Quantitative analyses of empirical fitness landscapes

@article{Szendro2012QuantitativeAO,
  title={Quantitative analyses of empirical fitness landscapes},
  author={Ivan G. Szendro and Martijn F. Schenk and Jasper Franke and Joachim H A Krug and J. Arjan G.M. de Visser},
  journal={Journal of Statistical Mechanics: Theory and Experiment},
  year={2012},
  volume={2013}
}
The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes was lacking, but since it became feasible to construct all possible genotypes containing combinations of a limited set of mutations, the number of studies has grown to a point where a classification of landscapes becomes possible. The aim of this review is to… 
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Epistasis and constraints in fitness landscapes

This work proposes two new sets of measures that explicitly capture two relevant features of fitness landscapes: epistasis and constraints, and shows how these measures can help uncovering the amount and the nature of epistatic interactions in two experimental landscapes.

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A new natural measure of the amount of epistasis based on the correlation of fitness effects of mutations, which has a natural interpretation, captures well the interaction between mutations and can be obtained analytically for most landscape models.

Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations.

A Family of Fitness Landscapes Modeled through Gene Regulatory Networks

This work investigates fitness landscape models through the lens of Gene Regulatory Networks (GRNs), where the regulatory products are computed from multiple genes and collectively treated as the phenotypes, and deduces a mesoscopic structure underlying GRN Fitness landscape models that retains necessary information for evolutionary dynamics with minimal complexity.

Measuring ruggedness in fitness landscapes

An elegant combination of simulations and experiments with Escherichia coli is used to show that even in adaptation over the course of a few weeks involving only a handful of mutations, interactions among those mutations can have very large effects.

Evolutionary Accessibility in Tunably Rugged Fitness Landscapes

Some measures of accessibility behave non-monotonically as a function of K, indicating a special role of the most sparsely connected, non-trivial cases K=1 and 2, and the relation between models for fitness landscapes and spin glasses is addressed.

Inferring fitness landscapes by regression produces biased estimates of epistasis

This work critically examine regression techniques used to approximate fitness landscapes from data, finding that such regressions are subject to two inherent biases that distort the biological quantities of greatest interest, often making evolution seem less predictable than it actually is.

Evolutionary constraints in fitness landscapes

This paper presents some measures of evolutionary constraints based on the similarity between accessible paths and the abundance and characteristics of “chains” of obligatory mutations, that are paths going through genotypes with a single fitter neighbor, and shows how they shed light on evolutionary constraints and predictability in experimentally resolved landscapes.

Key issues review: evolution on rugged adaptive landscapes

The concept of adaptive landscapes is introduced, the major theoretical studies of evolution on rugged landscapes are reviewed, and recent mathematical and statistical analyses motivated by empirical adaptive landscapes are discussed.

Epistasis and Adaptation on Fitness Landscapes

  • C. Bank
  • Biology
    Annual Review of Ecology, Evolution, and Systematics
  • 2022
Fitness landscape theory and experiments are reviewed and their implications for the role of epistasis in adaptation are discussed and theoretical expectations in the light of empirical fitness landscapes are discussed.
...

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