Tishkoff et al. observe close correspondence between genes and languages in Africa, and this is one good case in which languages and genes tell the same story. This story is different, however, from the common belief that Pygmies are relic African populations with roots Upper and Middle Pleistocene.

Another quote of note: "Thus, modern humans have existed continuously in Africa longer than
in any other geographic region and have maintained relatively large effective population sizes,
resulting in high levels of within-population genetic diversity (1, 2). Africa contains more than
2000 distinct ethnolinguistic groups representing nearly one-third of the world’s languages (3).
Except for a few isolates that show no clear relationship with other languages, these languages
have been classified into four major macrofamilies…" The fact languages and genes in Africa seem to be closely aligned with each other and that African linguistic diversity falls into a limited number of families again suggests that African genetic diversity may not be as old as it's usually assumed. In contrast, in America between-population diversity is high (see Razib's recent posts on Fst), languages fall into 140 language families, which may suggest high antiquity.

If one really was keen on using PCA, one could calculate a pairwise distance matrix and then use that instead of the correlation matrix (Principal Coordinates Analysis).

Just curious (Really. I’m not implying that TEH DARWINISMZ ARE FALSIFIED! or anything ludicrous like that).