Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544individuals from Africa, Asia, Europe, Oceania, and the New World.Phylogenetic analyses of these nine sites resulted in a tree for 10distinct Y haplotypes with a coalescence time of approximately 150,000years. The 10 haplotypes were unevenly distributed among human populations:5 were restricted to a particular continent, 2 were shared between Africaand Europe, 1 was present only in the Old World, and 2 were found in allgeographic regions surveyed. The ancestral haplotype was limited to Africanpopulations. Random permutation procedures revealed statisticallysignificant patterns of geographical structuring of this paternal geneticvariation. The results of a nested cladistic analysis indicated that thesegeographical associations arose through a combination of processes,including restricted, recurrent gene flow (isolation by distance) and rangeexpansions. We inferred that one of the oldest events in the nestedcladistic analysis was a range expansion out of Africa which resulted inthe complete replacement of Y chromosomes throughout the Old World, afinding consistent with many versions of the Out of Africa ReplacementModel. A second and more recent range expansion brought Asian Y chromosomesback to Africa without replacing the indigenous African male gene pool.Thus, the previously observed high levels of Y chromosomal geneticdiversity in Africa may be due in part to bidirectional populationmovements. Finally, a comparison of our results with those from nestedcladistic analyses of human mtDNA and beta-globin data revealed differentpatterns of inferences for males and females concerning the relative rolesof population history (range expansions) and population structure(recurrent gene flow), thereby adding a new sex-specific component tomodels of human evolution.