The origin of many of the defining features of animal body plans, such as symmetry,
nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty
regarding the emergence order of the early branching taxa: the sponge groups, ctenophores,
placozoans, cnidarians, and bilaterians. The "phylogenomic" approach [1] has recently
provided a robust picture for intrabilaterian relationships [2, 3] but not yet for
more early branching metazoan clades. We have assembled a comprehensive 128 gene data
set including newly generated sequence data from ctenophores, cnidarians, and all
four main sponge groups. The resulting phylogeny yields two significant conclusions
reviving old views that have been challenged in the molecular era: (1) that the sponges
(Porifera) are monophyletic and not paraphyletic as repeatedly proposed [4-9], thus
undermining the idea that ancestral metazoans had a sponge-like body plan; (2) that
the most likely position for the ctenophores is together with the cnidarians in a
"coelenterate" clade. The Porifera and the Placozoa branch basally with respect to
a moderately supported "eumetazoan" clade containing the three taxa with nervous system
and muscle cells (Cnidaria, Ctenophora, and Bilateria). This new phylogeny provides
a stimulating framework for exploring the important changes that shaped the body plans
of the early diverging phyla.