The eumetazoan clade of modern animals includes cnidarians, acoels, deuterostomes, and protostomes. Stem group eumetazoans evolved in the late Neoproterozoic, possibly before the Marinoan glaciation, according to a variety of different kinds of evidence. Here, we combine this evidence, including paleontological observations, results from molecular and morphological phylogeny, and paleoecological considerations, with deductions from the organization of the gene regulatory networks that underlie development of the bilaterian body plan. Eumetazoan body parts are morphologically complex in detail, and modern knowledge of gene regulatory network structure shows that the control circuitry required for their development is hierarchical and multilayered. Among the consequences is that the kernels of the networks that control the early allocation of spatial developmental fate canalize the possibilities of downstream evolutionary change, a mechanism that can account for the appearance of distinct clades in early animal evolution. We reconstruct preeumetazoan network organization and consider the process by which the eumetazoan regulatory apparatus might have been assembled. A strong conclusion is that the evolutionary process generating the genomic programs responsible for developmental formulation of basic eumetazoan body plans was in many ways very different from the evolutionary changes that can be observed at the species level in modern animals.
