Hierarchical patterns of global human Y-chromosome diversity

We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 m ales to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest leve ls of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of th e total variance of NRY haplotypes was attributable to differences among po pulations (i.e., Phi (ST) = 0.36). When a series of AMOVA analyses was perf ormed on different groupings of the 50 populations, high levels of among-gr oups variance (Phi (CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three pop ulation groupings formed distinct clusters in multidimensional scaling plot s. A nested cladistic analysis (NCA) demonstrated that both population stru cture processes (recurrent gene flow restricted by isolation by distance an d long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explainin g this tripartite division of global NRY diversity. As in our previous anal yses of smaller NRY data sets, the NCA detected a global contiguous range e xpansion out of Africa at the level of the total cladogram. Our new results support a,general scenario in which, after an early out-of-Africa range ex pansion, global-scale patterns of NRY variation were mainly influenced by m igrations out of Asia. Two other notable findings of the NCA were (1) Europ e as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analy ses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global leve ls. Finally, our results underscore the importance of subdivision of the hu man paternal gene pool and imply that caution should be exercised when usin g models and experimental strategies based on the assumption of panmixia.