Four chordate characters — dorsal hollow nerve cord, notochord, gill slits, and endostyle — are compared morphologically, molecularly, and functionally with similar structures in hemichordates to assess their putative homologies. The dorsal hollow nerve cord and enteropneust neurocord are probably homoplasies. The neurocord (= collar cord) may be an autapomorphy of Enteropneusta that innervates a unique pair of muscles, the perihemal coelomic muscles. Despite the apparent lack of organ-level homology, chordates and enteropneusts share a common pattern of neurulation that preserves a "contact innervation" between neuro- and myo-epithelia, which may be the primitive deuterostome pattern of neuromuscular innervation. The chordate notochord and hemichordate stomochord are probably homoplasies. Other potential notochord antecedents in hemichordates are examined, but no clear homolog is identified. The comparative morphology of notochords suggests that the "stack-of-coins" developmental stage, retained into adulthood only by cephalochordates, is the plesiomorphic notochord form. Hemichordate and chordate gill slits are probably homologs, but only at the level of simple ciliated circular or oval pores, lacking a skeleton, as occur in adults of Cephalodiscus spp., developmentally in some enteropneusts, and in many urochordates. Functional morphology, I125-binding experiments, and genetic data suggest that endostylar function may reside in the entire pharyngeal lining of Enteropneusta and is not restricted to a specialized midline structure as in chordates. A cladistic analysis of Deuterostomia, based partly on homologs discussed in this paper, indicates a sister-taxon relationship between Urochordata and Vertebrata, with Cephalochordata as the plesiomorphic clade.
A unique pair of triangles
