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Quantitative analyses of empirical fitness landscapes
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.
Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene
- M. Schenk, I. Szendro, M. Salverda, J. Krug, J. D. de Visser
- BiologyMolecular biology and evolution
- 15 May 2013
Understanding epistasis is central to biology. For instance, epistatic interactions determine the topography of the fitness landscape and affect the dynamics and determinism of adaptation. However,…
Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme
The distribution of mutation effects on cefotaxime (Ctx) resistance and fitness of 48 unique beneficial mutations in the bacterial enzyme TEM-1 β-lactamase is studied, finding that the distribution of both measures follows a Fréchet-type distribution characterized by a broad tail of a few exceptionally fit mutants.
Predictability of evolution depends nonmonotonically on population size
- I. Szendro, J. Franke, J. D. de Visser, J. Krug
- BiologyProceedings of the National Academy of Sciences
- 24 December 2012
An extensive computational study of evolutionary predictability based on an experimentally measured eight-locus fitness landscape for the filamentous fungus Aspergillus niger finds that these entropies display an initial decrease and a subsequent increase with population size N, governed by the scales Nμ and Nμ2.
Structure of characteristic Lyapunov vectors in spatiotemporal chaos.
- D. Pazó, I. Szendro, Juan M. López, Miguel A. Rodriguez
- PhysicsPhysical review. E, Statistical, nonlinear, and…
- 17 July 2008
This work focuses on characteristic LVs corresponding to the largest Lyapunov exponents in systems with spatiotemporal chaos, and proposes a minimal stochastic model that reproduces the results for chaotic systems.
Exact results for amplitude spectra of fitness landscapes.
Error growth patterns in systems with spatial chaos: from coupled map lattices to global weather models.
- C. Primo, I. Szendro, M. A. Rodríguez, J. Gutiérrez
- Physics, Environmental SciencePhysical review letters
- 6 March 2007
The spatial correlation and localization of relative fluctuations grow and decay indicating two different regimes, before and after saturation by nonlinear effects, which explains the increasing or decreasing trends previously observed in the exponential growth rate of these spatiotemporal systems.
Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model
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.
Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase
The results suggest that synonymous mutations may have beneficial effects by increasing the expression of an enzyme with low substrate activity, which may be realized via multiple, yet unknown, post-transcriptional mechanisms.
Van Kampen's expansion approach in an opinion formation model
Abstract. We analyze a simple opinion formation model consisting of two parties, A and B, and a group I, of undecided agents. We assume that the supporters of parties A and B do not interact among…