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Showing papers on "Genetic hitchhiking published in 2015"


Journal ArticleDOI
TL;DR: The output from SmileFinder can be used to plot percentile values to look for population diversity and divergence patterns that may suggest past actions of positive selection along chromosome maps, and to compare lists of suspected candidate genes under random gene sets to test for the overrepresentation of these patterns among gene categories.
Abstract: Background Adaptive alleles may rise in frequency as a consequence of positive selection, creating a pattern of decreased variation in the neighboring loci, known as a selective sweep. When the region containing this pattern is compared to another population with no history of selection, a rise in variance of allele frequencies between populations is observed. One challenge presented by large genome-wide datasets is the ability to differentiate between patterns that are remnants of natural selection from those expected to arise at random and/or as a consequence of selectively neutral demographic forces acting in the population.

349 citations


Journal ArticleDOI
29 May 2015-Science
TL;DR: Deep sequencing of a thermophilic cyanobacterial population and analysis of the statistics of synonymous single-nucleotide polymorphisms revealed a high rate of homologous recombination and departures from neutral drift consistent with the effects of genetic hitchhiking.
Abstract: Extensive fine-scale genetic diversity is found in many microbial species across varied environments, but for most, the evolutionary scenarios that generate the observed variation remain unclear. Deep sequencing of a thermophilic cyanobacterial population and analysis of the statistics of synonymous single-nucleotide polymorphisms revealed a high rate of homologous recombination and departures from neutral drift consistent with the effects of genetic hitchhiking. A sequenced isolate genome resembled an unlinked random mixture of the allelic diversity at the sampled loci. These observations suggested a quasisexual microbial population that occupies a broad ecological niche, with selection driving frequencies of alleles rather than whole genomes.

124 citations


Journal ArticleDOI
TL;DR: It is shown that during the experiment linkage disequilibrium increased almost uniformly over much greater distances than typically seen in Drosophila, and LD in such rising haplotype-blocks results in long range hitchhiking over multiple kilobase-sized regions.
Abstract: Whole-genome resequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype–phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an excess of candidate loci. Several explanations have been proposed for this phenomenon, but it is clear that information about the linkage structure during such experiments is needed. Until now only Pool-Seq (whole-genome sequencing of pools of individuals) data were available, which do not provide sufficient information about the correlation between linked sites. We address this problem in two complementary analyses of three replicate Drosophila melanogaster populations evolving to a new hot temperature environment for almost 70 generations. In the first analysis, we sequenced 58 haploid genomes from the founder population and evolved flies at generation 67. We show that during the experiment linkage disequilibrium (LD) increased almost uniformly over much greater distances than typically seen in Drosophila. In the second analysis, Pool-Seq time series data of the three replicates were combined with haplotype information from the founder population to follow blocks of initial haplotypes over time. We identified 17 selected haplotype-blocks that started at low frequencies in the base population and increased in frequency during the experiment. The size of these haplotype-blocks ranged from 0.082 to 4.01 Mb. Moreover, between 42% and 46% of the top candidate single nucleotide polymorphisms from the comparison of founder and evolved populations fell into the genomic region covered by the haplotype-blocks. We conclude that LD in such rising haplotype-blocks results in long range hitchhiking over multiple kilobase-sized regions. LD in such haplotype-blocks is therefore a major factor contributing to an excess of candidate loci. Although modifications of the experimental design may help to reduce the hitchhiking effect and allow for more precise mapping of causative variants, we also note that such haplotype-blocks might be well suited to study the dynamics of selected genomic regions during experimental evolution studies.

81 citations


Journal ArticleDOI
01 Oct 2015-Genetics
TL;DR: It is found that in general, adaptation from a unique standing variant will likely be difficult to detect on the basis of genetic polymorphism data from a single population time point alone, and when it can be detected, it will be hard to distinguish from other varieties of selective sweeps.
Abstract: The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical “hard sweep” hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite-alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep and multiple-mutation soft sweeps. We find that in general, adaptation from a unique standing variant will likely be difficult to detect on the basis of genetic polymorphism data from a single population time point alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps. Samples from multiple populations and/or time points have the potential to ease this difficulty.

