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Joachim Krug

Publications and source records attributed to Joachim Krug.

At least 55 records · Page 3Linked to original sources
arXiv2014

Evolutionary accessibility of modular fitness landscapes

A fitness landscape is a mapping from the space of genetic sequences, which is modeled here as a binary hypercube of dimension $L$, to the real numbers. We consider random models of fitness landscapes, where fitness values are assigned according to some probabilistic rule, and study the statistical properties of pathways to the global fitness maximum along which fitness increases monotonically. Such paths are important for evolution because they are the only ones that are accessible to an adapting population when mutations occur at a low rate. The focus of this work is on the block model introduced by A.S. Perelson and C.A. Macken [Proc. Natl. Acad. Sci. USA 92:9657 (1995)] where the genome is decomposed into disjoint sets of loci (`modules') that contribute independently to fitness, and fitness values within blocks are assigned at random. We show 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 path statistics. The block model can be viewed as a special case of Kauffman's NK-model, and we compare the analytic results to simulations of the NK-model with different genetic architectures. We find that the mean number of accessible paths in the different versions of the model are quite similar, but the distribution of the path number is qualitatively different in the block model due to its multiplicative structure. A similar statement applies to the number of local fitness maxima in the NK-models, which has been studied extensively in previous works. The overall evolutionary accessibility of the landscape, as quantified by the probability to find at least one accessible path to the global maximum, is dramatically lowered by the modular structure.

q-bio.PE↗
arXiv2013

Rate of adaptation in sexuals and asexuals: A solvable model of the Fisher-Muller effect

The adaptation of large asexual populations is hampered by the competition between independently arising beneficial mutations in different individuals, which is known as clonal interference. Fisher and Muller proposed that recombination provides an evolutionary advantage in large populations by alleviating this competition. Based on recent progress in quantifying the speed of adaptation in asexual populations undergoing clonal interference, we present a detailed analysis of the Fisher-Muller mechanism for a model genome consisting of two loci with an infinite number of beneficial alleles each and multiplicative fitness effects. We solve the infinite population dynamics exactly and show that, for a particular, natural mutation scheme, the speed of adaptation in sexuals is twice as large as in asexuals. Guided by the infinite population result and by previous work on asexual adaptation, we postulate an expression for the speed of adaptation in finite sexual populations that agrees with numerical simulations over a wide range of population sizes and recombination rates. The ratio of the sexual to asexual adaptation speed is a function of population size that increases in the clonal interference regime and approaches 2 for extremely large populations. The simulations also show that the imbalance between the numbers of accumulated mutations at the two loci is strongly suppressed even by a small amount of recombination. The generalization of the model to an arbitrary number $L$ of loci is briefly discussed. If each offspring samples the alleles at each locus from the gene pool of the whole population rather than from two parents, the ratio of the sexual to asexual adaptation speed is approximately equal to $L$ in large populations. A possible realization of this scenario is the reassortment of genetic material in RNA viruses with $L$ genomic segments.

q-bio.PE↗
arXiv2013

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.

q-bio.PE↗
arXiv2013

Accessibility percolation on n-trees

Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in ascending order. For the case when the random variables are independent and identically distributed, we derive an asymptotically exact expression for the probability that there is at least one accessible path from the root to the leaves in an $n$-tree. This probability tends to 1 (0) if the branching number is increased with the height of the tree faster (slower) than linearly. When the random variables are biased such that the mean value increases linearly with the distance from the root, a percolation threshold emerges at a finite value of the bias.

cond-mat.stat-mech↗
arXiv2013

Record occurrence and record values in daily and monthly temperatures

We analyze the occurrence and the values of record-breaking temperatures in daily and monthly temperature observations. Our aim is to better understand and quantify the statistics of temperature records in the context of global warming. Similar to earlier work we employ a simple mathematical model of independent and identically distributed random variables with a linearly growing expectation value. This model proved to be useful in predicting the increase (decrease) in upper (lower) temperature records in a warming climate. Using both station and re-analysis data from Europe and the United States we further investigate the statistics of temperature records and the validity of this model. The most important new contribution in this article is an analysis of the statistics of record values for our simple model and European reanalysis data. We estimate how much the mean values and the distributions of record temperatures are affected by the large scale warming trend. In this context we consider both the values of records that occur at a certain time and the values of records that have a certain record number in the series of record events. We compare the observational data both to simple analytical computations and numerical simulations. We find that it is more difficult to describe the values of record breaking temperatures within the framework of our linear drift model. Observations from the summer months fit well into the model with Gaussian random variables under the observed linear warming, in the sense that record breaking temperatures are more extreme in the summer. In winter however a significant asymmetry of the daily temperature distribution hides the effect of the slow warming trends. Therefore very extreme cold records are still possible in winter. This effect is even more pronounced if one considers only data from subpolar regions.

