Model describing regulatory reorganization of the echinoderm mesoderm and evolution of the larval skeletogenic mesenchyme. (A) Regulatory states for the mesoderm of sea urchins, sea cucumbers and sea stars are shown in the top row of the schematic. The dark blue ring represents the endodermal territory that surrounds the mesoderm. Orange regions indicate derived alx1 expression. Genes expressed in each territory are listed. (B) In later development, these territories will form two types of mesenchyme: the alx1+ SM and the blastocoelar cells (orange and purple, respectively). Gene expression patterns not described in this work have been previously reported [20–30, 32–34, 39]. Of the organisms studied, only sea cucumbers and sea urchins are known to make skeletogenic mesenchyme, though brittle stars also form a larval skeleton. By comparing gene expression in the mesodermal territories of sea urchins, sea cucumbers and sea stars, we extrapolated the regulatory state of the mesoderm of the echinoderm ancestor (the proto-mesoderm), shown at the base of the tree (phylogeny after [11, 14, 15]). The broad expression of most TFs within the mesoderm of sea cucumbers and sea stars supports the hypothesis that there was a pan proto-mesoderm during blastula stages. Subsequent regulatory changes within the mesoderm in the lineage leading to at least sea urchins and sea cucumbers created a population of cells, marked by their expression of alx1, that go on to form the larval skeleton.