Evolution of pharyngeal patterning in deuterostomes. The last common ancestor of all deuterostomes possessed a segmented pharynx with alternating pharyngeal arches and tongue bars and with an extracellular collagenous skeleton secreted by endodermal cells. This ancestral pharynx was patterned by Pax1/9, Six1/2 and Eya genes, with Hox1 likely establishing the posterior boundary of the pharynx. The involvement of RA signaling in pharyngeal patterning in hemichordates is possible, but further work is required to validate this hypothesis. In the ancestral chordate, the pharyngeal apparatus was elaborated by Tbx1/10-expressing mesoderm originating from the anterior paraxial mesoderm. Engrailed (En) was co-expressed with Tbx1/10 in the anterior somites and the gene network controlling chordate pharyngeal patterning further included Pitx and Pax2/5/8 as well as fibroblast growth factor (FGF) and bone morphogenetic protein (BMP) signaling. In the vertebrate lineage, neural crest cells contribute extensively to the developing pharynx and segmentation of the head mesoderm was likely lost. Genes shown in bold are directly involved in mediating RA signaling in the pharynx. *Pharyngeal expression unknown in hemichordates; **Pharyngeal expression has not been assessed in hemichordates and vertebrates; ***Pharyngeal expression lost in terrestrial mammals. Abbreviations: ea, external branchial arches; ec, extrabranchial cartilage; gs, gill slits; mu, muscles; pa, pharyngeal arches; sc, superficial branchial constrictions; sy, synapticles; tb, tongue bar. For the sake of clarity, tunicates have not been included in the diagram.