Phylogenetic positions of cephalochordates, urochordates, and vertebrates, showing their Hox contents. The cephalochordate amphioxus represents the basal branch of chordates and possesses a single Hox cluster of 15 genes in both B. floridae and B. lanceolatum, although the whole genomic sequence of the latter has not been reported yet (indicated by dashed lines in the corresponding regions). Urochordates, the sister group of vertebrates, possess a disintegrated Hox cluster at different levels. Whereas the ascidian Ciona intestinalis has a highly disintegrated cluster with several reorganizations, the larvacean Oikopleura dioica has a completely atomized cluster where only two Hox9 genes remain linked, probably arising from an independent duplication. Vertebrates have multiple clusters, such as four in the mouse caused by two rounds of genome duplication (2R), or the seven clusters of zebrafish after a third teleost-specific round of genome duplication (3R). Squares represent Hox genes, with the same gray-scale colors indicating different paralogous groups (PG1 and PG2, PG3, central PG4-8, and posterior PG9-13/15). White boxes with dashed outlines represent pseudogenes.