The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 
111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the 
early evolutionary history of sub-Saharan Africans and the out-of-Africa 
expansion. The analyses revealed a complex genetic structure of the Africans 
that contributed to the emergence of modern humans. We observed partitioning of 
two thirds of old lineages among southern, west/central and east African 
populations indicating ancient population stratification predating the out of 
Africa migration. Age estimates of these lineages, older than coalescence times 
of uniparentally inherited markers, raise the question whether contemporary 
humans originated from a single population or as an amalgamation of different 
populations separated by years of independent evolution, thus suggesting a 
greater antiquity of our species than generally assumed. While the oldest 
sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from 
southern-Africa, a distinct haplotype found among Biaka is likely due to 
admixture from an even older population. An East African population that gave 
rise to non-Africans underwent a selective sweep affecting the subcentromeric 
region where MTMR8 is located. This and similar sweeps in four other regions of 
the X chromosome, documented in the literature, effectively reduced genetic 
diversity of non-African chromosomes and therefore may have exacerbated the 
effect of the demographic bottleneck usually ascribed to the out of Africa 
migration. Our data is suggestive, however, that a bottleneck, occurred in 
Africa before range expansion.