相关论文: Statistical properties of neutral evolution

The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…

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…

We investigate the evolutionary dynamics of a finite population of RNA sequences adapting to a neutral fitness landscape. Despite the lack of differential fitness between viable sequences, we observe typical properties of adaptive…

The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…

Neutral evolution assumes that there are no selective forces distinguishing different variants in a population. Despite this striking assumption, many recent studies have sought to assess whether neutrality can provide a good description of…

We give a overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of nonspecialists, especially statistical physicists. In particular, we focus mostly on neutral models in…

System Evolution Analytics on a system that evolves is a challenge because it makes a State Series SS = {S1, S2... SN} (i.e., a set of states ordered by time) with several inter-connected entities changing over time. We present stability…

Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…

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…

In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…

There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…

Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…

An important parameter in the study of population evolution is $\theta=4N\nu$, where $N$ is the effective population size and $\nu$ is the rate of mutation per locus per generation. Therefore, $\theta$ represents the mean number of…

The evolutionary and ecological processes behind the origin of species are among the most fundamental problems in biology. In fact, many theoretical hypothesis on different type of speciation have been proposed. In particular, models of…

Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…

We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population are governed by correlation…

We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…

Motivated by landscape models in string theory, cosmic nuclear evolution is analyzed allowing the Standard Model Higgs expectation value w to take values different from that in our world (w=1), while holding the Yukawa couplings fixed.…

Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…

The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network…