Dynamical Modularity of the Genotype-Phenotype Map

An organism’s phenotype can be thought of as consisting of a set of discrete traits, able to evolve relatively independently of each other. This implies that the developmental processes generating these traits—the underlying genotype-phenotype map—must also be functionally organised in a modular manner. The genotype-phenotype map lies at the heart of evolutionary systems biology. Recently, it has become popular to define developmental modules in terms of the structure of gene regulatory networks. This approach is inherently limited: gene networks often do not have structural modularity. More generally, the connection between structure and function is quite loose. In this chapter, we discuss an alternative approach based on the concept of dynamical modularity, which overcomes many of the limitations of structural modules. A dynamical module consists of the activities of a set of genes and their interactions that generate a specific dynamic behaviour. These modules can be identified and characterised by phase-space analysis of data-driven models. We showcase the power and the promise of this new approach using several case studies. Dynamical modularity forms an important component of a general theory of the evolution of regulatory systems and the genotype-phenotype map they define.