physics.ao-ph↗
arXiv2012

Evolutionary accessibility in tunably rugged fitness landscapes

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 questions about the accessibility of optimal genotypes under natural selection. Depending on population dynamic parameters such as mutation rate and population size, evolutionary accessibility can be quantified through the statistics of accessible mutational pathways (along which fitness increases monotoncially), or through the study of the basin of attraction of the optimal genotype under greedy (steepest ascent) dynamics. Here we investigate these two measures of accessibility in the framework of Kauffman's $LK$-model, a paradigmatic family of random fitness landscapes with tunable ruggedness. The key parameter governing the strength of genetic interactions is the number $K$ of interaction partners of each of the $L$ sites in the genotype sequence. In general, accessibility increases with increasing genotype dimensionality $L$ and decreases with increasing number of interactions $K$. Remarkably, however, we find that some measures of accessibility behave non-monotonically as a function of $K$, indicating a special role of the most sparsely connected, non-trivial cases K=1 and 2. The relation between models for fitness landscapes and spin glasses is also addressed.

q-bio.PE↗
arXiv2012

Quantitative analyses of empirical fitness landscapes

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.

q-bio.PE↗
arXiv2012

Non-conserved dynamics of steps on vicinal surfaces during electromigration-induced step bunching

We report new results on the non-conserved dynamics of parallel steps on vicinal surfaces in the case of sublimation with electromigration and step-step interactions. The derived equations are valid in the quasistatic approximation and in the limit $f^{-1}\gg l_D\gg l_{\pm} \gg l_i$, where $f$ is the inverse electromigration length, $l_D$ the diffusion length, $l_{\pm}$ the kinetic lengths and $l_i$ the terrace widths. The coupling between crystal sublimation and step-step interactions induces non-linear, non-conservative terms in the equations of motion. Depending on the initial conditions, this leads to interrupted coarsening, anticoarsening of step bunches or periodic switching between step trains of different numbers of bunches.

cond-mat.stat-mech↗
arXiv2011

Correlations between record events in sequences of random variables with a linear trend

The statistics of records in sequences of independent, identically distributed random variables is a classic subject of study. One of the earliest results concerns the stochastic independence of record events. Recently, records statistics beyond the case of i.i.d. random variables have received much attention, but the question of independence of record events has not been addressed systematically. In this paper, we study this question in detail for the case of independent, non-identically distributed random variables, specifically, for random variables with a linearly moving mean. We find a rich pattern of positive and negative correlations, and show how their asymptotics is determined by the universality classes of extreme value statistics.

cond-mat.stat-mech↗
arXiv2011

Adaptive walks and extreme value theory

We study biological evolution in a high-dimensional genotype space in the regime of rare mutations and strong selection. The population performs an uphill walk which terminates at local fitness maxima. Assigning fitness randomly to genotypes, we show that the mean walk length is logarithmic in the number of initially available beneficial mutations, with a prefactor determined by the tail of the fitness distribution. This result is derived analytically in a simplified setting where the mutational neighborhood is fixed during the adaptive process, and confirmed by numerical simulations.

q-bio.PE↗
arXiv2011

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.

q-bio.PE↗
arXiv2011

Record statistics for biased random walks, with an application to financial data

We consider the occurrence of record-breaking events in random walks with asymmetric jump distributions. The statistics of records in symmetric random walks was previously analyzed by Majumdar and Ziff and is well understood. Unlike the case of symmetric jump distributions, in the asymmetric case the statistics of records depends on the choice of the jump distribution. We compute the record rate $P_n(c)$, defined as the probability for the $n$th value to be larger than all previous values, for a Gaussian jump distribution with standard deviation $σ$ that is shifted by a constant drift $c$. For small drift, in the sense of $c/σ\ll n^{-1/2}$, the correction to $P_n(c)$ grows proportional to arctan$(\sqrt{n})$ and saturates at the value $\frac{c}{\sqrt{2} σ}$. For large $n$ the record rate approaches a constant, which is approximately given by $1-(σ/\sqrt{2π}c)\textrm{exp}(-c^2/2σ^2)$ for $c/σ\gg 1$. These asymptotic results carry over to other continuous jump distributions with finite variance. As an application, we compare our analytical results to the record statistics of 366 daily stock prices from the Standard & Poors 500 index. The biased random walk accounts quantitatively for the increase in the number of upper records due to the overall trend in the stock prices, and after detrending the number of upper records is in good agreement with the symmetric random walk. However the number of lower records in the detrended data is significantly reduced by a mechanism that remains to be identified.