58 citations


Journal ArticleDOI
TL;DR: Analysis of population genetic models of selective sweeps in prokaryotes under negative frequency-dependent selection indicates that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low.
Abstract: Fixation of beneficial genes in bacteria and archaea (collectively, prokaryotes) is often believed to erase pre-existing genomic diversity through the hitchhiking effect, a phenomenon known as genome-wide selective sweep. Recent studies, however, indicate that beneficial genes spread through a prokaryotic population via recombination without causing genome-wide selective sweeps. These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena. We use mathematical modeling to investigate potential solutions to this apparent paradox. Most microbes in nature evolve in heterogeneous, dynamic communities, in which ecological interactions can substantially impact evolution. Here, we focus on the effect of negative frequency-dependent selection (NFDS) such as caused by viral predation (kill-the-winner dynamics). The NFDS maintains multiple genotypes within a population, so that a gene beneficial to every individual would have to spread via recombination, hence a gene-specific selective sweep. However, gene loci affected by NFDS often are located in variable regions of microbial genomes that contain genes involved in the mobility of selfish genetic elements, such as integrases or transposases. Thus, the NFDS-affected loci are likely to experience elevated rates of recombination compared with the other loci. Consequently, these loci might be effectively unlinked from the rest of the genome, so that NFDS would be unable to prevent genome-wide selective sweeps. To address this problem, we analyzed population genetic models of selective sweeps in prokaryotes under NFDS. The results indicate that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low. Although these conditions might seem to contradict the intuition that gene-specific selective sweeps require high recombination rates, they actually decrease the effective rate of recombination at loci affected by NFDS relative to the per-locus basal level, so that NFDS can cause gene-specific selective sweeps. Because many free-living prokaryotes are likely to evolve under NFDS caused by ubiquitous viruses, gene-specific selective sweeps driven by NFDS are expected to be a major, general phenomenon in prokaryotic populations.

48 citations


Journal ArticleDOI
01 Jun 2015-Genetics
TL;DR: A composite-likelihood-ratio (CLR) test for detecting incomplete selective sweeps based on the joint sampling probabilities for allele frequencies of two groups as a function of strength of selection and recombination rate is proposed.
Abstract: Adaptive evolution occurs as beneficial mutations arise and then increase in frequency by positive natural selection. How, when, and where in the genome such evolutionary events occur is a fundamental question in evolutionary biology. It is possible to detect ongoing positive selection or an incomplete selective sweep in species with sexual reproduction because, when a beneficial mutation is on the way to fixation, homologous chromosomes in the population are divided into two groups: one carrying the beneficial allele with very low polymorphism at nearby linked loci and the other carrying the ancestral allele with a normal pattern of sequence variation. Previous studies developed long-range haplotype tests to capture this difference between two groups as the signal of an incomplete selective sweep. In this study, we propose a composite-likelihood-ratio (CLR) test for detecting incomplete selective sweeps based on the joint sampling probabilities for allele frequencies of two groups as a function of strength of selection and recombination rate. Tested against simulated data, this method yielded statistical power and accuracy in parameter estimation that are higher than the iHS test and comparable to the more recently developed nSL test. This procedure was also applied to African Drosophila melanogaster population genomic data to detect candidate genes under ongoing positive selection. Upon visual inspection of sequence polymorphism, candidates detected by our CLR method exhibited clear haplotype structures predicted under incomplete selective sweeps. Our results suggest that different methods capture different aspects of genetic information regarding incomplete sweeps and thus are partially complementary to each other.

41 citations


01 Jan 2015
TL;DR: In this paper, the authors study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination.
Abstract: A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.

33 citations


Journal ArticleDOI
TL;DR: In this paper, the authors derived a recursive expression for the establishment probability of the beneficial allele after a single hybridization event and furthermore studied the probability that slightly deleterious alleles hitchhike to fixation.
Abstract: By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.

27 citations


Journal ArticleDOI
TL;DR: A pattern of gene decay on the X-specific region of the Y chromosome may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.
Abstract: Genes on non-recombining heterogametic sex chromosomes may degrade over time through the irreversible accumulation of deleterious mutations. In papaya, the non-recombining male-specific region of the Y (MSY) consists of two evolutionary strata corresponding to chromosomal inversions occurring approximately 7.0 and 1.9 MYA. The step-wise recombination suppression between the papaya X and Y allows for a temporal examination of the degeneration progress of the young Y chromosome. Comparative evolutionary analyses of 55 X/Y gene pairs showed that Y-linked genes have more unfavorable substitutions than X-linked genes. However, this asymmetric evolutionary pattern is confined to the oldest stratum, and is only observed when recently evolved pseudogenes are included in the analysis, indicating a slow degeneration tempo of the papaya Y chromosome. Population genetic analyses of coding sequence variation of six Y-linked focal loci in the oldest evolutionary stratum detected an excess of nonsynonymous polymorphism and reduced codon bias relative to autosomal loci. However, this pattern was also observed for corresponding X-linked loci. Both the MSY and its corresponding X-specific region are pericentromeric where recombination has been shown to be greatly reduced. Like the MSY region, overall selective efficacy on the X-specific region may be reduced due to the interference of selective forces between highly linked loci, or the Hill–Robertson effect, that is accentuated in regions of low or suppressed recombination. Thus, a pattern of gene decay on the X-specific region may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.

