Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition

We report the discovery of a polymorphic A to G transition found on the human Y chromosome by sequencing Y-specific sequence-tagged sites (STSs). It shows maximal linkage disequilibrium with a previously described Alu insertional polymorphism. We analyze further an apparently African Y chromosome which seems to have entered a Mexican Mayan population several generations ago. Using the newly discovered transition and the Y-speclfic polymorphic Alu insertion, we discuss how the chromosome's haplotype information might be used to answer questions of houman origins and migrations.