q-fin.ST↗
arXiv2011

Evolutionary advantage of small populations on complex fitness landscapes

Background: Recent experimental and theoretical studies have shown that small asexual populations evolving on complex fitness landscapes may achieve a higher fitness than large ones due to the increased heterogeneity of adaptive trajectories. Here we introduce a class of haploid three-locus fitness landscapes that allows to investigate this scenario in a precise and quantitative way. Results: Our main result derived analytically shows how the probability of choosing the path of largest initial fitness increase grows with the population size. This makes large populations more likely to get trapped at local fitness peaks and implies an advantage of small populations at intermediate time scales. The range of population sizes where this effect is operative coincides with the onset of clonal interference. Additional studies using ensembles of random fitness landscapes show that the results achieved for a particular choice of three-locus landscape parameters are robust and also persist as the number of loci increases. Conclusions: Our study indicates that an advantage for small populations is likely whenever the fitness landscape contains local maxima. The advantage 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.

q-bio.PE↗
arXiv2011

Rare events in population genetics: Stochastic tunneling in a two-locus model with recombination

We study the evolution of a population in a two-locus genotype space, in which the negative effects of two single mutations are overcompensated in a high fitness double mutant. We discuss how the interplay of finite population size, $N$, and sexual recombination at rate $r$ affects the escape times $t_\mathrm{esc}$ to the double mutant. For small populations demographic noise generates massive fluctuations in $t_\mathrm{esc}$. The mean escape time varies non-monotonically with $r$, and grows exponentially as $\ln t_{\mathrm{esc}} \sim N(r - r^\ast)^{3/2}$ beyond a critical value $r^\ast$.

q-bio.PE↗
arXiv2010

Record-breaking temperatures reveal a warming climate

We present a mathematical analysis of records drawn from independent random variables with a drifting mean. To leading order the change in the record rate is proportional to the ratio of the drift velocity to the standard deviation of the underlying distribution. We apply the theory to time series of daily temperatures for given calendar days, obtained from historical climate recordings of European and American weather stations as well as re-analysis data. We conclude that the change in the mean temperature has increased the rate of record breaking events in a moderate but significant way: For the European station data covering the time period 1976-2005, we find that about 5 of the 17 high temperature records observed on average in 2005 can be attributed to the warming climate.

physics.data-an↗
arXiv2010

Records and sequences of records from random variables with a linear trend

We consider records and sequences of records drawn from discrete time series of the form $X_{n}=Y_{n}+cn$, where the $Y_{n}$ are independent and identically distributed random variables and $c$ is a constant drift. For very small and very large drift velocities, we investigate the asymptotic behavior of the probability $p_n(c)$ of a record occurring in the $n$th step and the probability $P_N(c)$ that all $N$ entries are records, i.e. that $X_1 < X_2 < ... < X_N$. Our work is motivated by the analysis of temperature time series in climatology, and by the study of mutational pathways in evolutionary biology.

cond-mat.stat-mech↗
arXiv2010

A pedestrian's view on interacting particle systems, KPZ universality, and random matrices

These notes are based on lectures delivered by the authors at a Langeoog seminar of SFB/TR12 "Symmetries and universality in mesoscopic systems" to a mixed audience of mathematicians and theoretical physicists. After a brief outline of the basic physical concepts of equilibrium and nonequilibrium states, the one-dimensional simple exclusion process is introduced as a paradigmatic nonequilibrium interacting particle system. The stationary measure on the ring is derived and the idea of the hydrodynamic limit is sketched. We then introduce the phenomenological Kardar-Parisi-Zhang (KPZ) equation and explain the associated universality conjecture for surface fluctuations in growth models. This is followed by a detailed exposition of a seminal paper of Johansson that relates the current fluctuations of the totally asymmetric simple exclusion process (TASEP) to the Tracy-Widom distribution of random matrix theory. The implications of this result are discussed within the framework of the KPZ conjecture.

cond-mat.stat-mech↗