Developmental gene regulatory networks (GRNs) are assemblages of regulatory genes directing embryonic development of animal body plans. Alterations to GRN circuitry cause variation in developmental programs both during an individual’s development and evolution of individual lineages. These networks are best exemplified by the global embryonic GRN directing early development of the euechinoid sea urchin Strongylocentrotus purpuratus. Notably, research on closely-related euechinoids in the sea urchin order Camarodonta, e.g. Lytechinus variegatus and Paracentrotus lividus, has revealed marked conservation of circuitry in this global GRN, suggesting little appreciable alteration has occurred since the divergence of camarodonts at least 90 million years ago (mya). To test whether this observation extends to all echinoids, I undertook a systematic survey of global spatiotemporal activity and GRN circuitry of 65 regulatory genes in the cidaroid sea urchin Eucidaris tribuloides, which diverged from euechinoids at least 268 mya. These data reveal alterations to all levels of echinoid GRN architecture since the cidaroid-euechinoid divergence. Alterations to mesodermal subcircuits were particularly striking, including functional differences in specification of non-skeletogenic mesoderm, skeletogenic mesoderm and mesodermal segregation. Analyses of E. tribuloides aboral-oral (dorsal-ventral) specification further suggested that mesodermal regulatory genes incurred more alterations to their regulation than ectodermal regulatory genes. Collectively, these data highlight the remarkable lability of GRNs in developmental evolution and suggest that mesodermal regulatory genes have undergone disproportionate and extensive rewiring in this clade
