Molecular Systems Predict Equilibrium Distributions of Phenotype Diversity Available for Selection

Two long-standing challenges in theoretical population genetics and evolution are predicting the distribution of phenotype diversity generated by mutation and available for selection and determining the interaction of mutation, selection, and drift to characterize evolutionary equilibria and dynamics. More fundamental for enabling such predictions is the current inability to causally link population genetic parameters, selection and mutation, to the underlying molecular parameters, kinetic and thermodynamic. Such predictions would also have implications for understanding cryptic genetic variation and the role of phenotypic robustness. Here we provide a new theoretical framework for addressing these challenges. It is built on Systems Design Space methods that relate system phenotypes to genetically-determined parameters and environmentally-determined variables. These methods, based on the foundation of biochemical kinetics and the deconstruction of complex systems into rigorously defined biochemical phenotypes, provide several innovations that automate (1) enumeration of the phenotypic repertoire without knowledge of kinetic parameter values, (2) representation of phenotypic regions and their relationships in a System Design Space, and (3) prediction of values for kinetic parameters, concentrations, fluxes and global tolerances for each phenotype. We now show that these methods also automate prediction of phenotype-specific mutation rate constants and equilibrium distributions of phenotype diversity in populations undergoing steady-state exponential growth. We introduce this theoretical framework in the context of a case study involving a small molecular system, a primordial circadian clock, compare and contrast this framework with other approaches in theoretical population genetics, and discuss experimental challenges for testing predictions.