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Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life 1 , but the evolutionary mechanisms that operate on interactions with these networks remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyze genomes, epigenomes, and transcriptomes during early development in two sea urchin species in the genus Heliocidaris that exhibit highly divergent life histories and in an outgroup species. Signatures of positive selection and changes in chromatin status within putative gene regulatory elements are both enriched on the branch leading to the derived life history, and particularly so near core dGRN genes; in contrast, positive selection within protein-coding regions have at most a modest enrichment in branch and function. Singlecell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near dGRN genes with conserved roles in cell fate specification. Experimentally perturbing the function of three key transcription factors reveals profound evolutionary changes in the earliest events that

Significance Ctenophore cydippid larvae are not larvae at all and begin adult reproduction at an early age (∼14 vs. ∼60 d) and small size (∼1 vs. ∼100 mm) relative to attainment of what has been considered the adult stage. This overturns the previous understanding of the ctenophore life cycle, which was believed to be a unique form of biphasic life cycle with two separate sexually reproductive periods. Practically, these results clarify ecological controls regulating ctenophore reproduction and will aid management of this invasive species. Additionally, the 2-wk egg-to-egg generation time will open new avenues of research in this understudied but informative taxon.

BackgroundThe longstanding canonical model of spider gastrulation posits that cell internalization occurs only at a unitary central blastopore; and that the cumulus (dorsal organizer) arises from within the early deep layer by cell–cell interaction. Recent work has begun to challenge the canonical model by demonstrating cell internalization at extra-blastoporal sites in two species (Parasteatodatepidariorum and Zygiella x-notata); and showing in Zygiella that the prospective cumulus internalizes first, before other cells are present in the deep layer. The cell behaviors making up spider gastrulation thus appear to show considerable variation, and a wider sampling of taxa is indicated.ResultsWe evaluated the model in three species from two families by direct observation of living embryos. Movements of individual cells were traced from timelapse recordings and the origin and fate of the cumulus determined by CM-DiI labeling. We show that there are two distinct regions of internalization: most cells enter the deep layer via the central blastopore but many additional cells ingress via an extra-blastoporal ring, either at the periphery of the germ disc (Latrodectus spp.) or nearer the central field (Cheiracanthium mildei). In all species, the cumulus cells internalize first; this is shown by tracing cells in timelapse, histology, and by CM-DiI injection into the deep layer. Injection very early in gastrulation labels only cumulus mesenchyme cells whereas injections at later stages label non-cumulus mesoderm and endoderm.ConclusionsWe propose a revised model to accommodate the new data. Our working model has the prospective cumulus cells internalizing first, at the central blastopore. The cumulus cells begin migration before other cells enter the deep layer. This is consistent with early specification of the cumulus and suggests that cell–cell interaction with other deep layer cells is not required for its function. As the cumulus migrates, additional mesendoderm internalizes at two distinct locations: through the central blastopore and at an extra-blastoporal ring. Our work thus demonstrates early, cell-autonomous behavior of the cumulus and variation in subsequent location and timing of cell internalization during gastrulation in spiders.Electronic supplementary materialThe online version of this article (doi:10.1186/s13227-015-0029-z) contains supplementary material, which is available to authorized users.