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Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution.
Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans,
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A comparison of genotype-phenotype maps for RNA and proteins,
E. Ferrada, A. Wagner, · 1925
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R. A. Fisher, The genetical theory of natural selection, Clarendon Press, Oxford, 1930
1930
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The roles of mutation, inbreeding, crossbreeding and selection in evolution,
S. Wright, · 1932
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Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome,
B. A. Blount, G.-O. F. Gowers, J. C. H. Ho, R. Ledesma-Amaro, D. Jovicevic, R. M. McKiernan, Z. X. Xie, B. Z. Li, Y. J. Yuan, T. Ellis, · 1932
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Studies on hybrid sterility. ii. localization of sterility factors in drosophila pseudoobscura hybrids,
T. Dobzhansky, · 1936
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Isolating mechanisms, evolution and temperature,
H. Muller, · 1942
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Natural selection and the complexity of the gene,
F. B. Salisbury, · 1969
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Natural selection and the concept of a protein space,
J. Maynard Smith, · 1970
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Potato spindle tuber “virus”: IV. A replicating, low molecular weight rna,
T. O. Diener, · 1971
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Perspective: Evolution and detection of genetic robustness,
J. A. G. de Visser, J. Hermisson, G. P. Wagner, L. A. Meyers, H. Bagheri-Chaichian, J. L. Blanchard, L. Chao, J. M. Cheverud, S. F. Elena, W. Fontana, G. Gibson, T. F. Hansen, D. Krakauer, R. C. Lewontin, C. Ofria, S. H. Rice, G. v. Dassow, A. Wagner, M. C. Whitlock, · 1972
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The importance of molecular hierarchy in information processing,
M. Conrad, · 1972
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Enzyme recruitment in evolution of new function,
R. A. Jensen, · 1976
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Thresholds and breakpoints in ecosystems with a multiplicity of stable states,
R. M. May, · 1977
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Selection differentials and selection coefficients,
R. Milkman, · 1978
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Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination,
A. S. Perelson, G. F. Oster, · 1979
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Effective deme sizes during long-term evolution estimated from rates of chromosomal rearrangement,
R. Lande, · 1979
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Bootstrapping on the adaptive landscape,
M. Conrad, · 1979
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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information,
M. Zuker, P. Stiegler, · 1981
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Genetic revolutions, founder effects, and speciation,
N. H. Barton, B. Charlesworth, · 1984
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Expected time for random genetic drift of a population between stable phenotypic states,
R. Lande, · 1985
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The RNA world,
W. Gilbert, · 1986
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The frequency of shifts between alternative equilibria,
N. Barton, S. Rouhani, · 1987
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Free fitness that always increases in evolution,
Y. Iwasa, · 1988
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Multiplex DNA sequencing,
G. M. Church, S. Kieffer-Higgins, · 1988
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The equilibrium partition function and base pair binding probabilities for rna secondary structure,
J. S. McCaskill, · 1990
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Modelling neutral and selective evolution of protein folding,
D. J. Lipman, W. J. Wilbur, · 1991
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From genes to phenotype: dynamical systems and evolvability,
P. Alberch, · 1991
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Spiral wave structure in pre-biotic evolution: hypercycles stable against parasites,
M. C. Boerlijst, P. Hogeweg, · 1991
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Statistics of rna secondary structures,
W. Fontana, D. A. Konings, P. F. Stadler, P. Schuster, · 1993
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From sequences to shapes and back: A case study in RNA secondary structures,
P. Schuster, W. Fontana, P. F. Stadler, I. L. Hofacker, · 1994
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Fast folding and comparison of RNA secondary structures,
I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster, · 1994
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Pattern generation in molecular evolution: exploitation of the variation in rna landscapes,
M. A. Huynen, P. Hogeweg, · 1994
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The evolution of functionally novel proteins after gene duplication,
A. L. Hughes, · 1994
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Genome growth and the evolution of the genotype-phenotype map,
L. Altenberg, · 1995
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Exploring phenotype space through neutral evolution,
M. A. Huynen, · 1996
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Emergence of preferred structures in a simple model of protein folding,
H. Li, R. Helling, C. Tang, N. Wingreen, · 1996
