Evolution, development and homology of deuterostome pharyngeal arches

This dissertation addresses the development of the pharyngeal arch endoskeleton in three chondrichthyan fishes -- the little skate (Leucoraja erinacea), the whitespotted bamboo shark (Chiloscyllium plagiosum ), and the elephant fish (Callorhinchus milii) -- and also addresses the development and homology of the pharyngeal gill slits and arches of the hemichordate worm, Saccoglossus kowalevskii. All of the chondrichthyan species examined possess branchial rays on their hyoid and gill arches, though gill arch rays are vestigial in C. milii . This suggests that ray-bearing branchial arches are a primitive feature of the chondrichthyan crown group. In L. erinacea and C. milii, epithelial Sonic hedgehog (Shh) expression within a distal pseudostratified epithelial ridge (L. erinacea) or epithelial fold (C. milii ) correlates with branchial ray outgrowth. Experimental embryological studies in L. erinacea reveal that a retinoic acid (RA)- Shh-Fibroblast growth factor (Fgf) feedback loop regulates branchial ray outgrowth. Shh and Fgf8 are co-expressed within the epithelial ridge of the outgrowing gill septum, and loss-of-function experiments demonstrate that Shh and Fgf8 act synergistically to maintain branchial ray outgrowth. The application of exogenous RA induces ectopic epithelial Shh expression -- and supernumerary gill rays, in a mirror-image orientation relative to native rays -- on the epibranchial cartilages. The application of ectopic recombinant SHH is also sufficient to induce supernumerary, mirror-image branchial rays. These data demonstrate that ligand expression in the pharyngeal epithelium is necessary for normal patterning of the chondrichthyan pharyngeal arch endoskeleton, and also suggest that the gill rays of chondrichthyans and the vertebrate paired appendage endoskeleton are patterned by common developmental mechanisms. Finally, I demonstrate that S. kowalevskii expresses the transcription factors Pax1/9, Six1, FoxC and Hox1 in the endoderm of the developing gill slits. These patterns are similar to expression patterns observed in vertebrate pharyngeal endoderm, and likely represent a conserved feature of deuterostome pharyngeal endoderm. S. kowalevskii does not express that pan-vertebrate pharyngeal mesoderm marker Tbx1, and it exhibits divergent patterns of pharyngeal ligand and receptor expression relative to vertebrates. This, combined with an absence of pharyngeal mesoderm derivatives in the adult S. kowalevskii pharyngeal arches, suggests that hemichordates share a conserved pharyngeal endodermal developmental program with chordates, but that a defined pharyngeal mesenchyme population -- and associated pharyngeal epithelial-mesenchymal interactions -- are a vertebrate novelty.