We investigate the evolutionary dynamics of a finite population of sequences adapting to NK fitness landscapes. We find that, unlike in the case of an infinite population, the average fitness in a finite population is maximized at a small but finite, rather than vanishing, mutation rate. The highest local maxima in the landscape are visited for even larger mutation rates, close to a transition point at which the population delocalizes (i.e., leaves the fitness peak at which it was localized) and starts traversing the sequence space. If the mutation rate is increased even further, the population undergoes a second transition and loses all sensitivity to fitness peaks. This second transition corresponds to the standard error threshold transition first described by Eigen. We discuss the implications of our results for biological evolution and for evolutionary optimization techniques.
The idea of adaptive walks on fitness landscapes as a means of studying evolutionary processes on large time scales is extended to fitness landscapes that are slowly changing over time. The influence of ruggedness and of the amount of static fitness contributions are investigated for model landscapes derived from Kauffman's $NK$ landscapes. Depending on the amount of static fitness contributions in the landscape, the evolutionary dynamics can be divided into a percolating and a non-percolating phase. In the percolating phase, the walker performs a random walk over the regions of the landscape …
We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our method can be applied to both discrete time and continuous time systems. While the behavior of continuous time systems is dominated by the average fitness landscape for small mutation rates, in discrete time systems it is instead the geometric mean fitness that determines the system's properties. In both cases, we find that in situations in which the arithmeti…
Molecular evolution is often conceptualised as adaptive walks on rugged fitness landscapes, driven by mutations and constrained by incremental fitness selection. It is well known that epistasis shapes the ruggedness of the landscape's surface, outlining their topography (with high-fitness peaks separated by valleys of lower fitness genotypes). However, within the strong selection weak mutation (SSWM) limit, once an adaptive walk reaches a local peak, natural selection restricts passage through downstream paths and hampers any possibility of reaching higher fitness values. Here, in addition to …
Evolution in changing environments is an important, but little studied aspect of the theory of evolution. The idea of adaptive walks in fitness landscapes has triggered a vast amount of research and has led to many important insights about the progress of evolution. Nevertheless, the small step to time-dependent fitness landscapes has most of the time not been taken. In this work, some elements of a theory of adaptive walks on changing fitness landscapes are proposed, and are subsequently applied to and tested on a simple family of time-dependent fitness landscapes, the oscillating NK landscap…
We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment's resource composition lead to both non-constant replication and decay rates of the molecules. In general, therefore, molecular evolution takes place in a dynamic rather than a static fitness landscape. We incorporate dynamic replication and decay rates into the standard quasispecies theory of molecular evolution, and show that for periodic time-dependencies, a system of evolving molecules enters a limit cycle for $t\to\infty$. For fa…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection and mutation, and calculated the mean fitness. For the case of recombination, we formulated a model with a multidimensional fitness landscape (the dimension of the space is equal to the number of blocks) and derived a theorem about the dynamics of initially narrow distribution. We also considered the case of lethal mutations. We also formulated the finite po…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of non-equilibrium vi…
We present an extension of Eigen's model for quasi-species including the competition among individuals, proposed as the simplest mechanism for the formation of new species in a smooth fitness landscape. We are able to obtain analytically the critical threshold for species formation. The comparison with numerical simulations is very good.
A quasispecies evolving on a fitness landscape with a single peak of fluctuating height is studied. In the approximation that back mutations can be ignored, the rate equations can be solved analytically. It is shown that the error threshold on this class of dynamic landscapes is defined by the time average of the selection pressure. In the case of a periodically fluctuating fitness peak we also study the phase-shift and response amplitude of the previously documented low-pass filter effect. The special case of a small harmonic fluctuation is treated analytically.
In a co-evolutionary context, the survive probability of individual elements of a system depends on their relation with their neighbors. The natural selection process depends on the whole population, which is determined by local events between individuals. Particular characteristics assigned to each individual, as larger memory, usually improve the individual fitness, but an agent possess also endogenous characteristics that induce to re-evaluate her fitness landscape and choose the best-suited kind of interaction, inducing a non absolute value of the outcomes of the interaction. In this work,…
We consider a continuum version of a previously introduced and numerically studied model of macroevolution (PRL 75, 2055, (1995)) in which agents evolve by an optimization process in a rugged fitness landscape and die due to their competitive interactions. We first formulate dynamical equations for the fitness distribution and the survival probability. Secondly we analytically derive the $t^{-2}$ law which characterizes the life time distribution of biological genera. Thirdly we discuss other dynamical properties of the model such as the rate of extinction and conclude with a brief discussion.
