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… 
Analysis of adaptive walks on NK fitness landscapes with different interaction schemes
TLDR
This paper studies the NK model for fitness landscapes where the interaction scheme between genes can be explicitly defined and finds that the distribution of local maxima over the landscape is particularly sensitive to the choice of interaction pattern.
Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics
TLDR
This work introduces a broad class of high-dimensional random fitness landscapes for which the correlations between fitnesses of genomes are a general function of genetic distance, and studies the properties of these landscapes focusing on the simplest evolutionary process: random adaptive walks.
Key issues review: evolution on rugged adaptive landscapes
TLDR
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.
Universality Classes of Interaction Structures for NK Fitness Landscapes
TLDR
A unified framework for computing the exponential growth rate of the expected number of local fitness maxima as a function of L is developed, and two different universality classes of interaction structures that display different asymptotics of this quantity for large k are identified.
Fitness Landscapes, Adaptation and Sex on the Hypercube
TLDR
In this thesis, several models of fitness landscapes are analyzed with different analytical and numerical methods to identify characteristics in order to compare the model landscapes to experimental measurements.
Greedy adaptive walks on a correlated fitness landscape.
A Family of Fitness Landscapes Modeled through Gene Regulatory Networks.
TLDR
This work develops and study a model of evolution on fitness landscapes using the lens of Gene Regulatory Networks (GRNs), where the regulatory products are computed from multiple genes and collectively treated as phenotypes, and proves the existence of empirically observed, topographical features such as accessibility and connectivity.
Epistasis and constraints in fitness landscapes
TLDR
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.
Recombination and mutational robustness in neutral fitness landscapes
TLDR
It is demonstrated that genetic recombination acting in combination with selection massively enhances the effect of mutational robustness, suggesting that the increase of robustness may be a major driver underlying the evolution of sexual recombination and other forms of genetic exchange throughout the living world.
...
...

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.
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.
Adaptive walks by the fittest among finite random mutants on a Mt. Fuji-type fitness landscape II. Effect of small non-additivity
TLDR
Examining properties of adaptive walks by the fittest on “rough Mt. Fuji-type” fitness landscapes, which are modeled by superposing small uncorrelated random component on an additive fitness landscape, drew the “hill-climbing” vector field, where each vector represents the most probable step for a walker in a single step.
...
...