The mid-developmental transition and the evolution of animal body plans

Abstract

Animals are grouped into ~35 ‘phyla’ based upon the notion of distinct body plans1–4. Morphological and molecular analyses have revealed that a stage the middle of development—known as the phylotypic period—is conserved among species within some phyla5–9. While these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals10. Here, we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that, in all ten species, development comprises the coupling of early and late phases of gene expression. These conserved phases are linked by a divergent ‘mid-developmental transition’ that deploys species-specific suites of signaling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signaling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly-conserved among them, yet divergent relative to species in other phyla.

No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

“…A high proportion of H. dujardini mRNASeq (Fig. 1C) (42), transcriptome assembly (12), expressed sequence tags (ESTs), and genome survey sequences (GSSs) mapped to the assembly. We predicted a high-confidence set of 23,021 protein-coding genes using AUGUSTUS (44).…”

Phylogenetic evidence for the modular evolution of metazoan signalling pathways

“…Recent efforts to combine molecular (e.g. transcriptomics) and developmental techniques [5] have provided an opportunity to use expression data as a first attempt to imply function rather than relying on only presence/absence data from genomic studies. Despite having only limited data from several critical taxa, we take a first step towards integrating genomic and developmental studies from diverse nonbilaterian metazoans to attempt to reconstruct ancestral functions of several key signal transduction cascades.…”

Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

“…Establishing a timeline for the rates at which these novel structures arise, and the rate at which the developmental GRNs that encode them evolve, lies at the heart of evolutionary developmental biology (5). In recent years, identifying genetic regulatory differences between diverse organisms has become more feasible with broader phylogenetic sampling of developmental and gene expression data across Metazoa (6,7). These new data provide insight into genomically encoded developmental programs and the species-specific GRNs that direct animal development in previously unexplored branches of the tree of life.…”