Phylogenetic neighbor-joining tree showing the progressive specialization of H2A.Z-1 and H2A.Z-2 genes (indicated in Additional file 2) across chordates after estimating the nucleotide p -distances. Histone H2A.Z-1 variants are indicated in pink, H2A.Z-2 variants are indicated in purple and H2A.Z-e sequences from early chordates are indicated in brown. Histone variants from protostomes, plants and fungi/protists are indicated in blue, while the root of the tree is labeled in black. Pink, purple and red boxes in interior branches denote the monophyletic origin for each group. BP, CP and bootstrap confidence values for the maximum parsimony trees are indicated as in Fig. 1. Variant sequences predicted from databases and draft genomes data are indicated by PRED near the species name. The colored bar chart at the right indicates the codon usage bias for the corresponding sequence within each variant, estimated as the effective number of codons (ENC) and indicating the average (lines) and standard deviation (yellow box) for H2A.Z-1 and H2A.Z-2 sequences. The composition of the triresidue (amino acids and encoding triplets) is detailed in the right margin of the topology for each of the sequences analyzed and in different colors in case of variation in the codons.