Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data

We consider a data set of DNA sequence variation at three Y chromosome gene s (SMCY, DBY, and DFFRY) in a worldwide sample of human Y chromosomes. Betw een 53 and 70 chromosomes were fully screened for sequence variation at eac h locus by using the method of denaturing high-performance liquid chromatog raphy. The sum of the lengths of the three genes is 64,120 bp. We have used these data to study the ancestral genealogy of human Y chromosomes. In par ticular, we focused on estimating the expected time to the most recent comm on ancestor and the expected ages of certain mutations with interesting geo graphic distributions. Although the geographic structure of the inferred ha plotype tree is reminiscent of that obtained for other loci (the root is in Africa, and most of the oldest non-African lineages are Asian), the expect ed time to the most recent common ancestor is remarkably short, on the orde r of 50,000 years. Thus, although previous studies have noted that Y chromo some variation shows extreme geographic structure, we estimate that the spr ead of Y chromosomes out of Africa is much more recent than previously was thought. We also show that our data indicate substantial population growth in the effective number of human Y chromosomes.