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

Author

Manrubia, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F., García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., and Weiß, Marcel

Subjects
Quantitative Biology - Populations and Evolution, Physics - Biological Physics
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., Comment: 111 pages, 11 figures uses elsarticle latex class

Published
2020
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3. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Author

Manrubia, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F., García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., and Weiß, Marcel

Published
2021
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4. Robust genetic codes enhance protein evolvability.

Author

Rozhoňová, Hana, Martí-Gómez, Carlos, McCandlish, David M., and Payne, Joshua L.

Subjects
GENETIC code, BIOLOGICAL evolution, GENETIC engineering, BIOENGINEERING, AMINO acid sequence, PROTEIN engineering, SYNTHETIC biology
Abstract

The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein evolvability—the ability of mutation to bring forth adaptive variation in protein function. One of the most striking features of the standard genetic code is its robustness to mutation, yet it remains an open question whether such robustness facilitates or frustrates protein evolvability. To answer this question, we use data from massively parallel sequence-to-function assays to construct and analyze 6 empirical adaptive landscapes under hundreds of thousands of rewired genetic codes, including those of codon compression schemes relevant to protein engineering and synthetic biology. We find that robust genetic codes tend to enhance protein evolvability by rendering smooth adaptive landscapes with few peaks, which are readily accessible from throughout sequence space. However, the standard genetic code is rarely exceptional in this regard, because many alternative codes render smoother landscapes than the standard code. By constructing low-dimensional visualizations of these landscapes, which each comprise more than 16 million mRNA sequences, we show that such alternative codes radically alter the topological features of the network of high-fitness genotypes. Whereas the genetic codes that optimize evolvability depend to some extent on the detailed relationship between amino acid sequence and protein function, we also uncover general design principles for engineering nonstandard genetic codes for enhanced and diminished evolvability, which may facilitate directed protein evolution experiments and the bio-containment of synthetic organisms, respectively. Only "one in a million" possible genetic codes are as robust as the standard genetic code, but does this robustness accelerate or impede adaptive evolution? This study uses experimental data from six massively parallel sequence-to-function assays for four proteins to show that robust genetic codes enhance protein evolvability by producing smooth adaptive landscapes with few peaks. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Direct, physically motivated derivation of triggering probabilities for spreading processes on generalized random networks

Author

Harris, Kameron Decker, Payne, Joshua L., and Dodds, Peter Sheridan

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Physics - Physics and Society
Abstract

We derive a general expression for the probability of global spreading starting from a single infected seed for contagion processes acting on generalized, correlated random networks. We employ a simple probabilistic argument that encodes the spreading mechanism in an intuitive, physical fashion. We use our approach to directly and systematically obtain triggering probabilities for contagion processes acting on a collection of random network families including bipartite random networks. We find the contagion condition, the location of the phase transition into an endemic state, from an expansion about the disease-free state., Comment: 7 pages, 2 figures, 1 table

Published
2011

8. Exact solutions for social and biological contagion models on mixed directed and undirected, degree-correlated random networks

Author

Payne, Joshua L., Harris, Kameron Decker, and Dodds, Peter Sheridan

Subjects
Physics - Physics and Society, Condensed Matter - Disordered Systems and Neural Networks, Computer Science - Social and Information Networks
Abstract

We derive analytic expressions for the possibility, probability, and expected size of global spreading events starting from a single infected seed for a broad collection of contagion processes acting on random networks with both directed and undirected edges and arbitrary degree-degree correlations. Our work extends previous theoretical developments for the undirected case, and we provide numerical support for our findings by investigating an example class of networks for which we are able to obtain closed-form expressions., Comment: 10 pages, 3 figures

Published
2011
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9. Direct, physically-motivated derivation of the contagion condition for spreading processes on generalized random networks

Author

Dodds, Peter Sheridan, Harris, Kameron Decker, and Payne, Joshua L.

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Computer Science - Social and Information Networks, Physics - Physics and Society
Abstract

For a broad range single-seed contagion processes acting on generalized random networks, we derive a unifying analytic expression for the possibility of global spreading events in a straightforward, physically intuitive fashion. Our reasoning lays bare a direct mechanical understanding of an archetypal spreading phenomena that is not evident in circuitous extant mathematical approaches., Comment: 4 pages, 1 figure, 1 table

Published
2011

10. Analysis of a threshold model of social contagion on degree-correlated networks

Author

Dodds, Peter Sheridan and Payne, Joshua L.

Subjects
Physics - Physics and Society
Abstract

We analytically determine when a range of abstract social contagion models permit global spreading from a single seed on degree-correlated random networks. We deduce the expected size of the largest vulnerable component, a network's tinderbox-like critical mass, as well as the probability that infecting a randomly chosen individual seed will trigger global spreading. In the appropriate limits, our results naturally reduce to standard ones for models of disease spreading and to the condition for the existence of a giant component. Recent advances in the distributed, infinite seed case allow us to further determine the final size of global spreading events, when they occur. To provide support for our results, we derive exact expressions for key spreading quantities for a simple yet rich family of random networks with bimodal degree distributions., Comment: 7 Pages, 1 figure, submitted to Phys. Rev. E

Published
2009
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22. Robustness, Evolvability, and Accessibility in Linear Genetic Programming

Author

Hu, Ting, Payne, Joshua L., Banzhaf, Wolfgang, Moore, Jason H., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Silva, Sara, editor, Foster, James A., editor, Nicolau, Miguel, editor, Machado, Penousal, editor, and Giacobini, Mario, editor