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How to derive a protein folding potential? a new approach to an old problem,
L. A. Mirny, E. I. Shakhnovich, · 1996
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Smoothness within ruggedness: The role of neutrality in adaptation,
M. A. Huynen, P. F. Stadler, W. Fontana, · 1996
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Generic properties of combinatory maps: Neutral networks of RNA secondary structures,
C. Reidys, P. F. Stadler, P. Schuster, · 1997
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Mass survival of birds across the cretaceous-tertiary boundary: molecular evidence,
A. Cooper, D. Penny, · 1997
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Test of synergistic interactions among deleterious mutations in bacteria,
S. F. Elena, R. E. Lenski, · 1997
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Evolution and speciation on holey adaptive landscapes,
S. Gavrilets, · 1997
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Continuity in evolution: on the nature of transitions,
W. Fontana, P. Schuster, · 1998
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Shaping space: The possible and the attainable in RNA genotype-phenotype mapping,
W. Fontana, P. Schuster, · 1998
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The evolutionary genetics of speciation,
J. A. Coyne, H. A. Orr, · 1998
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Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins,
P. Závodszky, J. Kardos, A. Svingor, G. A. Petsko, · 1998
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Protein ground state candidates in a simple model: An enumeration study,
V. Shahrezaei, N. Hamedani, M. R. Ejtehadi, · 1999
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Effect of alphabet size and foldability requirements on protein structure designability,
N. E. G. Buchler, R. A. Goldstein, · 1999
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Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure,
D. H. Mathews, J. Sabina, M. Zuker, D. H. Turner, · 1999
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Complete suboptimal folding of RNA and the stability of secondary structures,
S. Wuchty, W. Fontana, I. L. Hofacker, P. Schuster, · 1999
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Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space,
E. Bornberg-Bauer, H. S. Chan, · 1999
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Neutral evolution of mutational robustness,
E. van Nimwegen, J. P. Crutchfield, M. Huynen, · 1999
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Inferring tree models for oncogenesis from comparative genome hybridization data,
R. Desper, F. Jiang, O.-P. Kallioniemi, H. Moch, C. H. Papadimitriou, A. A. Schäffer, · 1999
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On the possibility of constructive neutral evolution,
A. Stoltzfus, · 1999
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Preservation of duplicate genes by complementary, degenerative mutations,
A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan, J. Postlethwait, · 1999
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One sequence, two ribozymes: implications for the emergence of new ribozyme folds,
E. A. Schultes, D. P. Bartel, · 2000
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Plasticity, evolvability, and modularity in RNA,
L. W. Ancel, W. Fontana, · 2000
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Estimate of the mutation rate per nucleotide in humans,
M. W. Nachman, S. L. Crowell, · 2000
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Rapid speciation via parallel, directional selection on regulatory genetic pathways,
N. A. Johnson, A. H. Porter, · 2000
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Adaptive evolution on neutral networks,
C. O. Wilke, · 2001
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Replication and mutation on neutral networks,
C. M. Reidys, C. V. Forst, P. F. Stadler, · 2001
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Catastrophic shifts in ecosystems,
M. Scheffer, S. Carpenter, J. A. Foley, C. Folke, B. Walker, · 2001
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Evolution of digital organisms at high mutation rates leads to survival of the flattest,
C. O. Wilke, J. L. Wang, C. Ofria, R. E. Lenski, C. Adami, · 2001
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Phylogenetics and speciation,
T. G. Barraclough, S. Nee, · 2001
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Inferring speciation rates from phylogenies,
S. Nee, · 2001
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Developmental system drift and flexibility in evolutionary trajectories,
J. R. True, E. S. Haag, · 2001
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Toward a new synthesis: population genetics and evolutionary developmental biology,
N. A. Johnson, A. H. Porter, · 2001
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Direct estimate of the mutation rate and the distribution of fitness effects in the yeast Saccharomyces cerevisiae,
D. M. Wloch, K. Szafraniec, R. H. Borts, R. Korona, · 2001
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Multidimensional epistasis and the disadvantage of sex,
F. A. Kondrashov, A. S. Kondrashov, · 2001
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S. J. Gould, The structure of evolutionary theory, Harvard University Press, 2002
2002
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Enumerating designing sequences in the HP model,
A. Irbäck, C. Troein, · 2002
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Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix,
H. Li, C. Tang, N. S. Wingreen, · 2002
