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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Journal ArticleDOI
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)
Journal ArticleDOI
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
Towards a general theory of adaptive walks on rugged landscapes.
TL;DR: This article develops parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to "jump beyond" the correlation lengths in the underlying landscape.
Book
Fitness Landscapes and the Origin of Species
TL;DR: This book builds for the first time a general, quantitative theory for the origin of species based on the notion of fitness landscapes introduced by Sewall Wright in 1932, generalizing this notion to explore the consequences of the huge dimensionality of Fitness landscapes that correspond to biological systems.
Journal ArticleDOI
Darwinian evolution can follow only very few mutational paths to fitter proteins.
TL;DR: It is demonstrated that 102 mutational trajectories linking β-lactamase alleles are inaccessible to Darwinian selection and that many of the remaining trajectories have negligible probabilities of realization, which implies that the protein tape of life may be largely reproducible and even predictable.
Journal ArticleDOI
The genetic theory of adaptation: a brief history
TL;DR: The history of adaptation theory is surveyed, focusing on the rise and fall of various views over the past century and the reasons for the slow development of a mature theory of adaptation.
Journal ArticleDOI
Deleterious mutations and the evolution of sexual reproduction
TL;DR: If the deleterious mutation rate per genome per generation is greater than 1, then the greater efficiency of selection against these mutations in sexual populations may be responsible for the evolution of sex and related phenomena.