Ancestral-duplicon determination of the human Y-chromosomal euchromatin/heterochromatin transition regions. The upper layer displays the chromosomal position and extension of the regions containing highly duplicated sequences with respect to the heterochromatin. The chromosomal location of a defined ancestral duplicon is indicated by the color key. Duplicons are denoted according to the cytogenetic band position of their ancestral locus. Conserved genic structures are shown in parentheses. Gray blocks display sequences for which no ancestral state could be determined. (A) Duplication blocks accounting for a total of 866 kb were analyzed by phylogenetic analysis and comparative primate FISH to define their ancestral duplicon (colored bars) state (see Methods). (B) Duplicated sequences simultaneously subjected to DupMasker analysis (Jiang et al. 2008) for prediction of ancestral duplicons are compared against experimentally determined loci.