Related papers: An accurate model for genetic hitch-hiking
We consider a biological population in which a beneficial mutation is undergoing a selective sweep when a second beneficial mutation arises at a linked locus and we investigate the probability that both mutations will eventually fix in the…
Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function…
For a family of models of evolving population under selection, which can be described by noisy traveling wave equations, the coalescence times along the genealogical tree scale like $\log^\alpha N$, where $N$ is the size of the population,…
We study the simple genetic algorithm with a ranking selection mechanism (linear ranking or tournament). We denote by $\ell$ the length of the chromosomes, by $m$ the population size, by $p_C$ the crossover probability and by $p_M$ the…
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in…
In population genetics, diffusions on the unit interval are often used to model the frequency path of an allele. In this setting we derive approximations for fixation probabilities, expected hitting times and the expected…
The Wright-Fisher model and the Moran model are both widely used in population genetics. They describe the time evolution of the frequency of an allele in a well-mixed population with fixed size. We propose a simple and tractable model…
When long-lived, balancing selection can lead to trans-species polymorphisms that are shared by two or more species identical by descent. In this case, the gene genealogies at the selected sites cluster by allele instead of by species and,…
Motivation: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing…
Accurate estimates of subnational health and demographic indicators are critical for informing health policy decisions. Many countries collect relevant data using complex household surveys, but when data are limited, direct survey weighted…
When a population inhabits an inhomogeneous environment, the fitness value of traits can vary with the position in the environment. Gene flow caused by random mating can nevertheless prevent that a sexually reproducing population splits…
We propose a metric which can be used to compute the amount of heritable variation enabled by a given dynamical system. A distribution of selection pressures is used such that each pressure selects a particular fixed point via competitive…
We examine birth--death processes with state dependent transition probabilities and at least one absorbing boundary. In evolution, this describes selection acting on two different types in a finite population where reproductive events occur…
Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the…
Gene drive alleles bias their own inheritance to offspring. They can fix in a wild-type population in spite of a fitness cost, and even lead to the eradication of the target population if the fitness cost is high. However, this outcome may…
Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…
We construct an individual-based metapopulation model of population genetics featuring migration, mutation, selection and genetic drift. In the case of a single `island', the model reduces to the Moran model. Using the diffusion…
Our goal is to study the genetic composition of a population in which each individual has 2 parents, who contribute equally to the genome of their ospring. We use a biparental Moran model, which is characterized by its xed number N of…