A survey of long-range DNA polymorphisms on the human Y chromosome

The human Y chromosome is poor in conventional DNA polymorphisms, and this has hindered studies of the paternal lineage. However, three large hypervariable arrays exist, and haplotyping at these loci defines two groups in Caucasian and Asian populations, reflecting the existence of two ancestral Y chromosomes. In this study, the Y was systematically surveyed for further long-range polymorphisms, by the hybridization of 33 probes to SfiI digests of DNA from males of different ethnic origins and from the two groups. Five novel polymorphisms were identified, all showing variability consistent with a changing number of tandem repeats within an array. A search for conventional polymorphisms was also done, using 41 probes and the enzyme TaqI; three novel variants and one polymorphism with a frequency of 18% (n = 66) were found. The novel polymorphisms were typed in 66 Y chromosomes, including the set of 42 in which the two groups were originally defined. Known long-range and conventional polymorphisms were also extended to cover the whole set, yielding compound haplotypes comprising the states of twelve polymorphisms. This haplotyping distinguishes between all 66 chromosomes, and should distinguish between most in the population. The existence of the two groups is supported, and a third group can be defined; six of the eight members of this group are known to be from India. Twelve chromosomes do not fall into any of these groups, and are likely to be representatives of further groups.