Published
2011
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23. The long and winding road to understanding organismal construction: Reply to comments on 'From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics'

Author

Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo, Ahnert, Sebastian E, Altenberg, Lee, Cano, Alejandro V, Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F, García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S, Krug, Joachim, Louis, Ard A, Martin, Nora S, Payne, Joshua L, Tarnowski, Matthew J, Weiß, Marcel, Theoretical Biology and Bioinformatics, and Sub Theoretical Biology

Subjects
Genotype, Taverne, Biological Evolution
Published
2022

27. Sexual Recombination in Self-Organizing Interaction Networks

Author

Payne, Joshua L., Moore, Jason H., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Di Chio, Cecilia, editor, Cagnoni, Stefano, editor, Cotta, Carlos, editor, Ebner, Marc, editor, Ekárt, Anikó, editor, Esparcia-Alcazar, Anna I., editor, Goh, Chi-Keong, editor, Merelo, Juan J., editor, Neri, Ferrante, editor, Preuß, Mike, editor, Togelius, Julian, editor, and Yannakakis, Georgios N., editor

Published
2010
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29. The long and winding road to understanding organismal construction: Reply to comments on 'From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics'

Author

Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo, Ahnert, Sebastian E, Altenberg, Lee, Cano, Alejandro V, Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F, García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S, Krug, Joachim, Louis, Ard A, Martin, Nora S, Payne, Joshua L, Tarnowski, Matthew J, Weiß, Marcel, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo, Ahnert, Sebastian E, Altenberg, Lee, Cano, Alejandro V, Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F, García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S, Krug, Joachim, Louis, Ard A, Martin, Nora S, Payne, Joshua L, Tarnowski, Matthew J, and Weiß, Marcel

Published
2022

30. The long and winding road to understanding organismal construction Reply to comments on From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics comment

Author

Manrubia, Susanna, Cuesta, Jose A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalan, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F., Garcia-Martin, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., Weiss, Marcel, Manrubia, Susanna, Cuesta, Jose A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalan, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F., Garcia-Martin, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., and Weiss, Marcel

Published
2022

31. The long and winding road to understanding organismal construction: Reply to comments on “From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics”

Author

Manrubia Cuevas, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Díaz-Uriarte, Ramón, Elena, Santiago F., García-Martín, Juan A., Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., Weiß, Marcel, Manrubia Cuevas, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Díaz-Uriarte, Ramón, Elena, Santiago F., García-Martín, Juan A., Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., and Weiß, Marcel

Published
2022

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

Author

Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo, Ahnert, Sebastian E, Altenberg, Lee, Cano, Alejandro V, Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F, García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S, Krug, Joachim, Louis, Ard A, Martin, Nora S, Payne, Joshua L, Tarnowski, Matthew J, Weiß, Marcel, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo, Ahnert, Sebastian E, Altenberg, Lee, Cano, Alejandro V, Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F, García-Martín, Juan Antonio, Hogeweg, Paulien, Khatri, Bhavin S, Krug, Joachim, Louis, Ard A, Martin, Nora S, Payne, Joshua L, Tarnowski, Matthew J, and Weiß, Marcel

Published
2021

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

Author

Engineering and Physical Sciences Research Council (UK), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Ministerio de Economía y Competitividad (España), Gatsby Charitable Foundation, Foundational Questions Institute, Fetzer Institute, Silicon Valley Community Foundation, Stanford University, The Ohio State University, National Science Foundation (US), Generalitat Valenciana, Fundación Ramón Areces, German Research Foundation, Gates Cambridge Scholarships, Winton Foundation, Swiss National Science Foundation, Biotechnology and Biological Sciences Research Council (UK), Manrubia Cuevas, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Díaz-Uriarte, Ramón, Elena, Santiago F., García-Martín, Juan A., Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., Weiß, Marcel, Engineering and Physical Sciences Research Council (UK), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Ministerio de Economía y Competitividad (España), Gatsby Charitable Foundation, Foundational Questions Institute, Fetzer Institute, Silicon Valley Community Foundation, Stanford University, The Ohio State University, National Science Foundation (US), Generalitat Valenciana, Fundación Ramón Areces, German Research Foundation, Gates Cambridge Scholarships, Winton Foundation, Swiss National Science Foundation, Biotechnology and Biological Sciences Research Council (UK), Manrubia Cuevas, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Díaz-Uriarte, Ramón, Elena, Santiago F., García-Martín, Juan A., Hogeweg, Paulien, Khatri, Bhavin S., Krug, Joachim, Louis, Ard A., Martin, Nora S., Payne, Joshua L., Tarnowski, Matthew J., and Weiß, Marcel

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 with a critical and constructive attitude into 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.

Published
2021

49. The causes of evolvability and their evolution

Author

Payne, Joshua L, Wagner, Andreas, Payne, Joshua L, and Wagner, Andreas

Abstract

Evolvability is the ability of a biological system to produce phenotypic variation that is both heritable and adaptive. It has long been the subject of anecdotal observations and theoretical work. In recent years, however, the molecular causes of evolvability have been an increasing focus of experimental work. Here, we review recent experimental progress in areas as different as the evolution of drug resistance in cancer cells and the rewiring of transcriptional regulation circuits in vertebrates. This research reveals the importance of three major themes: multiple genetic and non-genetic mechanisms to generate phenotypic diversity, robustness in genetic systems, and adaptive landscape topography. We also discuss the mounting evidence that evolvability can evolve and the question of whether it evolves adaptively.

Published
2019

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