Journal ArticleDOI
Empirical fitness landscapes and the predictability of evolution
TLDR
This work reviews recent empirical and theoretical developments of the genotype–fitness map, identifies methodological issues and organizing principles, and discusses possibilities to develop more realistic fitness landscape models.Abstract:
A central topic in biology concerns how genotypes determine phenotypes and functions of organisms that affect their evolutionary fitness. This Review discusses recent advances in the development of empirical fitness landscapes and their contribution to theoretical analyses of the predictability of evolution. The genotype–fitness map (that is, the fitness landscape) is a key determinant of evolution, yet it has mostly been used as a superficial metaphor because we know little about its structure. This is now changing, as real fitness landscapes are being analysed by constructing genotypes with all possible combinations of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness landscapes inspire theoretical analyses of the predictability of evolution. Here, we review these recent empirical and theoretical developments, identify methodological issues and organizing principles, and discuss possibilities to develop more realistic fitness landscape models.read more
Citations
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Wonderful Life: The Burgess Shale and the Nature of History, Stephen Jay Gould. W. W. Norton, New York (1989), 347, Price $19.95 (U.S.A.), $27.95 (Canada)
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The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae
TL;DR: Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 emerged in the 2000s as important human pathogens, have spread extensively throughout the world, and are responsible for the rapid increase in antimicrobial resistance among E. coli and K. pneumoniae strains.
Journal ArticleDOI
Local fitness landscape of the green fluorescent protein.
Karen S. Sarkisyan,Dmitry A. Bolotin,Margarita Meer,Dinara R. Usmanova,Dinara R. Usmanova,Alexander S. Mishin,George V. Sharonov,Dmitry N. Ivankov,Dmitry N. Ivankov,Nina G. Bozhanova,Mikhail S. Baranov,Onuralp Soylemez,Natalya S. Bogatyreva,Natalya S. Bogatyreva,Peter K. Vlasov,Evgeny S. Egorov,Maria D. Logacheva,Maria D. Logacheva,Maria D. Logacheva,Alexey S. Kondrashov,Alexey S. Kondrashov,Dmitry M. Chudakov,Ekaterina V. Putintseva,Ilgar Z. Mamedov,Dan S. Tawfik,Konstantin A. Lukyanov,Fyodor A. Kondrashov,Fyodor A. Kondrashov +27 more
TL;DR: An extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) is visualize by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP, indicating congruence between the fitness landscape properties at the local and global scales.
Journal ArticleDOI
Contingency and determinism in evolution: Replaying life's tape.
TL;DR: The authors' review of many such experiments indicates that responses across replicate populations are often repeatable to some degree, although divergence increases as analyses move from overall fitness to underlying phenotypes and genetic changes.
Journal ArticleDOI
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
TL;DR: Improving enzymes by directed evolution requires the navigation of very large search spaces; this work surveys how to do this intelligently.
References
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Journal ArticleDOI
The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds.
TL;DR: This work examines epistasis for beneficial mutations at a broader genetic scale by measuring the fitness effects of two mutations beneficial for the ssDNA bacteriophage ID11 in eight different, related genotypes showing 0.3–3.7% nucleotide divergence from ID11 and finds evidence for diminishing-returns epistasis; the effects were more beneficial for lower-fitness genotypes.
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Epistasis in a model of molecular signal transduction.
Alain Pumir,Boris I. Shraiman +1 more
TL;DR: A complementary approach of studying theoretically the effect of varying multiple parameters in a validated model of molecular signal transduction, which defines a theoretical framework for interpretation of experimental data and provides statistical predictions for the structure of genetic interaction expected for moderately complex biological circuits.
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Long-term evolution is surprisingly predictable in lattice proteins.
TL;DR: It is shown that long-term outcomes are surprisingly predictable in this model of protein folding and binding called ‘lattice proteins’, suggesting that natural biological lineages will also have a predictive long- term fitness.