The pattern of genetic hitchhiking under recurrent mutation (original) (raw)
Related papers
Soft Sweeps III - The signature of positive selection from recurrent mutation
PLoS Genetics, 2005
Polymorphism data can be used to identify loci at which a beneficial allele has recently gone to fixation, given that an accurate description of the signature of selection is available. In the classical model that is used, a favored allele derives from a single mutational origin. This ignores the fact that beneficial alleles can enter a population recurrently by mutation during the selective phase. In this study, we present a combination of analytical and simulation results to demonstrate the effect of adaptation from recurrent mutation on summary statistics for polymorphism data from a linked neutral locus. We also analyze the power of standard neutrality tests based on the frequency spectrum or on linkage disequilibrium (LD) under this scenario. For recurrent beneficial mutation at biologically realistic rates, we find substantial deviations from the classical pattern of a selective sweep from a single new mutation. Deviations from neutrality in the level of polymorphism and in the frequency spectrum are much less pronounced than in the classical sweep pattern. In contrast, for levels of LD, the signature is even stronger if recurrent beneficial mutation plays a role. We suggest a variant of existing LD tests that increases their power to detect this signature. Citation: Pennings PS, Hermisson J (2006) Soft sweeps III: The signature of positive selection from recurrent mutation. PLoS Genet 2(12): e186.
Soft Sweeps II--Molecular Population Genetics of Adaptation from Recurrent Mutation or Migration
Molecular Biology and Evolution, 2006
In the classical model of molecular adaptation, a favored allele derives from a single mutational origin. This ignores that beneficial alleles can enter a population recurrently, either by mutation or migration, during the selective phase. In this case, descendants of several of these independent origins may contribute to the fixation. As a consequence, all ancestral haplotypes that are linked to any of these copies will be retained in the population, affecting the pattern of a selective sweep on linked neutral variation. In this study, we use analytical calculations based on coalescent theory and computer simulations to analyze molecular adaptation from recurrent mutation or migration. Under the assumption of complete linkage, we derive a robust analytical approximation for the number of ancestral haplotypes and their distribution in a sample from the population. We find that so-called ''soft sweeps,'' where multiple ancestral haplotypes appear in a sample, are likely for biologically realistic values of mutation or migration rates.
bioRxiv (Cold Spring Harbor Laboratory), 2023
We study the response of a quantitative trait to exponential directional selection in a finite haploid population, both on the genetic and the phenotypic level. We assume an infinite sites model, in which the number of new mutations per generation in the population follows a Poisson distribution (with mean Θ) and each mutation occurs at a new, previously monomorphic site. Mutation effects are beneficial and drawn from a distribution. Sites are unlinked and contribute additively to the trait. Assuming that selection is stronger than random genetic drift, we model the initial phase of the dynamics by a slightly supercritical Galton-Watson process. This enables us to obtain time-dependent results. We show that the copy-number distribution of the mutant in generation n, conditioned on survival until n, is described accurately by the deterministic increase from an initial distribution with mean 1. This distribution corresponds to the absolutely continuous part W + of the random variable, typically denoted W , that characterizes the stochasticity accumulating during the mutant's sweep. In bypassing, we prove the folklore result that W + is approximately exponentially distributed, but in general not exactly so by deriving its second and third moment.
The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations
Genetics, 2014
We study invasion and survival of weakly beneficial mutations arising in linkage to an established migration-selection polymorphism. Our focus is on a continent-island model of migration, with selection at two biallelic loci for adaptation to the island environment. Combining branching and diffusion processes, we provide the theoretical basis for understanding the evolution of islands of divergence, the genetic architecture of locally adaptive traits, and the importance of so-called 'divergence hitchhiking' relative to other mechanisms, such as 'genomic hitchhiking', chromosomal inversions, or translocations. We derive approximations to the invasion probability and the extinction time of a de-novo mutation. Interestingly, the invasion probability is maximised at a non-zero recombination rate if the focal mutation is sufficiently beneficial. If a proportion of migrants carries a beneficial background allele, the mutation is less likely to become established. Linked selection may increase the survival time by several orders of magnitude. By altering the time scale of stochastic loss, it can therefore affect the dynamics at the focal site to an extent that is of evolutionary importance, especially in small populations. We derive an effective migration rate experienced by the weakly beneficial mutation, which accounts for the reduction in gene flow imposed by linked selection. Using the concept of the effective migration rate, we also quantify the long-term effects on neutral variation embedded in a genome with arbitrarily many sites under selection. Patterns of neutral diversity change qualitatively and quantitatively as the position of the neutral locus is moved along the chromosome. This will be useful for population-genomic inference. Our results strengthen the emerging view that physically linked selection is biologically relevant if linkage is tight or if selection at the background locus is strong.
