Genetic variation within Africa (and the world)

Last year a paper came out in Science which made a rather large splash, The Genetic Structure and History of Africans and African Americans by Tishkoff et al. Since it’s more than a year old I recommend that those of you curious about the details of the paper and don’t have academic access go through the free registration, as you can then read it in full. Unlike Reich et al. the Science paper didn’t unveil a new method of analysis. It was the standard bread & butter, with PCA’s & STRUCTURE plots & phylogenetic trees. But the coverage of populations within Africa was massive. They had a lot of results and relationships to cover, and ended up with a 100 page supplement.

I commend the whole paper to you. But there are two elements I want to highlight. First, a three dimensional PCA plot. It has the first, second and third principal components of variation. In other words, the three largest independent dimensions in terms of explanatory power of genetic variation. Panel A includes all world populations, and panel B just Africans.

For panel A, PC1 = 20% of the variance, PC2 = 5%, and PC3 = 3.5%. For panel B the PCs didn’t drop off quite so much, PC1 = 11%, PC2 = 6%, PC3 = 5% and PC4 = 4%. In case you don’t know, the Hazda are Africa’s last obligate hunter-gatherers, and speak a language with clicks in it, just as the Bushmen do. The big division highlighted in this paper is that between the “indigenous” relict populations, the Hazda, Sandawe, Bushmen and Pygmies, and those who belong to the more widespread agriculturalist and pastoralist societies of Africa. Implicit within the paper is the model of a Bantu Expansion of farmers, as well as a possible later Nilotic expansion (which brought the Tutsi and Masaai) of herders, in a north-south direction. In the process they assimilated/and or/displaced the indigenous populations, of whom the aforementioned peoples are relict islands persisting in ecologically isolated or unfavorable domains.

The map to the left shows the population coverage within this paper of African groups. The pie graphs simply show ancestral quanta as inferred by STRUCTURE. You can read the paper for the blow-by-blow. But ultimately it seems there will be need for a finer-grained coverage to the south of the equator. If the Bantu expansion is as recent as archaeologists and linguists assume, on the order of ~2,000 years ago, then the gradients of genetic signals should persist. From what I can tell it is assumed on both genetic and phenotypic grounds that the Xhosa have a higher load of Khoisan ancestry than the Zulu or Tswana. The Bantu Expansion is recent enough that the semi-legendary Phoenician circumnavigation of Africa would have encountered many Khoisan peoples along the eastern coast.

Below are a selection of figures from the above paper. After selecting an image it is probably best to hit F11 for “Full Screen” if you aren’t a on a very big monitor (you can copy image location and view it in a separate window as well).