The deuterostomes are a well-circumscribed clade, comprising the Echinodermata (e.g., sea stars, sea lilies, sea urchins, sea cucumbers), Hemichordata (acorn worms and pterobranchs), and Chordata (sea squirts, lancelets, craniates plus vertebrates) (Figures 1 and 3-6). Traditionally, the membership of the Deuterostomia was considered to be wider, also including the three lophophorate phyla Brachiopoda (lamp shells), Phoronida, and Ectoprocta (moss animals), and frequently the Chaetognatha (arrow worms) as well. However, re-evaluation of morphological evidence (LUter, 2000; Bartolomaeus, 2001; Gruhl et al., 2005) is throwing serious doubt on the deuterostomian syna-pomorphies of brachiopods and phoronids, and accumulating molecular evidence now firmly places the lophophorates in the protostome clade Lophotrochozoa, while the phylogenetic position of the chaetognaths remains elusive. More recently, the enigmatic worm Xenoturbella bocki has been proposed to be a deuterostome as well.

Apart from clearly circumscribing the membership of the Deuterostomia, recent research has also reorganized the phylogenetic relationships within the deuterostomes on many levels (Blair and Hedges, 2005). In contrast to traditional ideas, the echinoderms and hemichordates are now united as sister groups in a clade Ambulacraria. Furthermore, within the chordates, the sister group relationship between the cephalochordates (lancelets) and the craniates (hagfish plus vertebrates) has been consolidated. However, the widely accepted position of the tunicates as the sister group to cephalochordates plus craniates has now come under fire from phylogenomic analyses that support instead an unexpected sister group relationship between tuni-cates and vertebrates, to the exclusion of the cephalochordates (Blair and Hedges, 2005; Delsuc et al., 2006). Intriguingly, a recent morphological phylogenetic analysis yielded the same result (Ruppert, 2005).

A large amount of new phylogenetic research within the vertebrates on many taxonomic levels has in several instances generated an evolutionary picture that is significantly at odds with established views, for example relationships within the placental mammals (Figure 6; Murphy et al., 2004; Springer et al., 2004). Since invertebrates comprise the vast majority of animal diversity this article is chiefly concerned with invertebrate phylogeny. However, in view of the fact that vertebrates are disproportionately represented in research on nervous systems, a brief overview of our current understanding of vertebrate phylogeny will also be presented (see Section; Figures 4-6).

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