25 citations


Journal ArticleDOI
01 Dec 2015-Genetics
TL;DR: A new phenomenon is characterized: mildly deleterious recessive alleles, thought to represent a wide fraction of newly arising mutations, on average survive in a population slightly longer than neutral ones, before getting lost.
Abstract: In finite populations, an allele disappears or reaches fixation due to two main forces, selection and drift. Selection is generally thought to accelerate the process: a selected mutation will reach fixation faster than a neutral one, and a disadvantageous one will quickly disappear from the population. We show that even in simple diploid populations, this is often not true. Dominance and recessivity unexpectedly slow down the evolutionary process for weakly selected alleles. In particular, slightly advantageous dominant and mildly deleterious recessive mutations reach fixation slightly more slowly than neutral ones (at most 5%). This phenomenon determines genetic signatures opposite to those expected under strong selection, such as increased instead of decreased genetic diversity around the selected site. Furthermore, we characterize a new phenomenon: mildly deleterious recessive alleles, thought to represent a wide fraction of newly arising mutations, on average survive in a population slightly longer than neutral ones, before getting lost. Consequently, these mutations are on average slightly older than neutral ones, in contrast with previous expectations. Furthermore, they slightly increase the amount of weakly deleterious polymorphisms, as a consequence of the longer unconditional sojourn times compared to neutral mutations.

24 citations


Journal ArticleDOI
TL;DR: A model of a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker, shows the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that is called Substitution Fleming–Viot Process (SFVP).
Abstract: How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

Journal ArticleDOI
TL;DR: In this paper, the authors identify the genetic signature of a selective sweep in a population described by a birth-and-death process with density dependent competition, and study the limit behavior for large K, where K scales the population size.

Journal ArticleDOI
TL;DR: Simulation is used to explore the utility of the joint site frequency spectrum to estimate selection and demography simultaneously, including developing an extension of the previously proposed Jaatha program and demonstrating that the common assumption of selective neutrality when estimating demographic models may lead to severe biases.
Abstract: The ability to infer the parameters of positive selection from genomic data has many important implications, from identifying drug-resistance mutations in viruses to increasing crop yield by genetically integrating favorable alleles. Although it has been well-described that selection and demography may result in similar patterns of diversity, the ability to jointly estimate these two processes has remained elusive. Here, we use simulation to explore the utility of the joint site frequency spectrum to estimate selection and demography simultaneously, including developing an extension of the previously proposed Jaatha program (Mathew et al., 2013). We evaluate both complete and incomplete selective sweeps under an isolation-with-migration model with and without population size change (both population growth and bottlenecks). Results suggest that while it may not be possible to precisely estimate the strength of selection, it is possible to infer the presence of selection while estimating accurate demographic parameters. We further demonstrate that the common assumption of selective neutrality when estimating demographic models may lead to severe biases. Finally, we apply the approach we have developed to better characterize the within-host demographic and selective history of human cytomegalovirus (HCMV) infection using published next generation sequencing data.

