A selective difference between human Y-chromosomal DNA haplotypes

DNA analysis is making a valuable contribution to the understanding of huma n evolution [1]. Much attention has focused on mitochondrial DNA (mtDNA) [2 ] and the Y chromosome [3,4], both of which escape recombination and so pro vide information on maternal and paternal lineages, respectively. It is oft en assumed that the polymorphisms observed at loci on mtDNA and the Y chrom osome are selectively neutral and, therefore, that existing patterns of mol ecular variation can be used to deduce the histories of populations in term s of drift, population movements, and cultural practices. The coalescence o f the molecular phylogenies of mtDNA and the Y chromosome to recent common ancestors in Africa [5,6], for example, has been taken to reflect a recent origin of modern human populations in Africa. An alternative explanation, t hough, could be the recent selective spread of mtDNA and Y chromosome haplo types from Africa in a population with a more complex history [7]. It is th erefore important to establish whether there are selective differences betw een classes (haplotypes) of mtDNA and Y chromosomes and, if so, whether the se differences could have been sufficient to influence the distributions of haplotypes in existing populations. A precedent for this hypothesis has be en established for mtDNA in that one mtDNA background increases susceptibil ity to Leber hereditary optic neuropathy [8]. Although studies of nucleotid e diversity in global samples of Y chromosomes have suggested an absence of recent selective sweeps or bottlenecks [9], selection may, in principle, b e very important for the Y chromosome because it carries several loci affec ting male fertility [10,11] and as many as 5% of males are infertile [11,12 ]. Here, we show that one class of infertile males, PRKX/PRKY translocation XX males, arises predominantly on a particular Y haplotypic background. Se lection is, therefore, acting on Y haplotype distributions in the populatio n.