Stanford University| Biochemistry| Stanford Genome Technology Center  

Am. J. Hum. Genet., 59 [Suppl.], 147

Amassing a wealth of Y chromosome polymorphisms for evolutionary studies.

P. A. Underhill†, L. Jin†, L. L. Cavalli-Sforza†, R. Davis‡ and P. J. Oefner‡.

Departments of ‡Genetics and †Biochemistry, Stanford University, Stanford, California




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The non-recombining portion of the Y chromosome preserves haplotype information over time scales spanning modem human history. In addition, most nucleotide substitutions, as well as small insertion/deletion polymorphisms on the Y display geographical localization making them particularly valuable indices of gene flow. Nearly 100 kb of primary Y chromosome sequence has been generated from cosmids, creating an abundant reservoir of new Y-specific STS's. Our ongoing screening effort for polymorphisms, which is based upon a sensitive and rapid heteroduplex detection method, is accomplished using denaturing high performance liquid chromatography (DHPLC) to comparatively sequence males (n >= 50) from globally diverse populations. Each automated analysis compares two genomes as a mixture of denatured and reannealed amplicons, in only minutes for ~ 20 ¢ per assay. We describe a collection of markers which are defined both in terms of geographic affiliation and frequency within indigenous populations. Approximately 50% of the markers display a frequency >= 15 %. The majority of polymorphisms discovered to date have accumulated in African and some Oceanian populations, reflecting the antiquity of those populations. Our updated estimate of nucleotide diversity for the Y is not much smaller then that observed in autosomes. This reinforces our earlier observation that selection is not a significant factor in explaining the reduction of variation observed on the Y chromosome.

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