plosone-phylo
pone.0000884.g003
A cladogram of primate species showing approximate appearance time of inactivating mutations.Species relationships were compiled from several sources [47]–[50], and a tree was plotted using MEGA3 (branch lengths not to scale). Inactivating mutations shared by more than one species (Table 1) are marked on the tree (e.g. 9A, etc) at the estimated time point of their appearance. The deletions of exons 2, 4 and 5 are marked as mutations 2A, 4A and 5A. We estimated mutation age conservatively – mutations are marked on the most recent ancestral branch shared by all species possessing the mutation (species known to lack the mutation were used to further pinpoint age). Some mutations may be older than shown, but outgroup data are not available to determine age more accurately. Mutations that appear to have arisen twice independently are marked in gray. Exon 19 mutations are not plotted or included in mutation counts, as their effect on protein sequence may be minimal. An “X” next to a species name indicates that GC-D is a pseudogene in that species, and the number in parentheses indicates the minimum estimate of total number of inactivating mutations (observed plus inferred) present. Species abbreviations: m., monkey; Rb. s., Red-backed squirrel; C. s., Common squirrel; mm., marmoset; or., orangutan.
pone.0000884.g003
A cladogram of primate species showing approximate appearance time of inactivating mutations.Species relationships were compiled from several sources [47]–[50], and a tree was plotted using MEGA3 (branch lengths not to scale). Inactivating mutations shared by more than one species (Table 1) are marked on the tree (e.g. 9A, etc) at the estimated time point of their appearance. The deletions of exons 2, 4 and 5 are marked as mutations 2A, 4A and 5A. We estimated mutation age conservatively – mutations are marked on the most recent ancestral branch shared by all species possessing the mutation (species known to lack the mutation were used to further pinpoint age). Some mutations may be older than shown, but outgroup data are not available to determine age more accurately. Mutations that appear to have arisen twice independently are marked in gray. Exon 19 mutations are not plotted or included in mutation counts, as their effect on protein sequence may be minimal. An “X” next to a species name indicates that GC-D is a pseudogene in that species, and the number in parentheses indicates the minimum estimate of total number of inactivating mutations (observed plus inferred) present. Species abbreviations: m., monkey; Rb. s., Red-backed squirrel; C. s., Common squirrel; mm., marmoset; or., orangutan.