What I find most interesting, however, is the presence of African-specific haplotypes that seem quite divergent from the most common human haplotypes.
For example (Table 1), haplotype B006 differs from the modal Eurasian haplotype B001 (which is common to Eurasians and Africans) at 13 sites, and B007 (which is African-specific) differs from B001 at 11 sites. It seems to me that B007 might represent archaic African admixture.
It is also not clear why the common haplotype in Neandertals and Eurasians cannot be due to modern human admixture in Neandertals.
An X-linked haplotype of Neandertal origin is present among all non-African populations
Vania Yotova et al.
Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of H. sapiens who left Africa between 80 Kya and 50 Kya to colonize the rest of the world. Here we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.