Structural properties of genotype–phenotype maps

The map between genotype and phenotype is fundamental to biology. Biological information is stored and passed on in the form of genotypes, and expressed in the form of phenotypes. A growing body of literature has examined a wide range of genotype–phenotype (GP) maps and has established a number of properties that appear to be shared by many GP maps. These properties are ‘structural’ in the sense that they are properties of the distribution of phenotypes across the point-mutation network of genotypes. They include: a redundancy of genotypes, meaning that many genotypes map to the same phenotypes, a highly non-uniform distribution of the number of genotypes per phenotype, a high robustness of phenotypes and the ability to reach a large number of new phenotypes within a small number of mutational steps. A further important property is that the robustness and evolvability of phenotypes are positively correlated. In this review, I give an overview of the study of GP maps with particular emphasis on these structural properties, and discuss a model that attempts to explain why these properties arise, as well as some of the fundamental ways in which the structure of GP maps can affect evolutionary outcomes.

[1]  Naturforschender Verein in Brünn.,et al.  Verhandlungen des naturforschenden Vereines in Brünn. , 1876 .

[2]  N. Pierce Origin of Species , 1914, Nature.

[3]  R. Fisher XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance. , 1919, Transactions of the Royal Society of Edinburgh.

[4]  W. E. Ritter AS TO THE CAUSES OF EVOLUTION. , 1923, Science.

[5]  J. Haldane,et al.  The Causes of Evolution , 1933 .

[6]  M. Kimura Evolutionary Rate at the Molecular Level , 1968, Nature.

[7]  FRANK B. SALISBURY,et al.  Natural Selection and the Complexity of the Gene , 1969, Nature.

[8]  John Maynard Smith,et al.  Natural Selection and the Concept of a Protein Space , 1970, Nature.

[9]  J. Crow The genetic basis of evolutionary change , 1975 .

[10]  K. Dill Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[11]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .

[12]  D. Lipman,et al.  Modelling neutral and selective evolution of protein folding , 1991, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[13]  Yoh Iwasa,et al.  Free fitness that always increases in evolution. , 1988, Journal of theoretical biology.

[14]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[15]  N. Wingreen,et al.  Emergence of Preferred Structures in a Simple Model of Protein Folding , 1996, Science.

[16]  R. Schaller,et al.  Moore's law: past, present and future , 1997 .

[17]  Dorothea Heiss-Czedik,et al.  An Introduction to Genetic Algorithms. , 1997, Artificial Life.

[18]  M. Karplus,et al.  Protein Folding: A Perspective from Theory and Experiment , 1998 .

[19]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[20]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[21]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[22]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[23]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[24]  Sarah A. Teichmann,et al.  3D Complex: A Structural Classification of Protein Complexes , 2006, PLoS Comput. Biol..

[25]  P. Schuster Prediction of RNA secondary structures: from theory to models and real molecules , 2006 .

[26]  Andreas Wagner,et al.  Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology , 2007, PLoS Comput. Biol..

[27]  A. Wagner Robustness and evolvability: a paradox resolved , 2008, Proceedings of the Royal Society B: Biological Sciences.

[28]  A. Wagner,et al.  Innovation and robustness in complex regulatory gene networks , 2007, Proceedings of the National Academy of Sciences.

[29]  Richard A Goldstein,et al.  The structure of protein evolution and the evolution of protein structure. , 2008, Current opinion in structural biology.

[30]  Eric L. Miller,et al.  The Ascent of the Abundant: How Mutational Networks Constrain Evolution , 2008, PLoS Comput. Biol..

[31]  Elhanan Borenstein,et al.  An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution , 2008, PLoS Comput. Biol..

[32]  Venky N. Iyer,et al.  Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation , 2008, PLoS genetics.

[33]  Andreas Wagner,et al.  Neutral network sizes of biological RNA molecules can be computed and are not atypically small , 2008, BMC Bioinformatics.

[34]  Andreas Wagner,et al.  Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks , 2009, PLoS Comput. Biol..

[35]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[36]  A. Wagner,et al.  Evolutionary Innovations and the Organization of Protein Functions in Genotype Space , 2010, PloS one.

[37]  Timothy R Hughes,et al.  Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. , 2010, Trends in genetics : TIG.

[38]  J. Doye,et al.  Self-assembly, modularity, and physical complexity. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[39]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[40]  Mark Newman,et al.  Networks: An Introduction , 2010 .

[41]  A. Wagner,et al.  Evolvability and robustness in a complex signalling circuit. , 2011, Molecular bioSystems.

[42]  Javier M. Buldú,et al.  Correction: Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks , 2011, PLoS ONE.

[43]  Sebastian E Ahnert,et al.  Evolutionary dynamics in a simple model of self-assembly. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[44]  Andreas Wagner,et al.  A comparison of genotype-phenotype maps for RNA and proteins. , 2012, Biophysical journal.

[45]  Joshua L. Payne,et al.  Constraint and Contingency in Multifunctional Gene Regulatory Circuits , 2013, PLoS Comput. Biol..

[46]  Helmut Schiessel,et al.  Exact enumeration of Hamiltonian walks on the 4 × 4 × 4 cube and applications to protein folding , 2013 .

[47]  Susanna Manrubia,et al.  toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map , 2014, Scientific Reports.

[48]  Joshua L. Payne,et al.  The Robustness and Evolvability of Transcription Factor Binding Sites , 2014, Science.

[49]  Jason H. Moore,et al.  Robustness, Evolvability, and the Logic of Genetic Regulation , 2014, Artificial Life.

[50]  Joshua L. Payne,et al.  Latent phenotypes pervade gene regulatory circuits , 2014, BMC Systems Biology.

[51]  Iain G. Johnston,et al.  A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure , 2014, Journal of The Royal Society Interface.

[52]  Ard A. Louis,et al.  The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima , 2014, PloS one.

[53]  E. Ibáñez-Marcelo,et al.  The topology of robustness and evolvability in evolutionary systems with genotype-phenotype map. , 2014, Journal of theoretical biology.

[54]  S. Ahnert,et al.  The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps , 2015, Journal of The Royal Society Interface.

[55]  Joshua L. Payne,et al.  Function does not follow form in gene regulatory circuits , 2015, Scientific Reports.

[56]  S. Teichmann,et al.  Principles of assembly reveal a periodic table of protein complexes , 2015, Science.

[57]  Kamaludin Dingle,et al.  The structure of the genotype–phenotype map strongly constrains the evolution of non-coding RNA , 2015, Interface Focus.

[58]  Sebastian E. Ahnert,et al.  Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability , 2015, PLoS Comput. Biol..

[59]  L. Penrose,et al.  THE CORRELATION BETWEEN RELATIVES ON THE SUPPOSITION OF MENDELIAN INHERITANCE , 2022 .