Citation: Thompson, J. R., Petsios, E., Davidson, E. H., Erkenbrack, E. M., Gao, F., & Bottjer, D. J. (2015). Reorganization of sea urchin gene regulatory networks at least 268 million years ago as revealed by oldest fossil cidaroid echinoid.Scientific reports, 5.
Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins
Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provides the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes. Paleogenomics unites the fossil record and all aspects of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. Recent work on the regulatory genomic basis of development in cidaroid echinoids, sand dollars, heart urchins, and other nonmodel echinoderms provides an ideal dataset with which to explore GRN evolution in a comparative framework. Using divergence time estimation and ancestral state reconstructions, we have determined the age of the double-negative gate (DNG), the subcircuit which specifies micromeres and skeletogenic cells in Strongylocentrotus purpuratus. We have determined that the DNG has likely been used for euechinoid echinoid micromere specification since at least the Late Triassic. The innovation of the DNG thus predates the burst of post-Paleozoic echinoid morphological diversification that began in the Early Jurassic. Paleogenomics has wide applicability for the integration of deep time and molecular developmental data, and has wide utility in rigorously establishing timelines for GRN evolution.
This work provides direct evidence of evolutionary rewiring of gene-regulatory circuitry accompanying divergence of two subclasses of echinoderm, the cidaroid and euechinoid sea urchins. These forms descend from a known common Paleo- zoic ancestor, and their embryos develop differently, offering an opportunity to probe the basic evolutionary process by which clade divergence occurs at the gene-regulatory net- work (GRN) level. We carried out a systematic analysis of the use of particular genes participating in embryonic skeleto- genic cell specification, building on an established euechinoid developmental GRN. This study revealed that the well-known and elegantly configured regulatory circuitry that underlies skeletogenic specification in modern sea urchins is largely a novel evolutionary invention. The results dramatically dis- play extensive regulatory changes in a specific developmental GRN, underlying an incidence of cladistic divergence at the subclass level.
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