We estimated nucleotide divergence in unique gap-free sequence, indicated at each node, from the alignment of rhesus macaque (yellow), gibbon (purple), orang-utan (orange), gorilla (aqua), chimpanzee (green) and human (blue) whole genome shotgun reads to the human reference (Hs.35; Supplementary Information section 3). Note that the Bornean (P. pygmaeus) and Sumatran (P. abelii) orang-utan species showed nucleotide identity comparable to that of bonobo (Pan paniscus) and chimpanzee (Pan troglodytes). Estimates of divergence time based on sequence identity are indicated at each node, ~1 Myr implies approximately 1 Myr or less. Values taken from refs 29 and 30 where indicated.
We identified six genes (indicated in yellow) under moderate to strong positive selection in primates (P < 0.05) that fall within the cerebroside-sulphatid region of the sphingolipid metabolism pathway (adapted from human KEGG pathway 00600). This pathway is associated with several human lysosomal storage disorders, such as Gaucher’s disease, Sandhoff’s disease, Tay-Sachs disease and metachromatic leukodystrophy. Abbreviations, annotations and connections are presented in accordance with KEGG standards: solid lines represent direct relationships between enzymes (boxes) and metabolites (circular nodes), dashed lines represent indirect relationships, arrowheads denote directionality (see http://www.genome.jp/kegg-bin/show_pathway?map00600 for further details).