The deuterostome phyla include Echinodermata, Hemichordata, and Chordata. Chordata is composed of three subphyla, Vertebrata, Cephalochordata (Branchiostoma), and Urochordata (Tunicata). Careful analysis of a new 18S rDNA data set indicates that deuterostomes are composed of two major clades: chordates and echinoderms + hemichordates. This analysis strongly supports the monophyly of each of the four major deuterostome taxa: Vertebrata + Cephalochordata, Urochordata, Hemichordata, and Echinodermata. Hemichordates include two distinct classes, the enteropneust worms and the colonial pterobranchs. Most previous hypotheses of deuterostome origins have assumed that the morphology of extant colonial pterobranchs resembles the ancestral deuterostome. A molecular phylogenetic analysis of hemichordates is presented that challenges this long-held view. 18S rRNA was used to infer evolutionary relationships of the hemichordate classes Pterobranchia and Enteropneusta. The data show that pterobranchs may be derived within enteropneust worms rather than being a sister clade to the enteropneusts. The nesting of the pterobranchs within the enteropneusts dramatically alters the view of the evolution of the chordate body plan and suggests that the ancestral deuterostome more closely resembled a mobile worm-like enteropneust than a sessile colonial pterobranch.

This analysis of the slow evolving rDNA sequences of the 16 deuterostome taxa is the first molecular study to define clearly the evolutionary relationships among all four major groups of deuterostomes. Vertebrata is found to be monophyletic and a sister clade to Cephalochordata. Urochordata is monophyletic and forms a sister group to Vertebrata + Cephalochordata. The sister relationship between urochordates and vertebrates + cephalochordates is supported by morphological evidence. The presence of a notochord unites urochordates, cephalochordates, and vertebrates, although some authors differentiate the notochord of vertebrates + cephalochordates from the urochord of urochordates. The characters that set vertebrates + cephalochordates apart from urochordates are the presence of myotomes in vertebrates + cephalochordates and the presence of the tunic in the urochordates. Urochordates are considered members of Chordata because the tadpole larva exhibits the chordate body plan. However, differences in adult body plan and life histories of urochordates compared with vertebrates + cephalochordates justify a reappraisal of the inclusion of urochordates within the phylum Chordata despite the presence of a notochord.