Related papers: An asymptotically normal test for the selective ne…
Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and population size remains constant over time. However, it is unclear how such tests are affected if the last…
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely determined by the network topology and…
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 study the dynamics of a population subject to selective pressures, evolving either on RNA neutral networks or in toy fitness landscapes. We discuss the spread and the neutrality of the population in the steady state. Different limits…
Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, $K$, at which these substitutions accumulate in the population coincides with the…
How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, many previous studies have used models…
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.…
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…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is…
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…
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…
The site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing…
The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual based model of Wright and Fisher, we…
Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…
We consider a population model where individuals behave independently from each other and whose genealogy is described by a chronological tree called splitting tree. The individuals have i.i.d. (non-exponential) lifetime durations and give…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the…
Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the…
We study the response of a quantitative trait to exponential directional selection in a finite haploid population at the genetic and the phenotypic level. We assume an infinite sites model, in which the number of new mutations per…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…