Related papers: Evolution models with base substitutions, insertio…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be…
The purpose of this Note is twofold: First, we introduce the general formalism of evolutionary genetics dynamics involving fitnesses, under both the deterministic and stochastic setups, and chiefly in discrete-time. In the process, we…
We simulate the evolution of model protein sequences subject to mutations. A mutation is considered neutral if it conserves 1) the structure of the ground state, 2) its thermodynamic stability and 3) its kinetic accessibility. All other…
The mutation process in evolution strategies has been interlinked with the normal distribution since its inception. Many lines of reasoning have been given for this strong dependency, ranging from maximum entropy arguments to the need for…
We consider a population of genotype sequences evolving on a rugged fitness landscape with many local fitness peaks. The population walks uphill until it encounters a local fitness maximum. We find that the statistical properties of the…
A deterministic mutation-selection model in the sequence space approach is investigated. Genotypes are identified with two-letter sequences. Mutation is modelled as a Markov process, fitness functions are of Hopfield type, where the fitness…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
The tempo and mode of an adaptive process is strongly determined by the structure of the fitness landscape that underlies it. In order to be able to predict evolutionary outcomes (even on the short term), we must know more about the nature…
Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multi-mutation leaps, that is, several mutations…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
The modelling of evolutionary game dynamics in finite populations requires microscopic processes that determine how strategies spread. The exact details of these processes are often chosen without much further consideration. Different types…
A bit-string model for the evolution of a population of haploid organisms, subject to competition, reproduction with mutation and selection is studied, using mean field theory and Monte Carlo simulations. We show that, depending on…
In this paper, we consider a fitness-level model of a non-elitist mutation-only evolutionary algorithm (EA) with tournament selection. The model provides upper and lower bounds for the expected proportion of the individuals with fitness…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
Exploiting the mathematical curiosity of intransitive dice, we present a simple theoretical model for co-evolution that captures scales ranging from the genome of the individual to the system-wide emergence of species diversity. We study a…
The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon slows down the adaptation speed and makes the theoretical…