We construct a pathwise formulation of a growing population of cells, based on two different samplings of lineages within the population, namely the forward and backward samplings. We show that a general symmetry relation, called fluctuation relation relates these two samplings, independently of the model used to generate divisions and growth in the cell population. These relations lead to estimators of the population growth rate, which can be very efficient as we demonstrate by an analysis of a set of mother machine data. These fluctuation relations lead to general and important inequalities …
In this paper we investigate error-thresholds on dynamics fitness-landscapes. We show that there exists both lower and an upper threshold, representing limits to the copying fidelity of simple replicators. The lower bound can be expressed as a correction term to the error-threshold present on a static landscape. The upper error-threshold is a new limit that only exists on dynamic fitness-landscapes. We also show that for long genomes on highly dynamic fitness-landscapes there exists a lower bound on the selection pressure needed to enable effective selection of genomes with superior fitness in…
Natural selection drives populations towards higher fitness, but crossing fitness valleys or plateaus may facilitate progress up a rugged fitness landscape involving epistasis. We investigate quantitatively the effect of subdividing an asexual population on the time it takes to cross a fitness valley or plateau. We focus on a generic and minimal model that includes only population subdivision into equivalent demes connected by global migration, and does not require significant size changes of the demes, environmental heterogeneity or specific geographic structure. We determine the optimal spee…
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model (REM) and by a ferromagnetic version of the REM. The solution method uses the mapping of the evolutionary dynamics into a quantum Ising chain in a transverse field and the Suzuki-Trotter formalism to calculate the transition probabilities between configurations at different times. We find that in the case of the REM landscape the dynamics can exhibit three d…
We study the evolution of mutation rates for an asexual population living on a static fitness landscape, consisting of multiple peaks forming an evolutionary staircase. The optimal mutation rate is found by maximizing the diffusion towards higher fitness. Surprisingly the optimal genomic copying fidelity is given by Q = e^(-1/ln(n)) (where n is the genome length), independent of all other parameters in the model. Simulations confirm this theoretical result. We also discuss the relation between the optimal mutation rate on static and dynamic fitness landscapes.
We investigate the problem of speciation and coexistence in simple ecosystems when the competition among individuals is included in the Eigen model for quasi-species. By suggesting an analogy between the competition among strains and the diffusion of a chemical inhibitor in a reaction-diffusion system, the speciation phenomenon is considered the analogous of chemical pattern formation in genetic space. In the limit of vanishing mutation rate we obtain analytically the conditions for speciation. Using different forms of the competition interaction we show that the speciation is absent for the g…
Stronger selection implies faster evolution---that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily supplied by mutation (i.e.\ mutation-driven evolution). Here, we show that this proposition does not actually hold for recombination-driven evolution, i.e.\ evolution in which genetic variation is primarily created by recombination rather than mutation. By numerically investigating population genetics models of recombination, migration and selection, we demo…
Stochastic gradient descent on the epigenetic landscape: a unified framework for cellular plasticity, tumor heterogeneity, and the asymptotic irrelevance of fitness
Instituto de Matemática e Computação, Universidade Federal de Itajubá（伊塔朱巴联邦大学数学与计算研究所）；Carl Gustav Carus School of Medicine, Technische Universität Dresden（德累斯顿工业大学卡尔·古斯塔夫·卡斯医学院）
The fitness landscape metaphor plays a central role on the modeling of optimizing principles in many research fields, ranging from evolutionary biology, where it was first introduced, to management research. Here we consider the ensemble of trajectories of the imitative learning search, in which agents exchange information on their fitness and imitate the fittest agent in the population aiming at reaching the global maximum of the fitness landscape. We assess the degree to which the starting and ending points determine the learning trajectories using two measures, namely, the predictability th…
