Figure 4

Schematic representation of the stepwise mutation model leading from the early chordate triresidue to the mammalian H2A.Z-1 and H2A.Z-2 triresidues. The model is presented independently for each of the positions in the triresidue. In the first step, the amino acid at a given position of the triresdue from early chordates is indicated. The second step involves the choice of either the H2A.Z-1 or the H2A.Z-2 pathway through a substitution of one of the positions in the codon which can result in a synonymous change or a residue replacement, configuring the triresidue in H2A.Z-1 and H2A.Z-2 proteins from non-mammalian vertebrates (usually Xenopus and zebrafish). The third step involves the transition of the already differentiated triresidues from non-mammalian vertebrates to those observed in mammalian H2A.Z-1 and H2A.Z-2 forms, through a single mutation in each of the three codons in most cases. The nature of the nucleotide substitutions mediating the transition from one step to another is indicated by open blue boxes (synonymous) and solid blue boxes (nonsynonymous) detailing the nucleotide change and the position at which it occurs. Multiple substitutions are indicated by solid grey boxes. The relative synonymous codon usage (RSCU) for each codon (black) is compared with the RSCU value for the preferred codon in that family (red) in each of the steps. In addition, substitutions fitting the Maximum composite likelihood estimation of the probability of substitution from one base to another simultaneously in H2A.Z-1 and H2A.Z-2 are identified in red as (ML).