Location and extent of sequenced great ape MSY-orthologous regions compared to the human reference sequence. (A) Schematic representation of the human Y Chromosome (Skaletsky et al. 2003) showing blocks of different sequence classes. (B) The analyzed subregions of MSY, shown as plots of read depth against chromosome position. Note that the order and orientation of MSY sequences in the great apes is not necessarily the same as that in the human reference sequence. In each plot, the y-axis ranges from zero to 150×. Sample size (N) for each species is given to the left, and mean depth (DP) and the extent of sequence obtained (bp) to the right. (Hsa) human; (Ptr) chimpanzee; (Ppa) bonobo; (Ggo) gorilla; (Ppy) Bornean orangutan; (Pab) Sumatran orangutan. Chimpanzees carry two distinct structural variant sequences (Ptr1 and 2) differing by insertion/deletions highlighted by magenta bars. Similarly highlighted is a Pan-specific duplication that extends palindrome P6. Below the species plots, black bars indicate sequenced regions shared across all 51 males (43 great apes and seven humans as a representative subset from the 448 sequenced samples, plus one haplogroup A00 human) (Hallast et al. 2015; Karmin et al. 2015), totaling 750,616 bp, and used in constructing the cross-species phylogeny shown in Figure 4 (see below). (C) Locations of single-copy MSY genes (Skaletsky et al. 2003; Bellott et al. 2014) shown as triangles (not drawn to scale) pointing in the direction of transcription.
