaic populations have contributed polymorphism to different African populations.

This question can be addressed empirically on the basis of whole genome sequence data. The Out-of-Africa bottleneck hypothesis suggests that reduced polymorphism in non-Africans is due to loss of variation as a limited number of founders exited Africa, carrying a subset of African variation. If Africans are descended primarily from the modern human groups left behind, then they will all carry the same "missing variation" set not found in Eurasians.

On the other hand, if, as I suggest, modern human groups encountered and admixed with different divergent African hominins, then different African populations will carry substantially disjoint sets of variants, reflecting deep population structure within Africa itself. Time will tell whether this prediction will prove to be true.