Related papers: Evolution of bacterial genomes under horizontal ge…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
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,…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
Evolutionary systems must learn to generalize, often extrapolating from a limited set of selective conditions to anticipate future environmental changes. The mechanisms enabling such generalization remain poorly understood, despite their…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They…
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.…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
We describe the evolution of $E.coli$ populations through a Bak-Sneppen type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial…
In this paper, we wish to investigate the dynamics of information transfer in evolutionary dynamics. We use information theoretic tools to track how much information an evolving population has obtained and managed to retain about different…
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…