Related papers: Modes of rapid polygenic adaptation
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 this work, we study how to use sampling to speed up mechanisms for answering adaptive queries into datasets without reducing the accuracy of those mechanisms. This is important to do when both the datasets and the number of queries asked…
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…
Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection…
In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in QTL mapping have begun to elucidate the genetic architectures underlying vast numbers of…
Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete…
The evolution of complex molecular traits such as disulphide bridges often requires multiple mutations. The intermediate steps in such evolutionary trajectories are likely to be selectively neutral or deleterious. Therefore, large…
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…
To understand the effect of assortative mating on the genetic evolution of a population, we consider a finite population in which each individual has a type, determined by a sequence of n diallelic loci. We assume that the population…
Selective sweeps affect neutral genetic diversity through hitchhiking. While this effect is limited to the local genomic region of the sweep in panmictic populations, we find that in spatially-extended populations the combined effects of…
We consider a single genetic locus with two alleles $A_1$ and $A_2$ in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
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…
Rapid adaptation has been observed in numerous organisms in response to selective pressures, such as the application of pesticides and the presence of pathogens. When rapid adaptation is driven by rare alleles from the standing genetic…
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak…
For a genetic locus carrying a strongly beneficial allele which has just fixed in a large population, we study the ancestry at a linked neutral locus. During this ``selective sweep'' the linkage between the two loci is broken up by…
Estimation of the allele frequency at genetic markers is a key ingredient in biological and biomedical research, such as studies of human genetic variation or of the genetic etiology of heritable traits. As genetic data becomes increasingly…
In considering evolution of transcribed regions, regulatory modules, and other genomic loci of interest, we are often faced with a situation in which the number of allelic states greatly exceeds the population size. In this limit, the…
The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the…