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We describe the first haploid minisatellite, the human Y chromosome-specific locus, MSY1. It consists of an array of 48-114 AT-rich 25 bp repeats of at least five different variant types. A minisatellite variant repeat PCR (MVR-PCR) system gives Y-specific DNA codes, with a virtual heterozygosity of 99.9%, making MSY1 by far the single most variable locus on the Y. African populations contain the most diverged MSY1 structures. MSY1 is the only Y-chromosomal system where the characteristics of large numbers of mutations can be studied in detail: it provides a uniquely powerful tool both for the investigation of mutation in a haploid system, and for the dating of paternal lineages.

We have identified a new T-->C transition on the human Y chromosome. C-allele chromosomes have been found only in a subset of the populations from Asia and northern Europe and reach their highest frequencies in Yakut, Buryats, and Finns. Examination of the microsatellite haplotypes of the C-allele chromosomes suggests that the mutation occurred recently in Asia. The Y chromosome thus provides both information about population relationships in Asia and evidence for a substantial paternal genetic contribution of Asians to northern European populations such as the Finns.

Deletion of the 50f2/C (DYS7C) locus in interval 6 of Yq has previously been reported as a polymorphism in three males. We describe a survey of worldwide populations for further instances of this deletion. Of 859 males tested, 55 (approximately 6%) show absence of the 50f2/C locus; duplication of the locus was also detected in eight out of 595 males (approximately 1.4%). Populations having the deletion are confined to Asia, Australasia, and southern and northern Europe; of those of reasonable sample size, Finns had the highest deletion frequency (55%; n = 21). The deletions vary in size and the larger ones remove some of the RBM (RNA Binding Motif) genes, but none of the deletion males lack DAZ (Deleted in AZoospermia), a candidate gene for the azoospermia factor. On a tree of Y haplotypes, 28 deletion and eight duplication chromosomes fall into six and four haplotypic groups respectively, each of which is likely to represent an independent deletion or duplication event. Microsatellite and other haplotyping data suggest the existence of at least two further classes of deletion. Thus duplications and deletions in this region of Yq have occurred many times in human evolution, but remain useful markers for paternal lineages.