On the networked architecture of genotype spaces and its critical effects on molecular evolution

Abstract

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at the macroevolutionary, ecological, and molecular level. Actually, when the complex architecture of genotype spaces is taken into account, the evolutionary dynamics of molecular populations becomes intrinsically non-uniform, sharing deep qualitative and quantitative similarities with slowly driven physical systems: non-linear responses analogous to critical transitions, sudden state changes, or hysteresis, among others. Furthermore, the phenotypic plasticity inherent to genotypes transforms classical fitness landscapes into multiscapes where adaptation in response to an environmental change may be very fast. The quantitative nature of adaptive molecular processes is deeply dependent on a networks-of-networks multilayered structure of the map from genotype to function that we begin to unveil.

arXiv comment48 pages, 4 figures

References in corpus (28)

• Catastrophic cascade of failures in interdependent networks
• Multilayer Networks
• The structure and dynamics of multilayer networks
• Robustness of a Network of Networks
• Why Do Proteins Look Like Proteins?
• Neutral Evolution of Mutational Robustness
• Evolution of public cooperation on interdependent networks: The impact of biased utility functions
• Epidemic spreading on interconnected networks
• Analysis of complex contagions in random multiplex networks
• Neutral genetic drift can aid functional protein evolution
• Synchronization of interconnected networks: the role of connector nodes
• Thermodynamics of Neutral Protein Evolution
• Are there laws of genome evolution?
• Successful strategies for competing networks
• The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima
• Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability
• Evolutionary Dynamics in a Simple Model of Self-Assembly
• Synchronization in interdependent networks
• Distribution of phenotype sizes in sequence-to-structure genotype-phenotype maps
• Evolution on neutral networks accelerates the ticking rate of the molecular clock
• Statistical theory of phenotype abundance distributions: a test through exact enumeration of genotype spaces
• toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map
• Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory
• Stronger selection can slow down evolution driven by recombination on a smooth fitness landscape
• Epidemics on Interconnected Networks
• Enumerating Designing Sequences in the HP Model
• Eigenvalues of neutral networks: interpolating between hypercubes
• RNAiFold2T: Constraint Programming design of thermo-IRES switches

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• Using quantum annealing to design lattice proteins
• From Spectra to Localized Networks: A Reverse Engineering Approach
• Entropic contribution to phenotype fitness
• Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes
• Epistasis between cultural traits drives paradigm shifts in cultural evolution