From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Abstract

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves into a critical and constructive attitude in our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.

arXiv comment111 pages, 11 figures uses elsarticle latex class

References in corpus (37)

• Catastrophic cascade of failures in interdependent networks
• Robustness of a Network of Networks
• Why Do Proteins Look Like Proteins?
• Neutral Evolution of Mutational Robustness
• Degeneracy: a design principle for achieving robustness and evolvability
• Synchronization of interconnected networks: the role of connector nodes
• Thermodynamics of Neutral Protein Evolution
• The context-dependence of mutations: a linkage of formalisms
• Successful strategies for competing networks
• Structural Determinant of Protein Designability
• CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data
• The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima
• Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer Progression
• Inferring fitness landscapes by regression produces biased estimates of epistasis
• Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability
• Protein folding and binding can emerge as evolutionary spandrels through structural coupling
• Physical epistatic landscape of antibody binding affinity
• A first-principles model of early evolution: Emergence of gene families, species and preferred protein folds
• Congruent evolution of genetic and environmental robustness in microRNA
• On the networked architecture of genotype spaces and its critical effects on molecular evolution
• Biophysical Fitness Landscapes for Transcription Factor Binding Sites
• Evolutionary Dynamics in a Simple Model of Self-Assembly
• Genotypic complexity of Fisher's geometric model
• Epistasis can lead to fragmented neutral spaces and contingency in evolution
• Complete RNA inverse folding: computational design of functional hammerhead ribozymes
• Distribution of phenotype sizes in sequence-to-structure genotype-phenotype maps
• Evolution of molecular phenotypes under stabilizing selection
• 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
• The Effect of Recombination on the Neutral Evolution of Genetic Robustness
• toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map
• Emergence of species in evolutionary simulated annealing
• Evolutionary stochastic dynamics of speciation and a simple genotype-phenotype map for protein binding DNA
• Robustness and epistasis in mutation-selection models
• Recombination and mutational robustness in neutral fitness landscapes
• Protein Ground State Candidates in a Simple Model: An Exact Enumeration
• Enumerating secondary structures and structural moieties for circular RNAs

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• Phenotypic-dependent variability and the emergence of tolerance in bacterial populations
• Evolutionary accessibility of random and structured fitness landscapes
• Dynamical Theory for Adaptive Systems
• Statistical Genetics in and out of Quasi-Linkage Equilibrium (Extended)
• Entropic contribution to phenotype fitness
• Why flatness does and does not correlate with generalization for deep neural networks
• Complexity and accessibility of random landscapes
• Information-theoretic characterization of the complete genotype-phenotype map of a complex pre-biotic world
• Eco-evolutionary constraints for the endemicity of rapidly evolving viruses
• Genotype networks drive oscillating endemicity and epidemic trajectories in viral evolution
• Functional bottlenecks can emerge from non-epistatic underlying traits