The evolution of embryogenesis is biased since many variations affect vital processes and lead to nonviable organisms. Species comparisons have enabled to evolutionary developmental biologists to characterize such constraints. For the animal embryo, it has been proposed that a stage in mid-development is conserved throughout the kingdom. As part of a consortium of ten labs, we test this hypothesis by identifying the developmental transcriptomes of ten species, each of a different animal phylum, including Nematodes, Ctenophores, Annelids, Chordates, Platyhelminthes, Tardigrades, Arthropods, Echinoderms, Cnidarians, and Poriferas. We find that animal embryonic development comprises the coupling of two conserved gene expression modules, primarily involved in proliferation and differentiation, where the switch between them occurs at the apparent phylotypic period of each phylum. Genes whose expression is coherent across the examined species are expressed in the first module, while clade specific variations occur in the second module and the transition to it. Our results are consistent with an inverse hour-glass model of animal evolution: gene expression differences across phyla are concentrated at the inter-module switch. Since, expression differences within a phylum appear to be minimal at the phylotypic stage, our work leads us to define a phylum as a collection of species where an hourglass model holds for gene expression differences. All together, we provide a map of embryology upon which ancestral constraints are mapped and distinguished from the stages in which variations are available to the agency of natural selection. [This work is a collaboration among the Arendt (Heidelberg), Rink (Dresden), Blaxter (Edinburgh), Goldstein (North Carolina), Salzberg (Haifa), deLeon (Haifa), Yaniv (Rehovot), Gat (Jerusalem), Degnan (Queensland), Martindale (Florida), and Yanai (Haifa) labs.].
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