Related papers: Analytic approach to the evolutionary effects of g…
We study the role of recombination, as practiced by genetically-competent bacteria, in speeding up Darwinian evolution. This is done by adding a new process to a previously-studied Markov model of evolution on a smooth fitness landscape;…
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
In large asexual populations, beneficial mutations have to compete with each other for fixation. Here, I derive explicit analytic expressions for the rate of substitution and the mean beneficial effect of fixed mutations, under the…
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…
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…
We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
One essential ingredient of evolutionary theory is the concept of fitness as a measure for a species' success in its living conditions. Here, we quantify the effect of environmental fluctuations onto fitness by analytical calculations on a…
Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…
How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material…
It has been a puzzling question why some organisms reproduce sexually. Fisher and Muller hypothesized that reproducing by sex can speed up the evolution. They explained that in the sexual reproduction, recombination can combine beneficial…
Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…
The effect of mechanical interactions between cells in the spreading of bacterial populations was investigated in one-dimensional space. A continuum-mechanics approach, comprising cell migration, proliferation, and exclusion processes, was…
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…
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…
Phenotypic fluctuations and plasticity can generally affect the course of evolution, a process known as the Baldwin effect. Several studies have recast this effect and claimed that phenotypic plasticity acceler- ates evolutionary rate (the…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…