相关论文: Bacterial evolution and the Bak-Sneppen model

Taking into account an evolutionary model of mutations in term of Levy Fights that was previously constructed, we designed an algorithm to reproduce the evolutionary dynamics of the Long-Term Evolution Experiment (LTEE) with E. Coli…

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…

In this paper we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement…

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…

Recent studies of in vitro evolution of DNA via protein binding indicate that the evolution behavior is qualitatively different in different parameter regimes. I here present a general theory that is valid for a wide range of parameters,…

These lectures contain a brief description of evolutionary models inspired by the statistical mechanics of disordered systems. After an introduction describing the Darwinian paradigm of evolving populations, the deterministic quasispecies…

We discuss the evaluation of Luria-Delbrueck fluctuation experiments under Bellman-Harris models of cell proliferation. It is shown that under certain very natural assumptions concerning the life-time distributions and the offspring…

It has long been posited that there is a connection between the dynamical equations describing evolutionary processes in biology and sequential Bayesian learning methods. This manuscript describes new research in which this precise…

We model the growth of a cell population using a piecewise deterministic Markov branching tree. In this model, each cell splits into two offspring at a division rate $B(x)$, which depends on its size $x$. The size of each cell increases…

In this work we study the effects of introducing long range interactions in the Bak-Sneppen (BS) model of biological evolution. We analyze a recebtly propopsed version of the BS model where the interactions decay as r^{-alpha}; in this way…

We show that the emergence of criticality in the locally-defined Bak-Sneppen model corresponds to separation over a hierarchy of timescales. Near to the critical point the model obeys scaling relations, with exponents which we derive…

We introduce a simple computational model that, with a microscopic dynamics driven by natural selection and mutation alone, allows the description of true speciation events. A statistical analysis of the so generated evolutionary tree…

Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…

Motivation: Gene blocks are genes co-located on the chromosome. In many cases, genes blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain,…

It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and…

In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general…

The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…

Bacteria and their viruses ("bacteriophages") coexist in natural environments forming complex infection networks. Recent empirical findings suggest that phage-bacteria infection networks often possess a nested structure such that there is a…

Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…

Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…