Neandertal/Denisovan admixture using PCA and ADMIXTURE (and another African surprise)

I have repeated the previous experiment, but this time I created K=5 synthetic populations from the components inferred by ADMIXTURE in the Harvard HGDP set. At K=5, the five inferred components corresponded to Sub-Saharan, West-Eurasian, East-Asian, Amerindian, and Australasian populations.
It is noteworthy, that for the first time, some deep Sub-Saharan African populations show evidence of Eurasian admixture; the type of this admixture is not clear, but it seems to be mostly West rather than East Eurasian. It may, in fact, reflect an element that was already West Eurasian-like, since there is a definite excess of the West Eurasian-centered component in the Sub-Saharan populations.

Note that this element was picked up because the SNP ascertainment was done on a San individual.  The San were not generally used for the ascertainment of SNPs in commercial SNP arrays designed for association studies, and hence their SNP diversity is generally under-reported. But, the panel4 of SNPs was ascertained in a San individual with full genome sequencing (as described in the Harvard HGDP materials).

Hence, it appears that Yoruba are 82.9% of the San-centered component, BantuKenya 78.3%, BantuSouthAfrica 86.9%, BiakaPygmy 94.7%, Mandenka 80.9%, MbutiPygmy 97.9%. San-centered components have appeared before in ADMIXTURE experiments, but the crucial difference here is that the remainder of the African populations' ancestry does not fall in another Sub-Saharan-centered component, but rather in the Eurasian ones.

Remembering that ~0% in an ADMIXTURE component means minimum -in the context of the studied set of populations- not zero, influence, we can reasonably infer that the San and Pygmy groups have minimal Eurasian influence, and not that it is absent entirely. Just as the Eurasian ancestry in other Sub-Saharan Africans turned up when we ascertained SNPs in the San, so could the Eurasian ancestry in the San turn up if we ascertain SNPs in an even more divergent African population. Unfortunately, we're out of luck, because the San are the most divergent African population currently in existence, having barely survived the recent Bantu onslaught.

In order to determine how much, i.e., whether there has indeed been a major episode of admixture between a Eurasian-like and a very divergent (unknown) African hominin, we would have to have the genome of that hominin (like we do with Neandertals and Denisovans), and measure how shifted towards it different populations are. I don't hold high hopes that the African heat will provide such an ancient genome, but if such a population did in fact persist down to the Holocene boundary, there may yet be hope of discovering their DNA directly. Otherwise, it will take ingenuity with full genomes of modern populations to test the hypothesis.

Getting back on topic, below is the projection of the 5 ancestral components onto the PCA created by chimp, Denisova, and Neandertal

The exact average positions of the different groups are:

# Population Sample_Size PC1 PC2

1         Chimp  1  0.815 -0.051
2       Neander  1 -0.452 -0.680
3      Denisova  1 -0.363  0.731
4    East-Asian 50  0.034 -0.011
5 West-Eurasian 50  0.033 -0.013
6   Sub-Saharan 50  0.050 -0.001
7  Australasian 50  0.024  0.000
8    Amerindian 50  0.034 -0.012