Quantitative analyses of empirical fitness landscapes

Abstract

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 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 various measures of epistasis that have been proposed in the literature appear to be equivalent. Our comparison shows that the ruggedness of the empirical landscape is affected by whether the included mutations are beneficial or deleterious and by whether intra- or intergenic epistasis is involved. Finally, the empirical landscapes are compared to landscapes generated with the Rough Mt.\ Fuji model. Despite the simplicity of this model, it captures the features of the experimental landscapes remarkably well.

arXiv comment24 pages, 5 figures; to appear in Journal of Statistical Mechanics: Theory and Experiment

References in corpus (7)

• Neutral Evolution of Mutational Robustness
• Evolutionary accessibility of mutational pathways
• The speed of evolution in large asexual populations
• Statistical Genetics and Evolution of Quantitative Traits
• Predictability of evolutionary trajectories in fitness landscapes
• Adaptive walks and extreme value theory
• More rigorous results on the Kauffman-Levin model of evolution

Cited by in corpus (29)

• Adaptation in tunably rugged fitness landscapes: The Rough Mount Fuji Model
• Inferring fitness landscapes by regression produces biased estimates of epistasis
• Protein folding and binding can emerge as evolutionary spandrels through structural coupling
• Exact Results for Amplitude Spectra of Fitness Landscapes
• Universality classes of interaction structures for NK fitness landscapes
• Quantifying the role of population subdivision in evolution on rugged fitness landscapes
• Evolving generalists via dynamic sculpting of rugged landscapes
• Adapt or perish: Evolutionary rescue in a gradually deteriorating environment
• Evolutionary accessibility of modular fitness landscapes
• Analysis of adaptive walks on NK fitness landscapes with different interaction schemes
• Phase transition in random adaptive walks on correlated fitness landscapes
• Multidimensional epistasis and the transitory advantage of sex
• Accessibility percolation on n-trees
• Antibiotic resistance: a physicist's view
• On the Fourier transform of a quantitative trait: Implications for compressive sensing
• Spectral Analysis of the Quantum Random Energy Model
• Accessibility Percolation on Cartesian Power Graphs
• Evolutionary accessibility of random and structured fitness landscapes
• Distribution of the number of fitness maxima in Fisher's Geometric Model
• Impact of population size on early adaptation in rugged fitness landscapes
• Length of adaptive walk on uncorrelated and correlated fitness landscapes
• Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes
• Scaling properties of evolutionary paths in a biophysical model of protein adaptation
• Complexity and accessibility of random landscapes
• Intermittency as metastability: a predictive approach to evolution in disordered environments
• Evolutionary adaptation is facilitated by the presence of lethal genotypes
• Universal distribution of the number of minima for random walks and Lévy flights
• The number of minima in random landscapes generated by constrained random walk and Lévy flights: universal properties
• RMF accessibility percolation on oriented graphs