相关论文: A model for mutation in bacterial populations

Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…

Bacteria populate the colon where they replicate and migrate in response to nutrient availability. Here I model the colon bacterial population as a sandpile model, the colon-pile. Sand addition mimics bacterial replication and grains…

We consider the evolution of large but finite populations on arbitrary fitness landscapes. We describe the evolutionary process by a Markov, Moran process. We show that to $\mathcal O(1/N)$, the time-averaged fitness is lower for the finite…

In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…

Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will…

With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…

Cooperation is a major factor in the evolution of human societies. The structure of human social networks, which affects the dynamics of cooperation and other interpersonal phenomena, have common structural signatures. One of these…

The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and…

We present an explicit solution to a classic model of cell-population growth introduced by Luria and Delbrueck 70 years ago to study the emergence of mutations in bacterial populations. In this model a wild-type population is assumed to…

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…

We consider an exactly solvable model of branching random walk with random selection, which describes the evolution of a population with $N$ individuals on the real line. At each time step, every individual reproduces independently, and its…

The aim of this paper is to study two models for a bacterial population subject to antibiotic treatments. It is known that some bacteria are sensitive to antibiotics. These bacteria are in a state called persistence and each bacterium can…

This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it…

We consider the evolution of a population of fixed size with no selection. The number of generations $G$ to reach the first common ancestor evolves in time. This evolution can be described by a simple Markov process which allows one to…

Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly…

Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…

We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…

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…

We consider a general class of Markovian models describing the growth in a randomly fluctuating environment of a clonal biological population having several phenotypes related by stochastic switching. Phenotypes differ e.g. by the level of…