Evolutionary Accessibility in Tunably Rugged Fitness Landscapes

@article{Franke2012EvolutionaryAI,
  title={Evolutionary Accessibility in Tunably Rugged Fitness Landscapes},
  author={Jasper Franke and Joachim H A Krug},
  journal={Journal of Statistical Physics},
  year={2012},
  volume={148},
  pages={706-723}
}
The adaptive evolution of a population under the influence of mutation and selection is strongly influenced by the structure of the underlying fitness landscape, which encodes the interactions between mutations at different genetic loci. Theoretical studies of such landscapes have been carried out for several decades, but only recently experimental fitness measurements encompassing all possible combinations of small sets of mutations have become available. The empirical studies have spawned new… 

Evolutionary Accessibility of Modular Fitness Landscapes

TLDR
The block model can be viewed as a special case of Kauffman’s NK-model, and it is shown that the number of accessible paths can be written as a product of the path numbers within the blocks, which provides a detailed analytic description of the paths statistics.

Properties of Random Fitness Landscapes and Their Influence on Evolutionary Dynamics. A Journey through the Hypercube

TLDR
The individual-based Wright-Fisher model is used to study recombination of genotypes, interactions between individuals and the influence of the underlying fitness landscape on these mechanisms.

Evolutionary constraints in fitness landscapes

TLDR
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.

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.

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

TLDR
A simple fitness landscape model with tunable ruggedness based on the rough Mount Fuji (RMF) model originally introduced by Aita et al. in the context of protein evolution is proposed and compared to the known behavior in the MLM model.

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.

Impact of population size on early adaptation in rugged fitness landscapes

TLDR
It is shown that the accessibility of the different fitness peaks is key to determining whether this height overall increases or decreases with population size, and early adaptation in rugged fitness landscapes can be more efficient and predictable for relatively small population sizes than in the large-size limit.

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.

Role of phenotype switching during biological evolution in static environments

TLDR
Traditional models of evolution over genotype space fail to account for the observation that biological diversity is rife, even amongst genetically identical cells that exist in the same environment, and should consider different fitness landscapes for each of the distinct phenotypic states that exist.

Multidimensional Epistasis and the Transitory Advantage of Sex

TLDR
It is shown that the adaptive advantage of recombination on static rugged landscapes is strictly transitory and can be prolonged indefinitely in fluctuating environments, and it is maximal when the environment fluctuates on the same time scale on which trapping at local optima typically occurs.

References

SHOWING 1-10 OF 68 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.

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.

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

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.

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.

Impact of epistasis and pleiotropy on evolutionary adaptation

TLDR
It is implied that the synergism between loci that interact epistatically is crucial for evolving genetic modules with high fitness, while too much ruggedness stalls the adaptive process.

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.

RAPID EVOLUTIONARY ESCAPE BY LARGE POPULATIONS FROM LOCAL FITNESS PEAKS IS LIKELY IN NATURE

TLDR
A novel expression for this critical recombination rate is developed, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes.

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.

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.
...