Studies of large sets of SNP data have proven to be a powerful tool in the analysis of the genetic structure of human populations. In this work, we analyze genotyping data for 2,841 SNPs in 12 Sub-Saharan African populations, including a previously unsampled region of south-eastern Africa (Mozambique). We show that robust results in a world-wide perspective can be obtained when analyzing only 1,000 SNPs. Our main results both confirm the results of previous studies, and show new and interesting features in Sub-Saharan African genetic complexity. There is a strong differentiation of Nilo-Saharans, much beyond what would be expected by geography. Hunter-gatherer populations (Khoisan and Pygmies) show a clear distinctiveness with very intrinsic Pygmy (and not only Khoisan) genetic features. Populations of the West Africa present an unexpected similarity among them, possibly the result of a population expansion. Finally, we find a strong differentiation of the south-eastern Bantu population from Mozambique, which suggests an assimilation of a pre-Bantu substrate by Bantu speakers in the region.

This research was supported by Dirección General de Investigación, Ministerio de Ciencia y Tecnología, Spain (grants SAF2007-63171, BFU2007-63657) and Direcció General de Recerca, Generalitat de Catalunya (2009 SGR 1101). SNP genotyping services were provided by the Spanish "Centro Nacional de Genotipado" (CEGEN; http://www.cegen.org); Bioinformatic services were kindly provided by the Genomic Diversity node, Spanish Bioinformatic Institute (www.inab.org). MS was supported by a PhD fellowship from the Programa de becas FPU del Ministerio de Educación y Ciencia, Spain (AP2005-3982).