Related papers: Landscape construction in non-gradient dynamics: A…
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…
Growing efforts to measure fitness landscapes in molecular and microbial systems are premised on a tight relationship between landscape topography and evolutionary trajectories. This relationship, however, is far from being straightforward:…
Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a…
Starting from the well-known field theory for directed percolation, we describe an evolving population, near extinction, in an environment with its own nontrivial spatio-temporal dynamics. Here, we consider the special case where the…
We propose a simple model for genetic adaptation to a changing environment, describing a fitness landscape characterized by two maxima. One is associated with "specialist" individuals that are adapted to the environment; this maximum moves…
Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding…
Landscape paradigm is ubiquitous in physics and other natural sciences, but it has to be supplemented with both quantitative and qualitatively meaningful tools for analyzing the topography of a given landscape. We here consider dynamic…
These notes introduce probabilistic landscape models defined on high-dimensional discrete sequence spaces. The models are motivated primarily by fitness landscapes in evolutionary biology, but links to statistical physics and computer…
The expansion of a population into new habitat is a transient process that leaves its footprints in the genetic composition of the expanding population. How the structure of the environment shapes the population front and the evolutionary…
In both natural and artificial studies, evolution is often seen as synonymous to natural selection. Individuals evolve under pressures set by environments that are either reset or do not carry over significant changes from previous…
Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel…
Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We…
Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its…
This chapter is about Complexity and Spatial Dynamics in Urban Systems. Strong inequalities in the size of cities and the apparent difficulty of limiting their growth raise practical issues for spatial planning. At a time when new…
Logit dynamics are evolution equations that describe transitions to equilibria of actions among many players. We formulate a pair-wise logit dynamic in a continuous action space with a generalized exponential function, which we call a…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Urban structures encompass settlements, characterized by the spatial distribution of built-up areas, but also transportation structures, to connect these built-up areas. These two structures are very different in their origin and function,…
This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different…
We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…
The metaphor of holey adaptive landscapes provides a pictorial representation of the process of speciation as a consequence of genetic divergence. In this metaphor, biological populations diverge along connected clusters of well-fit…