相关论文: Can we predict the mutation rate at the single nuc…

Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…

In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…

We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…

This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…

The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…

When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a…

Observations that rates of molecular evolution vary widely within and among lineages have cast doubts upon the existence of a single molecular clock. Differences in the timing of evolutionary events estimated from genetic and fossil…

Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…

In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…

We consider the accumulation of beneficial and deleterious mutations in large asexual populations. The rate of adaptation is affected by the total mutation rate, proportion of beneficial mutations and population size $N$. We show that…

We show how to incorporate fluctuations of the recombination rate along the chromosome into standard gene-genealogical models for the decorrelation of gene histories. This enables us to determine how small-scale fluctuations (Poissonian…

The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes…

We propose a one mutation model for cancer with a mutation rate that increases with time. Under rather general hypotheses the number of mutations is necessarily a (non homogeneous) Poisson process with the prescribed mutation rate. We show…

In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…

Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…

We consider a model of a population of fixed size N in which each individual gets replaced at rate one and each individual experiences a mutation at rate \mu. We calculate the asymptotic distribution of the time that it takes before there…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

Consider a supercritical birth and death process where the children acquire mutations. We study the mutation rates along the ancestral lineages in a sample of size $n$ from the population at time $T$. The mutation rate is time-inhomogenous…

In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments. A model with multiple fitness coding loci tracking a moving fitness peak is developed and an analytical expression for the optimal…

We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…