Phylogenetic tree of the class 4 HDACs. The represented tree is a maximum-likelihood (ML) tree produced with PHYML (using the WAG model of protein evolution). Rooting is arbitrary. Numbers above the internal branches are their bootstrap support values (100 bootstrap replicates). Only bootstrap support values >50% are shown. Other internal branches (with bootstrap support <50%) should be considered unreliable. In addition to the values shown for the other statistically supported internal branches (ML WAG), some key internal branches are labelled with additional statistical support values obtained by other methods of phylogenetic reconstruction or other models of evolution: bootstrap support in PHYML analysis with the JTT model of evolution (ML JTT; 100 bootstrap replicates), ML quartet puzzling support (QP; 25,000 puzzling steps), bootstrap support in neighbour-joining (NJ) analysis (BioNJ algorithm, 10,000 bootstrap replicates), bootstrap support in maximum-parsimony (MP) analysis (heuristic search; 500 bootstrap replicates), and posterior probabilities (Bayesian inference, BI). More details on the phylogenetic analyses can be found in the Methodssection and additional trees can be found in Additional Files 3, 4, 5. Eukaryotic lineages are marked by a bold "E". Colored circles highlight internal nodes defining monophyletic groups discussed in the main text. Black circles define two large groups: the "eukaryotic group" including proteins of species belonging to three of the main eukaryotic lineages, namely the opisthokonta (metazoa), plantae (viridiplantae), and chromalveolata (alveolata), and the "mixed group" comprising proteins of species belonging to various eubacterial and eukaryotic lineages. The grey circle denotes, inside the mixed group, a monophyletic group containing both eukaryotic and eubacterial sequences. The red circle indicates a monophyletic group comprising class 4 HDACs of nine animals; these HDACs show closer resemblance to eubacterial proteins than to those of other animals. The yellow circle defines a group comprising four HDACs of distantly related eukaryotic planctonic species. The orange circle denotes a group comprising an HDAC sequence of the cnidarian Nematostella vectensis and those of two unrelated eubacteria. The multiple alignment on which this tree is based is available as Additional File 8.