Adaptation in tunably rugged fitness landscapes: The Rough Mount Fuji Model

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 analyse a simple fitness landscape model with tunable ruggedness based on the Rough Mount Fuji (RMF) model originally introduced by Aita et al. [Biopolymers 54:64-79 (2000)] in the context of protein evolution. We provide a comprehensive collection of results pertaining to the topographical structure of RMF landscapes, including explicit formulae for the expected number of local fitness maxima, the location of the global peak, and the fitness correlation function. The statistics of single and multiple adaptive steps on the RMF landscape are explored mainly through simulations, and the results are compared to the known behavior in the MLM model. Finally, we show that the RMF model can explain the large number of second-step mutations observed on a highly-fit first step backgound in a recent evolution experiment with a microvirid bacteriophage [Miller et al., Genetics 187:185-202 (2011)].Comment: 43 pages, 12 figures; revised version with new results on the number of fitness maxim

Exact Results for Amplitude Spectra of Fitness Landscapes

Starting from fitness correlation functions, we calculate exact expressions for the amplitude spectra of fitness landscapes as defined by P.F. Stadler [J. Math. Chem. 20, 1 (1996)] for common landscape models, including Kauffman's NK-model, rough Mount Fuji landscapes and general linear superpositions of such landscapes. We further show that correlations decaying exponentially with the Hamming distance yield exponentially decaying spectra similar to those reported recently for a model of molecular signal transduction. Finally, we compare our results for the model systems to the spectra of various experimentally measured fitness landscapes. We claim that our analytical results should be helpful when trying to interpret empirical data and guide the search for improved fitness landscape models.Comment: 13 pages, 5 figures; revised and final versio

Equilibrium of anchored interfaces with quenched disordered growth

The roughening behavior of a one-dimensional interface fluctuating under quenched disorder growth is examined while keeping an anchored boundary. The latter introduces detailed balance conditions which allows for a thorough analysis of equilibrium aspects at both macroscopic and microscopic scales. It is found that the interface roughens linearly with the substrate size only in the vicinity of special disorder realizations. Otherwise, it remains stiff and tilted.Comment: 6 pages, 3 postscript figure

Multidimensional epistasis and the transitory advantage of sex

Identifying and quantifying the benefits of sex and recombination is a long standing problem in evolutionary theory. In particular, contradictory claims have been made about the existence of a benefit of recombination on high dimensional fitness landscapes in the presence of sign epistasis. Here we present a comparative numerical study of sexual and asexual evolutionary dynamics of haploids on tunably rugged model landscapes under strong selection, paying special attention to the temporal development of the evolutionary advantage of recombination and the link between population diversity and the rate of adaptation. We show that the adaptive advantage of recombination on static rugged landscapes is strictly transitory. At early times, an advantage of recombination arises through the possibility to combine individually occurring beneficial mutations, but this effect is reversed at longer times by the much more efficient trapping of recombining populations at local fitness peaks. These findings are explained by means of well established results for a setup with only two loci. In accordance with the Red Queen hypothesis the transitory advantage 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.Comment: 34 pages, 9 figures and 8 supplementary figures; revised and final versio

Driven Lattice Gases with Quenched Disorder: Exact Results and Different Macroscopic Regimes

We study the effect of quenched spatial disorder on the steady states of driven systems of interacting particles. Two sorts of models are studied: disordered drop-push processes and their generalizations, and the disordered asymmetric simple exclusion process. We write down the exact steady-state measure, and consequently a number of physical quantities explicitly, for the drop-push dynamics in any dimensions for arbitrary disorder. We find that three qualitatively different regimes of behaviour are possible in 1-$d$ disordered driven systems. In the Vanishing-Current regime, the steady-state current approaches zero in the thermodynamic limit. A system with a non-zero current can either be in the Homogeneous regime, chracterized by a single macroscopic density, or the Segregated-Density regime, with macroscopic regions of different densities. We comment on certain important constraints to be taken care of in any field theory of disordered systems.Comment: RevTex, 17pages, 18 figures included using psfig.st

Evolutionary accessibility of mutational pathways

Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield a fitness landscape that determines which mutational states can be reached from a given initial genotype. Understanding the accessibility properties of fitness landscapes is conceptually important in answering questions about the predictability and repeatability of evolutionary adaptation. Here we theoretically investigate accessibility of the globally optimal state on a wide variety of model landscapes, including landscapes with tunable ruggedness as well as neutral `holey' landscapes. We define a mutational pathway to be accessible if it contains the minimal number of mutations required to reach the target genotype, and if fitness increases in each mutational step. Under this definition accessibility is high, in the sense that at least one accessible pathwayexists with a substantial probability that approaches unity as the dimensionality of the fitness landscape (set by the number of mutational loci) becomes large. At the same time the number of alternative accessible pathways grows without bound. We test the model predictions against an empirical 8-locus fitness landscape obtained for the filamentous fungus \textit{Aspergillus niger}. By analyzing subgraphs of the full landscape containing different subsets of mutations, we are able to probe the mutational distance scale in the empirical data. The predicted effect of high accessibility is supported by the empirical data and very robust, which we argue to reflect the generic topology of sequence spaces.Comment: 16 pages, 4 figures; supplementary material available on reques

Dynamics of a disordered, driven zero range process in one dimension

We study a driven zero range process which models a closed system of attractive particles that hop with site-dependent rates and whose steady state shows a condensation transition with increasing density. We characterise the dynamical properties of the mass fluctuations in the steady state in one dimension both analytically and numerically and show that the transport properties are anomalous in certain regions of the density-disorder plane. We also determine the form of the scaling function which describes the growth of the condensate as a function of time, starting from a uniform density distribution.Comment: Revtex4, 5 pages including 2 figures; Revised version; To appear in Phys. Rev. Let