Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model

@article{Neidhart2014AdaptationIT,
  title={Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model},
  author={Johannes Neidhart and Ivan G. Szendro and Joachim H A Krug},
  journal={Genetics},
  year={2014},
  volume={198},
  pages={699 - 721}
}
Much of the current theory of adaptation is based on Gillespie’s mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a growing body of empirical evidence shows that real fitness landscapes, while possessing a considerable amount of ruggedness, are smoother than predicted by the MLM. In the present article we propose and analyze a simple fitness landscape model with tunable… 

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References

SHOWING 1-10 OF 90 REFERENCES

THE POPULATION GENETICS OF ADAPTATION ON CORRELATED FITNESS LANDSCAPES: THE BLOCK MODEL

  • H. A. Orr
  • Biology
    Evolution; international journal of organic evolution
  • 2006
TLDR
It is shown that all previous results characterizing single steps in adaptation in the mutational landscape model hold at least approximately on correlated landscapes in the block model; many entire-walk results, however, do not.

Evolutionary Accessibility in Tunably Rugged Fitness Landscapes

TLDR
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.

ADAPTIVE WALKS AND DISTRIBUTION OF BENEFICIAL FITNESS EFFECTS

TLDR
On taking large effect mutations into account, this work finds that the length of the walk shows different qualitative trends from those derived using small selection coefficient approximation, and can be exploited in experiments to determine the extreme value domain of the distribution of beneficial fitness effects.

ESTIMATING SOME FEATURES OF NK FITNESS LANDSCAPES

Kauffman and Levin introduced a class of models for the evolution of hereditary systems which they called NK fitness landscapes. Inspired by spinglasses, these models have the attractive feature of

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.

Quantitative analyses of empirical fitness landscapes

TLDR
The aim of this review is to identify measures of epistasis that allow a meaningful comparison of fitness landscapes and then apply them to the empirical landscapes to discern factors that affect ruggedness.

The dynamics of adaptation on correlated fitness landscapes

TLDR
A theory that predicts how a population's mean fitness and the number of accumulated substitutions are expected to increase over time, depending on the underlying fitness landscape is developed and it is shown that linear substitution trajectories, long considered the hallmark of neutral evolution, can arise even when mutations are strongly selected.

Correlated and uncorrelated fitness landscapes and how to tell the difference

TLDR
A framework for the mathematical treatment of multi-peaked “fitness landscapes”, including an explicit mathematical model, is suggested, which might be useful in the “tuning” of combinatorial optimization algorithms, and in modelling in the experimental sciences.

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.

EVOLUTIONARY ADVANTAGE OF SMALL POPULATIONS ON COMPLEX FITNESS LANDSCAPES

TLDR
This study indicates that an advantage for small populations is likely whenever the fitness landscape contains local maxima, which appears at intermediate time scales, which are long enough for trapping at local fitness maxima to have occurred but too short for peak escape by the creation of multiple mutants.
...