Fig. 6: Gene evolution on the Y chromosome.

Significant gains and losses in ampliconic gene copy number (Supplementary Note 10) are shown on the phylogenetic tree. Copy numbers of ampliconic genes are indicated with numbers and by circle size; no circle indicates absence of annotated protein-coding copies. Presence, pseudogenization or absence (that is, deletion) of ancestral (X-degenerate) genes are shown by squares of different colours. Genes showing signatures of purifying selection (Methods) are underlined. XKRY was found to be a pseudogene in all species studied and is therefore not shown. The protein-coding status of PRY was confirmed for human⁸, and we found evidence of expression of a similar transcript in gorilla (Supplementary Table 36b). The RBMY gene family harboured two distinct gene variants, each present in multiple copies in Pongo (Supplementary Fig. 19).