Extended Data Fig. 10: Comparative transcriptomic analysis of metazoan life cycles.

a, Matrix of heatmaps of normalised transcriptomic Jensen–Shannon divergence (JSD) from pairwise comparisons of all single copy one-to-one orthologs between all eleven metazoan lineages. From top to bottom and left to right: the annelids O. fusiformis and C. teleta, the bivalve C. gigas, the nematode C. elegans, the insect D. melanogaster, the vertebrate D. rerio, the cephalochordate B. lanceolatum, the sea urchin S. purpuratus, the cnidarians N. vectensis and C. hemisphaerica, and the poriferan A. queenslandica. b, Proposed evolutionary scenario for larval and life cycle evolution in Annelida. Post-embryonic trunk patterning is likely an ancestral condition with the convergent pre-displacement of trunk differentiation to embryogenesis concurring with the evolution of indirect development with feeding larva and direct development. Drawings are not to scale. c, Expression dynamics of Hox genes across the developmental RNA-seq time courses of all eleven species from a and the echiuran annelid U. unicinctus. Heatmaps were vertically aligned at the blastula, gastrula, and juvenile stages for all species. Lophotrochozoan lineages with trochophore larvae were also vertically aligned at the trochophore stage. Dotted lines encompass the larval stages of species with ciliated larvae. See Extended Data Fig. 5e and Supplementary Fige. 33 for the fully labelled and non-deformed heatmaps. d, Alternative evolutionary scenarios for the deployment of Hox genes (as proxy for trunk patterning and assuming the staggered expression along the directive axis of cnidarians and anteroposterior axis of bilaterians is homologous, which does not necessarily imply homology of the two axes). Given our current understanding of Hox gene deployment in cnidarian and bilaterian taxa, a late post-embryonic Hox patterning ancestral to Bilateria and Cnidaria, as seen in extant lineages with maximal indirect development, is a more parsimonious scenario (on the right).