A new study is out on Africa, and while there unfortunately aren't any new ancient genomes or even many new samples from what I've noticed, it's pretty hulking and while some of it, after having sifted through it, seems a little lackluster; it does have some interesting things to share such as the following:
"To quantify the extent of the genetic difference between groups we used two different metrics. First, we used the classical measure FST [Hudson et al., 1992; Bhatia et al., 2013] which measures the differentiation in allele frequencies between populations. It can be thought of as measuring the proportion of the heterozygosity at SNPs explained by the group labels. The second metric uses the similarity in copying patterns between two groups to estimate the total variation difference (TVD) at the haplotypic level...
...When compared to non-African populations, FST measured at our integrated set of SNPs is relatively low between many groups from West, Central, and East Africa (yellows on the upper right triangle), whereas TVD in the same populations can reveal haplotypic differences as strong as between Europe and Asia (pink and purples in lower left triangle). For example, the Chonyi from Kenya have relatively low FST but high TVD with West African groups, like the Jola (Chonyi-Jola FST = 0.019; Chonyi-Jola TVD = 0.803) suggesting that, whilst allele frequency differences between the two populations are relatively low, when we compare the populations’ ancestry vectors, the haplotypic differences are some the strongest between sub-Saharan groups."
It's interesting that for various African populations, Fst, which measures differences in allele frequencies, is not as useful for measuring divergence as it is for Eurasian / Out-of-Africa populations who've suffered through lower population sizes in early Human pre-history (+ dips like the "Eurasian-bottleneck") which were more conducive to genetic drift. For African populations, like the "Khoisan" for example, they've had larger population sizes throughout a good chunk of Human pre-history and have maintained greater genetic diversity as a result:
For these sorts of populations, it seems that haplotypic differences and Haplogroup divergence dating (like formation dates for E-V95, E-M329 and E-M215) is much more relevant to seeing how divergent they are. I.e. both these methods would imply that the African element in Somalis and Habeshas diverged from the African element in Yorubas roughly ~40,000 years ago.
That's a time-depth comparable to when the shared Homo Sapien Sapien ancestors of Eastern Non-