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Roles of mutation and recombination in the evolution of protein thermodynamics,
Y. Xia, M. Levitt, · 2002
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Gene location and bacterial sequence divergence,
A. Mira, H. Ochman, · 2002
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Modelling ‘evo-devo’ with RNA,
W. Fontana, · 2002
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Why are proteins marginally stable?,
D. M. Taverna, R. A. Goldstein, · 2002
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The evolution of evolvability,
R. Dawkins, · 2003
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Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution,
U. Bastolla, M. Porto, H. E. Roman, M. Vendruscolo, · 2003
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Structural determinant of protein designability,
J. L. England, E. I. Shakhnovich, · 2003
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How the global structure of protein interaction networks evolves,
A. Wagner, · 2003
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Transcription-associated mutational asymmetry in mammalian evolution,
P. Green, B. Ewing, W. Miller, P. J. Thomas, N. C. S. Program, E. D. Green, · 2003
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Evolution’s cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes,
W. J. Kent, R. Baertsch, A. Hinrichs, W. Miller, D. Haussler, · 2003
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Organismal complexity, protein complexity, and gene duplicability,
J. Yang, R. Lusk, W.-H. Li, · 2003
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Avida: A software platform for research in computational evolutionary biology,
C. Ofria, C. O. Wilke, · 2004
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Adaptive evolution of transcription factor binding sites,
J. Berg, S. Willmann, M. Lässig, · 2004
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Rates of evolution of hybrid inviability in birds and mammals,
B. M. Fitzpatrick, · 2004
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The contribution of epistasis to the architecture of fitness in an rna virus,
R. Sanjuán, A. Moya, S. F. Elena, · 2004
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Evidence for positive epistasis in hiv-1,
S. Bonhoeffer, C. Chappey, N. T. Parkin, J. M. Whitcomb, C. J. Petropoulos, · 2004
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Modularity in evolution: Some low-level questions,
L. Altenberg, · 2004
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The’evolvability’of promiscuous protein functions,
A. Aharoni, L. Gaidukov, O. Khersonsky, S. M. Gould, C. Roodveldt, D. S. Tawfik, · 2005
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Compact and ordered collapse of randomly generated rna sequences,
E. A. Schultes, A. Spasic, U. Mohanty, D. P. Bartel, · 2005
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A. Wagner, Robustness and evolvability in living systems, Princeton University Press, Princeton, NJ, 2005
2005
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Accessibility between neutral networks in indirect genotype-phenotype mappings,
P. K. Lehre, P. C. Haddow, · 2005
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An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus,
D. R. Rokyta, P. Joyce, S. B. Caudle, H. A. Wichman, · 2005
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The application of statistical physics to evolutionary biology,
G. Sella, A. E. Hirsh, · 2005
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Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies,
V. Mustonen, M. Lässig, · 2005
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The biochemical architecture of an ancient adaptive landscape,
M. Lunzer, S. P. Miller, R. Felsheim, A. M. Dean, · 2005
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Perspective: sign epistasis and genetic constraint on evolutionary trajectories,
D. M. Weinreich, R. A. Watson, L. Chao, · 2005
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Evolution of genetic potential,
L. A. Meyers, F. D. Ancel, M. Lachmann, · 2005
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Spontaneous evolution of modularity and network motifs,
N. Kashtan, U. Alon, · 2005
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Genotype-phenotype maps,
P. F. Stadler, B. M. R. Stadler, · 2006
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Prediction of RNA secondary structures: from theory to models and real molecules,
P. Schuster, · 2006
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Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet,
E. Shakhnovich, · 2006
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Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories,
S. Smit, M. Yarus, R. Knight, · 2006
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Direct evolution of genetic robustness in microrna,
E. Borenstein, E. Ruppin, · 2006
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Balancing robustness and evolvability,
R. E. Lenski, J. E. Barrick, C. Ofria, · 2006
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Sexual reproduction selects for robustness and negative epistasis in artificial gene networks,
R. B. Azevedo, R. Lohaus, S. Srinivasan, K. K. Dang, C. L. Burch, · 2006
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Darwinian evolution can follow only very few mutational paths to fitter proteins,
D. M. Weinreich, N. F. Delaney, M. A. DePristo, D. L. Hartl, · 2006
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Quantifying antagonistic epistasis in a multifunctional rna secondary structure of the rous sarcoma virus,
R. Sanjuán, · 2006
