Fig. 2.

Evolution of Y chromosome gene content in great apes. The reconstructed history of gene birth and death for X-degenerate (blue) and ampliconic (red) genes was overlaid on the great ape phylogenetic tree (not drawn to scale), using macaque as an outgroup. The rates of gene birth and death (in events per million years) are shown in parentheses (for complete data, see SI Appendix, Fig. S6 and Table S4). The list at the root includes the genes that were present in the common ancestor of great apes and macaque. In addition to most of the genes on the human Y, the macaque Y harbors the X-degenerate MXRA5Y gene, which we found to be deleted in orangutan and pseudogenized in bonobo, chimpanzee, gorilla, and human. We currently cannot find a full-length copy of the VCY gene in bonobo (SI Appendix, Supplemental Note S7). TXLNGY and DDX3Y are also known as CYorf15B and DBY, respectively.