Soft Sweeps II--Molecular Population Genetics of Adaptation from Recurrent Mutation or Migration (original) (raw)
Related papers
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.
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.
The evolution of genomic islands by increased establishment probability of linked alleles
Molecular ecology, 2016
Genomic islands are clusters of loci with elevated divergence that are commonly found in population genomic studies of local adaptation and speciation. One explanation for their evolution is that linkage between selected alleles confers a benefit, which increases the establishment probability of new mutations that are linked to existing locally adapted polymorphisms. Previous theory suggested there is only limited potential for the evolution of islands via this mechanism, but involved some simplifying assumptions that may limit the accuracy of this inference. Here, we extend previous analytical approaches to study the effect of linkage on the establishment probability of new mutations and identify parameter regimes that are most likely to lead to evolution of islands via this mechanism. We show how the interplay between migration and selection affects the establishment probability of linked vs. unlinked alleles, the expected maximum size of genomic islands, and the expected time req...
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.
The pattern of genetic hitchhiking under recurrent mutation
2008
Genetic hitchhiking describes evolution at a neutral locus that is linked to a selected locus. If a beneficial allele rises to fixation at the selected locus, a characteristic polymorphism pattern (so-called selective sweep) emerges at the neutral locus. The classical model assumes that fixation of the beneficial allele occurs from a single copy of this allele that arises by mutation. However, recent theory (Pennings and Hermisson, 2006a,b) has shown that recurrent beneficial mutation at biologically realistic rates can lead to markedly different polymorphism patterns, so called soft selective sweeps. We extend an approach that has recently been developed for the classical hitchhiking model (Schweinsberg and Durrett, 2005; Etheridge et al., 2006) to study the recurrent mutation scenario. We show that the genealogy at the neutral locus can be approximated (to leading orders in the selection strength) by a marked Yule process with immigration. Using this formalism, we derive an improv...
A simple method for computing exact probabilities of mutation numbers
Theoretical Population Biology, 2004
We describe a method for the recursive computation of exact probability distributions for the number of neutral mutations segregating in samples of arbitrary size and configuration. Construction of the recursions requires only characterization of evolutionary changes as a Markov process and determination of one-step transition matrices. We address the pattern of nucleotide diversity at a neutral marker locus linked to a determinant of mating type. Under a reformulation of parameters, the method also applies directly to metapopulation models with island migration among demes. Characterization of complete probability distributions facilitates parameter estimation and hypothesis testing by likelihood-as well as moment-based approaches. r
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.
Journal of molecular evolution, 2006
Analysis of the genome-wide patterns of single-nucleotide substitution reveals that the human GC content structure is out of equilibrium. The substitutions are decreasing the overall GC content (GC), at the same time making its range narrower. Investigation of single-nucleotide polymorphisms (SNPs) revealed that presently the decrease in GC content is due to a uniform mutational preference for A:T pairs, while its projected range is due to a variability in the fixation preference for G:C pairs. However, it is important to determine whether lessons learned about evolutionary processes operating at the present time (that is reflected in the SNP data) can be extended back into the evolutionary past. We describe here a new approach to this problem that utilizes the juxtaposition of forward and reverse substitution rates to determine the relative importance of variability in mutation rates and fixation probabilities in shaping long-term substitutional patterns. We use this approach to demonstrate that the forces shaping GC content structure over the recent past (since the appearance of the SNPs) extend all the way back to the mammalian radiation $90 million years ago. In addition, we find a small but significant effect that has not been detected in the SNP data-relatively high rates of C:G fi A:T germline mutation in low-GC regions of the genome.
Genetics, 1992
We investigate the evolution of a multigene family incorporating the forces of drift, mutation, gene conversion, unequal crossing over and selection. The use of simulation studies is required due to the complexity of the model. Selection is modeled in two modes: positive selection as a function of the number of different beneficial alleles and negative selection against deleterious alleles. We assume that gene conversion is unbiased, and that all mutations are initially deleterious. Compensation between mutants creates beneficial and neutral alleles, and allowances are made for compensatory mutations either within or between the members of a multigene family. We find that gene conversion can enhance the rate of acquisition of compensatory advantageous mutations when genes are redundant.
Multi-site adaptation in the presence of infrequent recombination
Theoretical population biology, 2010
The adverse effect of co-inheritance linkage of a large number of sites on adaptation has been studied extensively for asexual populations. However, it is insufficiently understood for multi-site populations in the presence of recombination. In the present work, motivated by our studies of HIV evolution in infected patients, we consider a model of haploid populations with infrequent recombination. We assume that small quantities of beneficial alleles preexist at a large number of sites and neglect new mutation. Using a generalized form of the traveling wave method, we show that the effectiveness of recombination is impeded and the adaptation rate is decreased by inter-sequence correlations, arising due to the fact that some pairs of homologous sites have common ancestors existing after the onset of adaptation. As the recombination rate per individual becomes smaller, site pairs with common ancestors become more frequent, making recombination even less effective. In addition, an incr...