I had previously posted about how Hammer et al. discovered a 2-million year old East Asian polymorphism, thus rejecting the pure Out of Africa model. Now, in a paper published in the journal Genetics they report a haplotype over a 17.5 kilobase sequence of the X chromosome where 2 out of 3 Mbuti (pygmoid) Africans have a haplotype that is over a million years old. Moreover, in the context of their statistical framework, the authors are able to reject the null hypothesis of "a single, historically panmictic population" originating in Africa.
These findings do not negate the fact that most human variation has a "shallow" time depth, but it is strong evidence that some humans have ancestry that is much more ancient than that of the bulk of mankind. In this case, the Mbuti pygmoids have apparently assimilated elements from archaic Africans.
This result may lend some support to my pet theory that the main differentiation in human genetic variation is between Paleoafricans who were reproductively isolated for a long time from the Afrasians, with subsequent hybridizaton between Afrasians and Paleoafricans in Africa. In this scheme, the Paleoafricans, perhaps descended from the earliest Homo sapiens population of East Africa picked up some pre-sapiens ancestry as they spread to the interior of Africa.
Genetics (online early)
Deep haplotype divergence and long-range linkage disequilibrium at Xp21.1 provide evidence that humans descend from a structured ancestral population.
Garrigan D, Mobasher Z, Kingan SB, Wilder JA, Hammer MF.
Fossil evidence links human ancestry with populations that evolved modern gracile morphology in Africa 130,000 - 160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of non-coding 17.5 kilobase sequence that has survived for over one million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.