Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback

We use in silico evolution to study the generation of gene regulatory structures. A particular area of interest in evolutionary development (evo-devo) is the correspondence between gene regulatory sequences on the DNA (cis-regulatory modules, CRMs) and the spatial expression of the genes. We use computation to investigate the incorporation of new CRMs into the genome. Simulations allow us to characterize different cases of CRM to spatial pattern correspondence. Many of these cases are seen in biological examples; our simulations indicate relative advantages of the different scenarios. We find that, in the absence of specific constraints on the CRM-pattern correspondence, CRMs controlling multiple spatial domains tend to evolve very quickly. Genes constrained to a one-to-one CRM-pattern domain correspondence evolve more slowly. Of these, systems in which pattern domains appear in a particular order in evolution, as in insect segmentation mechanisms, take the longest time in in silico evolutionary searches. For biological cases of this type, it is likely that other selective advantages outweigh the time costs.