PHYLOGENETICS AND THE RECONSTRUCTION OF ANCIENT GENE REGULATORY NETWORKS

The evolution of animal body plans has been hypothesized to be intrinsically controlled by the evolution of developmental gene regulatory networks GRNs which encode for organismal morphology. The rate at which morphological characters evolve is thus a function of the rate at which the underlying GRNs that specify them, in turn evolve. If we hope to know at what rate GRNs evolve, we must first have a rigorous timeline in which to explore their evolution and understand ancestral regulatory states. Echinoderms provide an ideal model system for the analysis of gene regulatory network evolution due to the well-characterized networks known from a number of model echinoderms, and gene expression data from a growing number of echinoderm non-model systems. We herein undertake comparative analysis of echinoderm expression patterns for three genes, Alx1, Ets, and Tbr, to reconstruct the evolutionary history of the expression patterns of these genes, and thus the GRNs which regulate their expression. Using expression data from echinoids, holothurians, asteroids, and ophiuroids, we utilize ancestral state reconstruction, paired with fossil-calibrated divergence time estimation to estimate the ancestral expression patterns in extinct echinoderm embryos. Our approach provides a robust framework for the estimation of ancient gene expression patterns, and has broad utility for understanding the evolution of gene expression and regulation in a number of other model and non-model systems.