The mechanisms underpinning the evolution of new and complex phenotypes is a difficult and outstanding question in biology. Until recently, the tools required for a sophisticated understanding of genotype to phenotype relationship dictated that only model organisms could be compared. The current progress in genetic manipulation and live imaging has made it possible to appraise a far wider diversity of organisms. In parallel, functional genomics has highlighted how change and reorganization of the genome regulatory landscape could generate cell-type and morphological innovations, highlighting new paths and constraints for evolutionary change. The breadth of new experimental systems is revealing innovations in gene regulation and molecular mechanisms and challenging some of our fundamental assumptions about evolution and developmental biology. We think this joint meeting is an excellent opportunity to re-address this enduring question.