The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear¹. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting^2,3. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel^1,4, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses^4,5. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres⁶. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinor-hynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other.

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. We present a molecular phylogenetic analysis of hemichordates that challenges this long-held view. We used 18S rRNA to infer evolutionary relationships of the hemichordate classes Pterobranchia and Enteropneusta. Our 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 our 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.