相关论文: Statistical properties of neutral evolution

The ratio of non-synonymous to synonymous substitutions $\omega(=d_{N}/d_{S})$ has been widely used as a measure of adaptive evolution in protein coding genes. Omega can be defined in terms of population genetics parameters as the fixation…

Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with…

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…

We investigate the evolutionary dynamics of a population structured in phenotype, subjected to trait dependent selection with a linearly moving optimum and an asexual mode of reproduction. Our model consists of a non-local and non-linear…

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…

Competition is the main driver of population dynamics, which shapes the genetic composition of populations and the assembly of ecological communities. Neutral models assume that all the individuals are equivalent and that the dynamics is…

Temporal environmental variations are ubiquitous in nature, yet most of the theoretical works in population genetics and evolution assume fixed environment. Here we analyze the effect of variations in carrying capacity on the fate of a…

The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…

The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…

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,…

In this paper we explore the eco-evolutionary dynamics of a predator-prey model, where the prey population is structured according to a certain life history trait. The trait distribution within the prey population is the result of interplay…

Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…

In this review some simple models of asexual populations evolving on smooth landscapes are studied. The basic model is based on a cellular automaton, which is analyzed here in the spatial mean-field limit. Firstly, the evolution on a fixed…

We present a simple yet effective method for structure prediction of two-dimensional structures. The method is based on a combination of neural networks and evolutionary techniques. It allows finding pristine 2D structures as well as…

The concept of neutral evolutionary networks being a significant factor in evolutionary dynamics was first proposed by Huynen {\em et al.} about 7 years ago. In one sense, the principle is easy to state -- because most mutations to an…

Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…

Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

We compare an evolutionary chemical model with simple empirical models of the abundance and with static chemical models. We focus on the prediction of molecular line profiles that are commonly observed in low mass star forming cores. We…