Related papers: Bacterial evolution and the Bak-Sneppen model
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…
We revisit the model by Wiser, Ribeck, and Lenski (Science \textbf{342} (2013), 1364--1367), which describes how the mean fitness increases over time due to beneficial mutations in Lenski's long-term evolution experiment. We develop the…
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…
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…
In the present work we analyze the problem of adaptation and evolution of RNA virus populations, by defining the basic stochastic model as a multivariate branching process in close relation with the branching process advanced by Demetrius,…
Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
This paper theoretically analyzes a phenomenological stochastic model for bacterial growth. This model comprises cell division and the linear growth of cells, where growth rates and cell cycles are drawn from lognormal distributions. We…
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…
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…
Stochastic models, based on random processes, may lead to power law distributions, which provide long range correlations. The observation of power law behavior and the presence of long range correlations in biological systems has been…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
In the Bak-Sneppen model, the lowest fitness particle and its two nearest neighbors are renewed at each temporal step with a uniform (0,1) fitness distribution. The model presents a critical value that depends on the interaction criteria…
We study a class of Markovian systems of $N$ elements taking values in $[0,1]$ that evolve in discrete time $t$ via randomized replacement rules based on the ranks of the elements. These rank-driven processes are inspired by variants of the…
In this paper we develop and test algorithmic techniques to estimate genotypes fitnesses by analysis of observed daily frequency data monitoring the long-term evolution of bacterial populations. In particular, we develop a non-linear least…
We considered a stochastic version of the Bak-Sneppen model (SBSM) of ecological evolution where the the number $M$ of sites mutated in a mutation event is restricted to only two. Here the mutation zone consists of only one site and this…
Radical shifts in the genetic composition of large cell populations are rare events with quite low probabilities, which direct numerical simulations generally fail to evaluate accurately. In this paper, we develop a theoretical large…
We study models of biological evolution and investigate a key factor to yield self-organized criticality (SOC). The Bak-Sneppen (BS) model is the most basic model that shows an SOC state, which is developed based on minimal and plausible…
We propose a purely probabilistic model to explain the evolution path of a population maximum fitness. We show that after $n$ births in the population there are about $\ln n$ upwards jumps. This is true for any mutation probability and any…