The well defined phylogeny of the echinoderm clade represents the relationships of a number of useful research models. A deep and diverse fossil record and extensive biochemical studies together establish confident divergence times for many points in the phylogenetic tree for echinoderms (see figure). Other sea urchin species (Echinoidea)have diverged from the reference species (Strongylocentrotus purpuratus at intervals covering 265 million years. Other eleutherozoan echinoderm classes: sea stars (Asteroidea), sea cucumbers (Holothuroidea), and brittle stars (Ophiuroidea) diverged earlier at about 540 million years ago. This is also the time at which hemichordates and the chordate branch to which humans diverged from echinoderms.

Evolutionary comparisons been especially useful for the description of gene regulatory networks (GRN) and the cis-regulatory modules (CRM) of which they are made. One of the most comprehensive examples of a GRN sufficiently mature to demonstrate their full range of predictive and explanatory power are at present those worked out experimentally for the embryo of the sea urchin (Strongylocentrotus purpuratus, Sp). Genomic comparisons with another echinoid species Lytechinus variegatus (Lv) identifies conserved non-coding regions that include CRMs. The full genomic sequence of this species leads to the first algorithms (that work) for large scale prediction of overall GRN structure from genomic sequence. Acquisition of the genome sequence of the sea star, Patiria miniata (Pm) will produce direct evidence, and provide predictive principles, for assessing what types of GRN subcircuit are flexible in evolution and thus could be reorganized or altered, and which are virtually unchanging and inflexible. Similar comparisons to the brittle star Ophiothrix spiculata and the sea cucumber Parastichopus parvamensis will deepen the inferences on flexibility and constraint of the evolution of GRNs. An echinoid species of intermediate divergence, Eucidaris tribuloides (Et) exhibits interesting variation in developmental pattern which can also be used to contrast with that of the reference.

We presently have available transcriptome data from a variety of echinoderm species that can be used for gene discovery. For each set there is a BLAST database and a search function that returns the best matches to the well annotated genes of the reference species and matches to the non-redundant mRNA database at NCBI. These can be searched by gene name or matching SPU number. In some cases transcript assemblies were available and we imported these in toto and then performed the BLAST analysis to the reference genes. In other cases we have performed assemblies locally.