Related papers: Adaptive evolution of hybrid bacteria by horizonta…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Massive binary evolution models are needed to predict massive star populations in star forming galaxies, the supernova diversity, and the number and properties of gravitational wave sources. Such models are often computed using so called…
The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…
Background: Hybridogenesis is a very interesting example of reproduction which seems to integrate the sexual and clonal processes in one system. In a case of frogs, described in the paper, two parental species - Rana lessonae and Rana…
We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…
Phenotypic heterogeneity is a strategy commonly used by bacteria to rapidly adapt to changing environmental conditions. Here, we study the interplay between phenotypic heterogeneity and genetic diversity in spatially extended populations.…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Many biological populations, such as bacterial colonies, have developed through evolution a protection mechanism, called bet-hedging, to increase their probability of survival under stressful environmental fluctutation. In this context, the…
When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
When a biological population expands into new territory, genetic drift develops an enormous influence on evolution at the propagating front. In such range expansion processes, fluctuations in allele frequencies occur through stochastic…
When simulating biological populations under different evolutionary genetic models, backward or forward strategies can be followed. Backward simulations, also called coalescent-based simulations, are computationally very efficient. However,…
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…
In unicellular organisms such as bacteria and in most viruses, mutations mainly occur during reproduction. Thus, genotypes with a high birth rate should have a higher mutation rate. However, standard models of asexual adaptation such as the…
Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…
During an epidemic outbreak, individuals often modify their behavior in response to global prevalence cues, using spatially mediated adaptations such as reduced mobility or transmission range. In this work, we investigate the impact of…
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…
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…