GTPases are integral components of virtually every known signal transduction pathway, and mutations in GTPases frequently cause disease. A genomic analysis identified and annotated 174 GTPases in the sea urchin genome (with 90% expressed in the embryo), covering five classes of GTP-binding proteins: the Ras superfamily, the heterotrimeric G proteins, the dynamin superfamily, the SRP/SR GTPases, and the translational GTPases. The sea urchin genome was found to contain large lineage-specific expansions within the Ras superfamily. For the Rho, Rab, Arf and Ras subfamilies, the number of sea urchin genes relative to vertebrate orthologs suggests reduced genomic complexity in the sea urchin. However, gene duplications in the sea urchin increased overall numbers, such that total sea urchin gene numbers of these GTPase families approximate vertebrate gene numbers. This suggests lineage-specific expansions as an important component of genomic evolution in signal transduction. A focused analysis on RhoA, a monomeric GTPase, shows it contributes to multiple signal transduction pathways during sea urchin development. The data reveal that RhoA inhibition in the sea urchin results in a failure to invaginate during gastrulation. Conversely, activated RhoA induces precocious archenteron invagination, complete with the associated actin rearrangements and extracellular matrix secretion. Although RhoA regulates convergent extension movements in vertebrates, our experiments show RhoA activity does not regulate convergent extension in the sea urchin. Instead, the results suggest RhoA serves as a trigger to initiate invagination, and once initiation occurs RhoA activity is no longer involved in subsequent gastrulation movements. RhoA signaling was also observed during endomesodermal specification in the sea urchin. Data show that LvRhoA activity is required, downstream of a partially characterized Early Signal, for SoxB1 clearance from endomesodermal nuclei (and subsequent expression of GataE and Endo16 genes). Investigations also suggest that within the endomesoderm, RhoA clears SoxB1 as part of Wnt8 signaling, as activated RhoA is sufficient to rescue Wnt8-inhibited embryos. These data provide evidence of the first molecular components involved in SoxB1 clearance, as well as highlight a previously unrecognized role for RhoA during endomesodermal specification. These analyses suggest RhoA signaling is integral to the proper specification and morphogenesis of the sea urchin endomesoderm. / dissertation