Related papers: Why Mutant Allele Frequencies in Oncogenes Peak Ar…

In the Admixture Model, the probability of an individual having a certain number of alleles at a specific marker depends on the allele frequencies in $K$ ancestral populations and the fraction of the individual's genome originating from…

Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…

The Moran process is a foundational model of genetic drift and mutation in finite populations. In its standard two-allele form with population size $n$, allele counts, and hence allele frequencies, change through stochastic replacement and…

Tumor recurrence, driven by the evolution of drug resistance is a major barrier to therapeutic success in cancer. Resistance is often caused by genetic alterations such as point mutation, which refers to the modification of a single genomic…

The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…

Many experimental and field studies have shown that adaptation can occur very rapidly. Two qualitatively different modes of fast adaptation have been proposed: selective sweeps wherein large shifts in the allele frequencies occur at a few…

The site frequency spectrum (SFS) is a popular summary statistic of genomic data. While the SFS of a constant-sized population undergoing neutral mutations has been extensively studied in population genetics, the rapidly growing amount of…

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…

We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…

We aim to understand the evolution of the genetic composition of cancer cell populations. To achieve this, we consider an individual-based model representing a cell population where cells divide, die and mutate along the edges of a finite…

Recurrent mutations are a common phenomenon in population genetics. They may be at the origin of the fixation of a new genotype, if they give a phenotypic advantage to the carriers of the new mutation. In this paper, we are interested in…

The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for…

We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. We consider unlinked biallelic markers mutating according to a finite sites, or…

The shape of allele-frequency clines maintained by migration-selection balance depends not only on the properties of migration and selection, but also on the dominance relations among alleles and on linkage to other loci under selection. We…

The mean fixation time of a deleterious mutant allele is studied beyond the diffusion approximation. As in Kimura's classical work [M. Kimura, Proc. Natl. Acad. Sci. U.S.A. Vol.77, 522 (1980)], that was motivated by the problem of fixation…

In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by…

In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as…

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 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…

The stationary distribution of allele frequencies under a variety of Wright--Fisher $k$-allele models with selection and parent independent mutation is well studied. However, the statistical properties of maximum likelihood estimates of…