Related papers: Bacterial Evolution and Bak-Sneppen Model
The idea of this review is to connect the different models of evolution to those of biological ageing through Darwin's theory. We start with the Eigen model of quasispecies for microevolution, then introduce the Bak-Sneppen model for…
The dynamics of complex systems in nature often occurs in terms of punctuations, or avalanches, rather than following a smooth, gradual path. A comprehensive theory of avalanche dynamics in models of growth, interface depinning, and…
We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to…
The Lenski experiment is a long term daily reproduction of Escherichia coli, that has evidenced phenotypic and genetic evolutions along the years. Some mathematical models, that could be usefull in understanding the results of that…
We study the dynamics of the Bak-Sneppen model on small-world networks. For each site in the network, we define a ``connectance,'' which measures the distance to all other sites. We find radically different patterns of activity for…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
A new delay equation is introduced to describe the punctuated evolution of complex nonlinear systems. A detailed analytical and numerical investigation provides the classification of all possible types of solutions for the dynamics of a…
We study here the Bak and Sneppen model, a prototype model for the study of Self-Organized Criticality. In this model several species interact and undergo extinction with a power law distribution of activity bursts. Species are defined…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…
The Bak-Sneppen model displaying punctuated equilibria in biological evolution is studied on random complex networks. By using the rate equation and the random walk approaches, we obtain the analytic solution of the fitness threshold $x_c$…
Current evolutionary biology models usually assume that a phenotype undergoes gradual change. This is in stark contrast to biological intuition, which indicates that change can also be punctuated-the phenotype can jump. Such a jump could…
We present evidence that the Bak-Sneppen model of evolution on $N$ vertices requires $N^3$ iterates to reach equilibrium. This is substantially more than previous authors suggested (on the order of $N^2$). Based on that estimate, we present…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
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…
Levy flights in the space of mutations model time evolution of bacterial DNA. Parameters in the model are adjusted in order to fit observations coming from the Long Time Evolution Experiment with E. Coli.
One of the key problems related to the Bak-Sneppen evolution model on the circle is to compute the limit distribution of the fitness at a fixed observation vertex in the stationary regime, as the size of the system tends to infinity.…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
By driven to extinction species less or poorly adapted, the Darwinian evolutionary theory is intrinsically an optimization theory. We investigate two optimization algorithms with such evolutionary characteristics: the Bak-Sneppen and the…
The modification of the model of P.Bak and K.Sneppen of the self-organized biological evolution is proposed on the basis of a formalization of the scheme of the biosphere evolution suggested by O.V.Kovalev. This scheme is regarded as one…
How adaptive evolution to one environmental stress improves or suppresses adaptation to another is an important problem in evolutionary biology. For instance, in microbiology, the evolution of bacteria to be resistant to different…