Related papers: Adaptive evolution of hybrid bacteria by horizonta…
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
Plasmids are major players in Horizontal Gene Transfer mechanisms, hence they are highly variable in their gene content and length. We propose a model for the fitness of a plasmid as a function of its length, which predicts diminishing…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
The purpose of this roadmap article is to draw attention to a paradigm shift in our understanding of evolution towards a perspective of ecological-evolutionary feedback, highlighted through two recent highly simplified examples of rapid…
The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but…
Gene expression levels are important molecular quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies in recent years have revealed substantial adaptive evolution at the genomic…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…
Using Monte Carlo model of biological evolution we have discovered that populations can switch between two different strategies of their genomes' evolution; Darwinian purifying selection and complementing the haplotypes. The first one is…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
We show how concepts from statistical physics, such as order parameter, thermodynamic limit, and quantum phase transition, translate into biological concepts in mutation-selection models for sequence evolution and can be used there. The…
A hybrid phase transition (HPT) that exhibits properties of continuous and discontinuous phase transitions at the same transition point has been observed in diverse complex systems. Previous studies of the HPTs on complex networks mainly…
Genetic diversity is central to the process of evolution. Both natural selection and random genetic drift are influenced by the level of genetic diversity of a population; selection acts on diversity while drift samples from it. At a given…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…