Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability

A major goal of evolutionary developmental biology (evo-devo) is to understand how multicellular body plans of increasing complexity have evolved, and how the corresponding developmental programs are genetically encoded. It has been repeatedly argued that key to the evolution of increased body plan complexity is the modularity of the underlying developmental gene regulatory networks (GRNs). This modularity is considered essential for network robustness and evolvability. In our opinion, these ideas, appealing as they may sound, have not been sufficiently tested. Here we use computer simulations to study the evolution of GRNs' underlying body plan patterning. We select for body plan segmentation and differentiation, as these are considered to be major innovations in metazoan evolution. To allow modular networks to evolve, we independently select for segmentation and differentiation. We study both the occurrence and relation of robustness, evolvability and modularity of evolved networks. Interestingly, we observed two distinct evolutionary strategies to evolve a segmented, differentiated body plan. In the first strategy, first segments and then differentiation domains evolve (SF strategy). In the second scenario segments and domains evolve simultaneously (SS strategy). We demonstrate that under indirect selection for robustness the SF strategy becomes dominant. In addition, as a byproduct of this larger robustness, the SF strategy is also more evolvable. Finally, using a combined functional and architectural approach, we determine network modularity. We find that while SS networks generate segments and domains in an integrated manner, SF networks use largely independent modules to produce segments and domains. Surprisingly, we find that widely used, purely architectural methods for determining network modularity completely fail to establish this higher modularity of SF networks. Finally, we observe that, as a free side effect of evolving segmentation and differentiation in combination, we obtained in-silico developmental mechanisms resembling mechanisms used in vertebrate development. Author Summary: An important question in evolutionary developmental biology is how the complex organisms we see around us have evolved, and how this complexity is encoded in their DNA. An often heard statement is that the gene regulatory networks underlying developmental processes are modular; that is, different functions are carried out by largely independent network parts. It is argued that this network modularity allows both for robust functioning and evolutionary tinkering, and that selection thus produces modular networks. Here we use a simulation model for the evolution of animal body plan patterning to investigate these ideas. To allow for the evolution of modular networks we independently select for both body plan segmentation and differentiation. We find two distinct evolutionary trajectories, one in which segments evolve before domains, and one in which segments and domains evolve simultaneously. In addition, the two evolved network types also differ in terms of developmental dynamics. We show that indirect selection for robustness favors the segments first type networks. Furthermore, as a free side effect, these more robust networks are also more evolvable. Finally, we take into account both functional and architectural aspects to determine the modularity of the network types. We show that segments simultaneous networks generate segments and domains in a integrated manner, whereas segments first networks use largely independent modules to generate segments and domains. Finally, although mimicking natural developmental mechanisms was not part of our model design, the segments first developmental mechanisms resembles vertebrate axial patterning mechanisms. This resemblance arises for free, simply from considering segmentation and differentiation in combination.