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Robustness and evolvability: a paradox resolved,
A. Wagner, · 2007
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Robustness can evolve gradually in complex regulatory gene networks with varying topology,
S. Ciliberti, O. C. Martin, A. Wagner, · 2007
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Innovation and robustness in complex regulatory gene networks,
S. Ciliberti, O. C. Martin, A. Wagner, · 2007
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A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds,
K. B. Zeldovich, P. Chen, B. E. Shakhnovich, E. I. Shakhnovich, · 2007
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frnadb: a platform for mining/annotating functional rna candidates from non-coding rna sequences,
T. Kin, K. Yamada, G. Terai, H. Okida, Y. Yoshinari, Y. Ono, A. Kojima, Y. Kimura, T. Komori, K. Asai, · 2007
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Phenotypic complexity and local variations in neutral degree,
P. K. Lehre, P. C. Haddow, · 2007
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The distribution of fitness effects of new mutations,
A. Eyre-Walker, P. D. Keightley, · 2007
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Protein stability imposes limits on organism complexity and speed of molecular evolution,
K. B. Zeldovich, P. Chen, E. I. Shakhnovich, · 2007
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Thermodynamics of neutral protein evolution,
J. D. Bloom, A. Raval, C. O. Wilke, · 2007
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Evolution of functional diversification within quasispecies,
E. S. Colizzi, P. Hogeweg, · 2007
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The biological Big Bang model for the major transitions in evolution,
E. V. Koonin, · 2007
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Empirical fitness landscapes reveal accessible evolutionary paths,
F. J. Poelwijk, D. J. Kiviet, D. M. Weinreich, S. J. Tans, · 2007
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Distribution of fitness and virulence effects caused by single-nucleotide substitutions in tobacco etch virus,
P. Carrasco, F. de la Iglesia, S. F. Elena, · 2007
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Distributions of epistasis in microbes fit predictions from a fitness landscape model,
G. Martin, S. F. Elena, T. Lenormand, · 2007
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Chromosome rearrangements and the evolution of genome structuring and adaptability,
A. Crombach, P. Hogeweg, · 2007
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On the structural repertoire of pools of short, random RNA sequences,
M. Stich, C. Briones, S. C. Manrubia, · 2008
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Protein folding: Then and now,
Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, N. V. Dokholyan, · 2008
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Protein robustness promotes evolutionary innovations on large evolutionary time-scales,
E. Ferrada, A. Wagner, · 2008
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Survival of the sparsest: robust gene networks are parsimonious,
R. D. Leclerc, · 2008
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Emergence of species in evolutionary "simulated annealing",
M. Heo, L. Kang, E. I. Shakhnovich, · 2008
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The ascent of the abundant: How mutational networks constrain evolution,
M. C. Cowperthwaite, E. P. Economo, W. R. Harcombe, E. L. Miller, L. A. Meyers, · 2008
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Neutral network sizes of biological RNA molecules can be computed and are not atypically small,
T. Jörg, O. C. Martin, A. Wagner, · 2008
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Inverting the viterbi algorithm: An abstract framework for structure design,
M. Schnall-Levin, L. Chindelevitch, B. Berger, · 2008
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The effect of recombination on the neutral evolution of genetic robustness,
G. J. Szöllősi, I. Derényi, · 2008
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Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites,
V. Mustonen, J. Kinney, C. G. Callan, M. Lässig, · 2008
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Evolution of complexity in rna-like replicator systems,
N. Takeuchi, P. Hogeweg, · 2008
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Virus adaptation by manipulation of host’s gene expression,
P. Agudelo-Romero, P. Carbonell, M. A. Perez-Amador, S. F. Elena, · 2008
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Oncogenetic trees,
A. Szabo, K. M. Boucher, · 2008
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An end to endless forms: Epistasis, phenotype distribution bias, and nonuniform evolution,
E. Borenstein, D. C. Krakauer, · 2008
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Evolution of evolvability in a developmental model,
J. Draghi, G. P. Wagner, · 2008
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Evolution of evolvability in gene regulatory networks,
A. Crombach, P. Hogeweg, · 2008
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The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA,
K. Dingle, S. Schaper, A. A. Louis, · 2015
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Evolution on genotype networks accelerates the ticking rate of the molecular clock,
S. Manrubia, J. A. Cuesta, · 2015
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Tipping points and early warning signals in the genomic composition of populations induced by environmental changes,
J. Aguirre, S. Manrubia, · 2015
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A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate,
