Phylogenetic relationships between the species used in this study. The tree is based on the current view of the phylogeny of the metazoans [73,74]. The total number of bHLHs and the number of represented bHLH metazoan families of orthologs in each genome is indicated. For the number of represented families, a range is indicated for most species, due to the uncertainty about the presence of some families in these species (see additional file 1 for details). The names of representative phylogenetic groups are indicated on the left of the nodes that define these different groups and along some of the terminal branches. The Ciona intestinalis data come from  and have not been reanalysed in this study.