Hidden role of mutations in the evolutionary process
Physical review, 2021
Mutations not only alter allele frequencies in a genetic pool but may also determine the fate of an evolutionary process. Here we study which allele fixes in a one-step, one-way model including the wild type and two adaptive mutations. We study the effect of the four basic evolutionary mechanisms-genetic drift, natural selection, mutation, and gene flow-on mutant fixation and its kinetics. Determining which allele is more likely to fix is not simply a question of comparing fitnesses and mutation rates. For instance, if the allele of interest is less fit than the other, then not only must it have a greater mutation rate, but also its mutation rate must exceed a specific threshold for it to prevail. We find exact expressions for such conditions. Our conclusions are based on the mathematical description of two extreme but important regimes, as well as on simulations.
Evolution, 1999
We investigate how a genetic polymorphism of distinctly different alleles can evolve in an initially monomorphic population under frequency-dependent selection if mutations have only a small phenotypic effect. We consider the case of a single additive locus with a continuum of potential allele types in a diploid outbreeding population. As a specific example, we use a version of soft selection model, where stabilizing selection acts on a continuous trait within each of two habitats. If the optimal phenotypes within the habitats are sufficiantly different, then two distinctly different alleles evolve gradually from a single ancestral allele. In a wide range of parameter values, the two locally optimal phenotypes will be realized by one of the homozygotes and the heterozygote, rather than the two homozygotes. Unlike in the haploid analogue of the model, there can be multiple polymorphic evolutionary attractors with different probabilities of convergence.
Soft Sweeps: Molecular Population Genetics of Adaptation From Standing Genetic Variation
Genetics, 2005
A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario-standing variation vs. new mutations-is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of "soft sweeps," where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.
Genetics, 2013
This work is concerned with the historical progression, to …xation, of an allele in a …nite population. This progression is characterised by the average frequency trajectory of alleles which achieve …xation before a given time, T . Under a di¤usion analysis, the average trajectory, conditional on …xation by time T , is shown to be equivalent to the average trajectory in an unconditioned problem involving additional selection. We call this additional selection '…ctitious selection'; it plays the role of a selective force in the unconditioned problem but does not exist in reality.
The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion
PLoS Computational Biology, 2012
Many theoretical and experimental studies suggest that range expansions can have severe consequences for the gene pool of the expanding population. Due to strongly enhanced genetic drift at the advancing frontier, neutral and weakly deleterious mutations can reach large frequencies in the newly colonized regions, as if they were surfing the front of the range expansion. These findings raise the question of how frequently beneficial mutations successfully surf at shifting range margins, thereby promoting adaptation towards a range-expansion phenotype. Here, we use individual-based simulations to study the surfing statistics of recurrent beneficial mutations on wave-like range expansions in linear habitats. We show that the rate of surfing depends on two strongly antagonistic factors, the probability of surfing given the spatial location of a novel mutation and the rate of occurrence of mutations at that location. The surfing probability strongly increases towards the tip of the wave. Novel mutations are unlikely to surf unless they enjoy a spatial head start compared to the bulk of the population. The needed head start is shown to be proportional to the inverse fitness of the mutant type, and only weakly dependent on the carrying capacity. The precise location dependence of surfing probabilities is derived from the nonextinction probability of a branching process within a moving field of growth rates. The second factor is the mutation occurrence which strongly decreases towards the tip of the wave. Thus, most successful mutations arise at an intermediate position in the front of the wave. We present an analytic theory for the tradeoff between these factors that allows to predict how frequently substitutions by beneficial mutations occur at invasion fronts. We find that small amounts of genetic drift increase the fixation rate of beneficial mutations at the advancing front, and thus could be important for adaptation during species invasions.