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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.

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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.
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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.
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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 NK model of rugged fitness landscapes and its application to maturation of the immune response.

TL;DR: This work analyzes a class of mathematical models the authors call NK models and shows that these models capture significant features of the maturation of the immune response, which is currently thought to share features with general protein evolution.
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The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

TL;DR: These estimates show that pleiotropy is highly restricted and are more in line with the notion of variational modularity than with universal Pleiotropy.
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Evolution of Hormone-Receptor Complexity by Molecular Exploitation

TL;DR: It is demonstrated how an integrated molecular system—the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor—evolved by a stepwise Darwinian process.
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Genome dynamics during experimental evolution.

TL;DR: The evolutionary forces and ecological processes that govern genome dynamics in various laboratory systems are discussed in the context of relevant population genetic theory, and these findings are related to evolution in natural populations.
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Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

TL;DR: P pervasive genetic hitchhiking is found: multiple mutations arise and move synchronously through the population as mutational ‘cohorts’, and patterns of sequence evolution are driven by a balance between these chance effects of hitchh hiking and interference.
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