PALEOGENOMICS OF ECHINOIDS AND THE EVOLUTION OF ECHINOID GENE REGULATORY NETWORKS

Establishing a timeline for the evolution of novelties, whether those be ecological, behavioral or genomic, lies at the heart of evolutionary biology. Molecular developmental biology lends the ability to understand the genetic underpinning behind the origin of evolutionary novelties through the study of Gene Regulatory Networks (GRN’s). Accurately dating GRN novelties, and establishing a timeline for GRN evolution is thus necessary to begin to answer questions on the rate at which GRN’s and their subcircuits evolve, and to tie the evolution of particular subcircuits to environmental and ecological changes. Paleogenomics attempts to unite the fossil record and all aspects of the study of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. Given the wealth of developmental and genomic data available for echinoids, they are an ideal target system for paleogenomic studies. The GRN’s controlling embryonic development in echinoids were until the past ten years only known from the indirect developing regular camaradont sea urchins, such as the model systems Strongylocentrutus purpuratus, Paracentrotus lividus, and Lytechinus variegatus. Recent work on the regulatory genomic basis for development in cidaroid echinoids, sand dollars, heart urchins, and other non-camaradonts provides an ever-expanding dataset with which to explore GRN evolution in a comparative perspective. Using molecular clocks, and phylogenetic comparative ancestral state reconstructions, it has been possible to date the appearance of the Double-Negative Gate, the GRN subcircuit responsible for specification of micromeres and the skeleton in euechinoid echinoids. The Double-Negative Gate has been demonstrated to be present in a number of euechinoid taxa, however, it is absent in their sister clade, the cidaroids. By using experimental molecular developmental data from numerous euechinoids and cidaroids, and across echinoderms, we have been able to date the appearance of the double negative gate in evolutionary time, and tie this to the early Mesozoic, or late Paleozoic. Paleogenomics thus has wide applicability for the integration of fossil and molecular developmental data, and serves to promote the utility of fossils in molecular developmental research.