One thing to keep in mind: a relatively small number of markers (by recent standards) were typed for this paper.
The combined dataset contains a total of 1,327 genotyped markers (consisting of 848 microsatellites, 476 indels and 3 SNPs) and 3,945 DNA samples. The overall overlap of markers genotyped in the combined dataset is 80% (not all markers were genotyped in all populations) [supplementary material]Though this should be enough to get the broad picture right, more markers would be nice. As Tishkoff acknowledges in this podcast interview (mp3), the use of "SNP panels [with] a million markers" in future studies should offer knowledge of more subtle variation.
 Sarah A. Tishkoff et al. The Genetic Structure and History of Africans and African Americans. Science doi:10.1126/science.1172257