B. S. Khatri, R. A. Goldstein, · 2015
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Simple biophysical model predicts faster accumulation of hybrid incompatibilities in small populations under stabilizing selection,
B. S. Khatri, R. A. Goldstein, · 2015
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A mixability theory for the role of sex in evolution,
A. Livnat, C. Papadimitriou, J. Dushoff, M. Feldman, · 2008
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Analysis of a complete dna–protein affinity landscape,
W. Rowe, M. Platt, D. C. Wedge, P. J. Day, D. B. Kell, J. Knowles, · 2009
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Evolutionary dynamics on networks of selectively neutral genotypes: Effects of topology and sequence stability,
J. Aguirre, J. M. Buldú, S. C. Manrubia, · 2009
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Evolutionary plasticity and innovations in complex metabolic reaction networks,
J. F. Matias Rodrigues, A. Wagner, · 2009
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Statistical mechanics of convergent evolution in spatial patterning,
B. S. Khatri, T. C. B. McLeish, R. P. Sear, · 2009
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Evolutionary constraints to viroid evolution,
S. F. Elena, G. Gómez, J.-A. Daròs, · 2009
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Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly megaselia abdita,
K. R. Wotton, E. Jiménez-Guri, A. Crombach, H. Janssens, A. Alcaine-Colet, S. Lemke, U. Schmidt-Ott, J. Jaeger, · 2015
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Are there ergodic limits to evolution? ergodic exploration of genome space and convergence,
T. C. B. McLeish, · 2015
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The pathogenicity of splicing effects: Mechanistic insights into pre-mRNA processing inform novel therapeutic approaches,
E. Daguenet, G. Dujardin, J. Valcárcel, · 2015
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Magellan: a tool to explore small fitness landscapes,
S. Brouillet, H. Annoni, L. Ferretti, G. Achaz, · 2015
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The impact of high-order epistasis in the within-host fitness of a positive-sense plant rna virus,
J. Lalić, S. F. Elena, · 2015
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Emerging viruses: why they are not jacks of all trades?,
S. Bedhomme, J. Hillung, S. F. Elena, · 2015
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Protein folding and binding can emerge as evolutionary spandrels through structural coupling,
M. Manhart, A. V. Morozov, · 2015
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Identifying restrictions in the order of accumulation of mutations during tumor progression: Effects of passengers, evolutionary models, and sampling,
R. Diaz-Uriarte, · 2015
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CAPRI: efficient inference of cancer progression models from cross-sectional data,
D. Ramazzotti, G. Caravagna, L. Olde Loohuis, A. Graudenzi, I. Korsunsky, G. Mauri, M. Antoniotti, B. Mishra, · 2015
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Breaking evolutionary constraint with a tradeoff ratchet,
M. G. De Vos, A. Dawid, V. Sunderlikova, S. J. Tans, · 2015
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Experimental evolution reveals hidden diversity in evolutionary pathways,
P. A. Lind, A. D. Farr, P. B. Rainey, · 2015
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Emergent speciation by multiple Dobzhansky-Muller incompatibilities,
T. Paixão, K. Bassler, R. B. R. Azevedo, · 2015
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The differential view of genotype–phenotype relationships,
V. Orgogozo, B. Morizot, A. Martin, · 2015
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Contingency, convergence and hyper-astronomical numbers in biological evolution,
A. A. Louis, · 2016
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Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability,
S. F. Greenbury, S. Schaper, S. E. Ahnert, A. A. Louis, · 2016
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Local fitness landscape of the green fluorescent protein,
K. S. Sarkisyan, D. A. Bolotin, M. V. Meer, D. R. Usmanova, A. S. Mishin, G. V. Sharonov, D. N. Ivankov, N. G. Bozhanova, M. S. Baranov, O. Soylemez, N. S. Bogatyreva, P. K. Vlasov, E. S. Egorov, M. D. Logacheva, A. S. Kondrashov, D. M. Chudakov, E. V. Putintseva, I. Z. Mamedov, D. S. Tawfik, K. A. Lukyanov, F. A. Kondrashov, · 2016
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RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory,
J. A. Garcia-Martin, A. H. Bayegan, I. Dotu, P. Clote, · 2016
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RNAiFold2T: constraint programming design of thermo-IRES switches,
J. A. Garcia-Martin, I. Dotu, J. Fernandez-Chamorro, G. Lozano, J. Ramajo, E. Martinez-Salas, P. Clote, · 2016
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Competition among networks highlights the power of the weak,
J. Iranzo, J. M. Buldú, J. Aguirre, · 2016
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The complete local genotype-phenotype landscape for the alternative splicing of a human exon,
P. Julien, B. Miñana, P. Baeza-Centurion, J. Valcárcel, B. Lehner, · 2016
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The fitness landscape of a tRNA gene,
C. Li, W. Qian, C. J. Maclean, J. Zhang, · 2016
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Network of epistatic interactions within a yeast snoRNA,
O. Puchta, B. Cseke, H. Czaja, D. Tollervey, G. Sanguinetti, G. Kudla, · 2016
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