Hierarchical Patterns of Global Human Y-Chromosome Diversity

Abstract

We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males 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 levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion 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 expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

“…Typing methods for six of these markers (P25, P297, M335, M18, M73, and M269) were described earlier. 18,28,[30][31][32][33] The marker P25, which has been shown to be liable to back mutation by gene conversion, 34 was analyzed in the Asian samples from CEPH and in the R1b (R-M343) chromosomes lacking any other internal mutation.…”

Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males

“…This problem is exacerbated for Y chromosomes because they lack sequence diversity 5 . To accommodate this difficulty, Y-chromosome researchers have adopted a strategy [6][7][8][9] to estimate levels of between-group variation using single-nucleotide polymorphisms (SNPs) discovered in small panels of globally diverse males and then genotyped in much larger population samples (e.g., the global data set 10 analyzed in ref. 1).…”

A Genetic Focus on the Peopling History of East Asia: Critical Views

“…Altogether, these results indicate that the genetic pool of NEAS is related to that of CAS and exhibits signatures of gene flow from multiple sources, while that of SEAS indicates greater isolation and population subdivision, although with a low level of differentiation among populations. Another crucial result related to these observations is the very high level of genetic diversity found in Central Asian populations (Comas et al 1998(Comas et al , 2004Hammer et al 2001;Quintana-Murci et al 2004;Wells et al 2001;Zerjal et al 2002), compatible with their connection to NEAS through gene flow, Central Asia being considered either as a source or as a receiver (Comas et al 1998(Comas et al , 2004Quintana-Murci et al 2004;Zerjal et al 2002) of human migrations.…”