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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References

SHOWING 1-10 OF 159 REFERENCES
Evolutionary Accessibility of Mutational Pathways
TLDR
Access to the globally optimal configuration should be accessible to genome wide evolution, but the repeatability of evolutionary trajectories is limited owing to the presence of a large number of alternative mutational pathways.
Exploring the Effect of Sex on Empirical Fitness Landscapes
TLDR
Fitness landscapes for two sets of strains of the asexual fungus Aspergillus niger involving all combinations of five mutations are described, finding that ∼30% of the single‐mutation fitness effects are positive despite their negative effect in the wild‐type strain and that several local fitness maxima and minima are present.
Predictability of Evolutionary Trajectories in Fitness Landscapes
TLDR
An exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding, which suggests smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics ofprotein folding.
Fitness Landscapes and the Origin of Species
TLDR
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.
Percolation on the fitness hypercube and the evolution of reproductive isolation.
TLDR
It is argued that macroevolution and speciation on "rugged" fitness landscapes proceed according to the properties of the corresponding holey landscapes, which may be related to the patterns of speciation.
Adaptive landscapes and protein evolution
TLDR
It is found that mutant sites in real proteins show significantly more additivity than those obtained from random simulations and is reflected in a summary statistic for adaptive landscapes known as the “roughness,” which for the actual proteins so far examined lies in the smallest 0.5% tail of random landscapes.
Microbial experiments on adaptive landscapes.
TLDR
It is shown that laboratory populations of microbes allow evolution to be observed in real time and, as such, provide key insights into the topology of adaptive landscapes.
The causes of epistasis
TLDR
It is concluded that pleiotropy is an important prerequisite for epistasis, and that epistasis may evolve as an adaptive or intrinsic consequence of changes in genetic robustness and evolvability.
Deterministic and Stochastic Regimes of Asexual Evolution on Rugged Fitness Landscapes
TLDR
Whether the evolutionary trajectory is deterministic or stochastic depends on the effective mutational distance deff up to which the population can spread in genotype space, which is relevant to the interpretation of evolution experiments with microbial populations.
...
...