This paper provides yet more evidence for my observation about the ancient split of humanity between Paleoafricans (having Af1 genotype and found in western/central Africa) and Afrasians (having Af2 genotype and found throughout Africa and Eurasia). The situation is similar in mtDNA, with Afrasians belonging exclusively to the L3 clade, and in Y chromosomes where they belong exclusively to the CR-M168 clade.
In other words, the Out-of-Africa population was not part of a single panmictic African population, but of a specific east African population (Afrasians) which dispersed both into Eurasia and into the rest of the African continent. In Eurasia, the Afrasians encountered Neandertals and other older humans, replacing them almost completely with little (and contested) intermixture. In Africa, which is the cradle of mankind, the Afrasians met with older populations of archaic sapiens (Paleoafricans) leading to a dual (Afrasian+Paleoafrican) structure of most Sub-Saharan populations which is not seen outside the African continent.
The new contribution of this particular paper is that the "Afrasian" Af2 clade is also split into a major clade encompassing most genotypes, and a minor one which represents an early movement of humans into southern Africa.
Am J Phys Anthropol. 2005 Dec 5; [Epub ahead of print]
Phylogenetic analysis of major African genotype (Af2) of JC virus: Implications for origin and dispersals of modern Africans.
Takasaka T, Kitamura T, Sugimoto C, Guo J, Zheng HY, Yogo Y.
Both mtDNA and the Y chromosome have been used to investigate how modern humans dispersed within and out of Africa. This issue can also be studied using the JC virus (JCV) genotype, a novel marker with which to trace human migrations. Africa is mainly occupied by two genotypes of JCV, designated Af1 and Af2. Af1 is localized to central/western Africa, while Af2 is spread throughout Africa and in neighboring areas of Asia and Europe. It was recently suggested that Af1 represents the ancestral type of JCV, which agrees with the African origin of modern humans. To better understand the origin of modern Africans, we examined the phylogenetic relationships among Af2 isolates worldwide. A neighbor-joining phylogenetic tree was constructed based on the complete JCV DNA sequences of 51 Af2 isolates from Africa and neighboring areas. According to the resultant tree, Af2 isolates diverged into two major clusters, designated Af2-a and -b, with high bootstrap probabilities. Af2-a contained isolates mainly from South Africa, while Af2-b contained those from the other parts of Africa and neighboring regions of Asia and Europe. These findings suggest that Af2-carrying Africans diverged into two groups, one carrying Af2-a and the other carrying Af2-b; and that the former moved to southern Africa, while the latter dispersed throughout Africa and to neighboring regions of Asia and Europe. The present findings are discussed with reference to relevant findings in genetic and linguistic studies.