Paper in “Evolution and Development” The Evolution of Signaling Pathways In Animal Development Andr é Pires-daSilva & Ralf J. Sommer Nature Reviews Genetics, January 2003 Department of Evolutionary Biology, Max-Planck-Institute für Entwicklungsbiologie, Germany

Background Knowledge The same set of seven pathways is used many times in animal development ↓ Generate so much cellular and morphological diversity

Essential Developmental Pathways Hh, Hedgehog, Wnt, Wingless related, TGF- , Transforming growth factor-  RTK, Receptor tyrosine kinase Notch, JAK/STAT, Janus kinase/signal transducer and activator of transcription Nuclear hormone pathways

Questions How a few signalling pathways can generate so much cellular and morphological diversity during the evolution and the individual development?

Properties of signaling pathways Signaling pathways are nonlinear, highly integrative biological modules. Property 1: Flexibility → generation of evolutionary novelty Property 2: Robustness → ensure reproducible outcomes of developmental processes

Signaling Flexibility: Mechanisms 1. The same receptor can activate different intracellular transducers in different tissues. 2. Differences in the kinetics of the ligand or receptor might generate distinct cellular outcomes. 3. Combinatorial activation by signaling pathways might result in the regulation of specific genes. 4. cells that express distinct transcription factors might respond differently when exposed to the same signals. 5. Compartmentalization of the signal in the cell can contribute to specificity.

a lethal-23 (LET-23) RTK signaling in C. elegans b The strength of receptor affinity for the Wnt ligand, results in the activation of alternative pathways. c Drosophila even-skipped (eve) gene contains functional binding sites for response to Wnt, TGF-  and RTK. Mutation at any of these sites abolishes eve expression.eve d In C. elegans, RTK stimulation results in vulva induction only in the hypodermis, owing to the tissue- specific expression of lineage-31. e GSK-3,its functional specificity relies on compartmentalization in the cell by cytosolic protein complexes during Wnt signaling Mechanisms of signaling specificity

Property 2 of signaling pathways : Robustness Gene network models: gene interactions for segmentation and neurogenetic networks in Drosophila embryos The interesting observation: changes in many variables can result in the same pattern of gene expression ↓ robustness Regulation mechanisms of robustness : positive- and negative-feedback loops

Aspects of the evolution of signaling pathways 1. The genetic repertoire seen in present-day species 2. The importance of the co-option of signaling pathways for the generation of morphological novelty. 3. The evolution of signaling pathways

Analysis of the evolution of signaling pathways The pre-genome era. Important findings: 1.The signaling pathways evolved before the occurrence of the bilaterians 2.The importance of gene duplication and subsequent protein sequence divergence Question 1.Evolution of signaling pathways →a prerequisite for the occurrence of animal multicellularity? “ maybe ” 2.Burst of gene duplications of signaling components→ Phylogenetic diversification of principal animal groups ? “ no ” The phylogenetic placement of organisms has important consequences on how the evolutionary pattern of signalling pathways is interpreted.

Gene duplication events do not correlate with the origin of the principal animal groups

The post-genome era. The availability of whole-genome sequences of different species Questions 1. Are there any general trends between the complexity of signaling pathways and body plans? gene expansion ; whole-genome duplication 2. Do all pathways evolve in similar ways, such as by an increase of paralogous proteins through gene duplications?

The post-genome era.

Two types of limitation restrict the findings solely on the basis of in silico analysis: 1.The most important limitation in comparing genomes and their proteins on a one-to-one level stems from the modular nature of proteins, most of which contain two or more domains. 2.A second limitation stems from the ability of gene-prediction programs to detect divergent gene sequences.

The in silico comparison of the evolution of signalling pathways allows several important conclusions 1. The evolution of these signaling systems might have been a prerequisite for the evolution of animal multicellularity. 2. Metazoan phyla differ in their number of signaling genes. 3. the availability of whole-genome sequences provides a framework for the analysis of pathway evolution.

Co-option of signaling pathways The process of re-using the existing genetic units has been termed 'co-option ‘ Co-option was originally recognized as a general principle for the evolution of transcription factors

Co-option of the Hedgehog signaling pathway for the induction of butterfly eyespots in the wing

Co-option of signaling pathways Conclusions: 1. All developmental processes that are involved in the generation of new structures require co-option events. 2. the co-option of signaling pathways and transcription factors is a common principle in animal evolution.

Case studies How do the pathways themselves evolve? Limitations of current case study: It remains unclear how many more components (often species and/or cell specific) exist.

Searching for case studies Somatic sex determination in C. elegans.

The evolution of nematode sex determination Wilkins' hypothesis, the bottom-up evolution of C. elegans sex determination, is testable by studying other nematodes. A study of more distantly related species, for which genetic tools are available that are comparable with those of C. elegans, can answer the question of how complex signaling pathways might have evolved.

Questions to be answer Correlation: the number of signaling genes → the diversification of body plans? Types of signaling pathway hamper? morphological evolution? Is the flexibility of signaling systems sufficient to explain the novelties of body plans? How are new components integrated into existing networks, and how does this change the behavior of a signaling network? How do signaling systems really evolve at the micro evolutionary level --- what type of mutations occur and how are such changes fixed in natural populations? Why do some pathways evolve faster than others?

Conclusions In all of these aspects, our understanding is far from complete. general principles in evolutionary developmental biology will emerge after a sophisticated analysis of several case studies has been carried out in selected animals. The light for answering the questions completely: whole-genome analysis

Critique Strength: directions of evolutionary developmental biology→ post genomic study The general tendency for the evolution of signaling pathways is still unclear. How did the seven types of the pathways related to each other during the evolution? Is there a co-evolution? Slight errors in Figure 2.