01 Jan 2015
TL;DR: There is an abundance of genetic variation in photosynthesis which can be used to improve the trait for agriculture and provide insights into novel evolutionary phenomena in the field.
Abstract: Oxygenic photosynthesis is the gateway of the sun’s energy into the biosphere, it is where light becomes life. Genetic variation is the fuel of evolution, without it natural selection is powerless and adaptation impossible. In this thesis I have set out to study a relatively unexplored field which sits at the intersection of these two topics, namely natural genetic variation in plant photosynthesis. To begin I reviewed the available literature (Chapter 2), from this it became clear that the main bottleneck restricting progress was the lack of high-throughput phenotyping platforms for photosynthesis. To address this an automated high-throughput chlorophyll fluorescence phenotyping system was developed, which could measure 1440 plants in less than an hour for ΦPSII, a measure of photosynthetic efficiency (Chapter 3). Using this phenotyping platform I screened five populations of Arabidopsis thaliana. Three of these populations resulted from bi-parental crosses and segregated for only two genomes, using these I conducted family mapping (Chapter 4). The final two populations were composed of natural, field collected, accessions and were analysed using a genome wide association approach (Chapter 5). The family mapping approach had greater statistical power due to within population replication and the genome wide association approach had higher mapping resolution due to historical recombination. Both approaches were used to identify genomic regions (loci) which were responsible for some of the variation in photosynthesis observed. The number and average effect of these loci was used to infer the genetic architecture of photosynthesis as a highly complex polygenic trait for which there are many loci of very small effect. In addition to screening these large populations a smaller subset of 18 lines was assayed for natural variation in phosphorylation of photosystem II (PSII) proteins in response to changing light (Chapter 6). This exploratory study indicated that this process shows considerable variation and may be important for adaptation of the photosynthetic apparatus to photosynthetic extremes. The genetic mapping studies just described, focus exclusively on genetic variation in the nuclear genome, whilst this contains the majority of the plants genetic information there is also a store of genetic information in the chloroplast and mitochondria. These genetic repositories contain genes which are essential for photosynthesis and energy metabolism. Any variation in these genes could have a large impact on photosynthesis. To study natural variation in these genomes I developed a new population of reciprocal nuclear-organellar hybrids (cybrids) which could be used to study the effect of genetic variation in organelles whilst controlling for nuclear genetic variation (Chapter 7). Preliminary results indicate that this resource will be of great use in disentangling natural genetic variation in nucleo-organelle interactions. Finally I looked at one chloroplast encoded photosynthetic mutation in more detail (Chapter 8). This mutation had evolved in response to herbicide application and had spread along British railways. When studying this population of resistant plants I found empirical evidence for organelle mediated nuclear genetic hitchhiking. This is a previously undescribed evolutionary phenomenon and is likely to be quite common. In conclusion there is an abundance of genetic variation in photosynthesis which can be used to improve the trait for agriculture and provide insights into novel evolutionary phenomena in the field.

Posted ContentDOI
16 Nov 2015-bioRxiv
TL;DR: The presence of recombination in the plastid is consistent with laboratory studies in C. reinhardtii and demonstrates that although the plastsid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.
Abstract: Plastids perform crucial cellular functions, including photosynthesis, across a wide variety of eukaryotes. Since endosymbiosis, plastids have maintained independent genomes that now display a wide diversity of gene content, genome structure, gene regulation mechanisms, and transmission modes. The evolution of plastid genomes depends on an input of de novo mutation, but our knowledge of mutation in the plastid is limited to indirect inference from patterns of DNA divergence between species. Here, we use a mutation accumulation experiment, where selection acting on mutations is rendered ineffective, combined with whole-plastid genome sequencing to directly characterize de novo mutation in Chlamydomonas reinhardtii. We show that the mutation rates of the plastid and nuclear genomes are similar, but that the base spectra of mutations differ significantly. We integrate our measure of the mutation rate with a population genomic dataset of 20 individuals, and show that the plastid genome is subject to substantially stronger genetic drift than the nuclear genome. We also show that high levels of linkage disequilibrium in the plastid genome are not due to restricted recombination, but are instead a consequence of increased genetic drift. One likely explanation for increased drift in the plastid genome is that there are stronger effects of genetic hitchhiking. The presence of recombination in the plastid is consistent with laboratory studies in C. reinhardtii and demonstrates that although the plastid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.

Posted ContentDOI
01 Apr 2015-bioRxiv
TL;DR: Using an agent-based model, it is demonstrated that there exists a broad set of conditions allowing the evolution of cooperation through the Hankshaw effect, and the feasibility of the theoretical assumptions for natural systems is discussed, not only for the case of cooperation, but also for other costly social behaviors such as spite.
Abstract: The evolution of cooperation—costly behavior that benefits others—faces one clear obstacle. Namely, cooperators are always at a competitive disadvantage relative to defectors, individuals that reap the same social benefits, but evade the personal cost. One solution to this problem involves genetic hitchhiking, where the allele encoding cooperative behavior becomes linked to a beneficial mutation. While traditionally seen as a passive process driven purely by chance, here we explore a more active form of hitchhiking. Specifically, we model hitchhiking in the context of adaptation to a stressful environment by cooperators and defectors with spatially limited dispersal. Under such conditions, clustered cooperators reach higher local densities, thereby experiencing more opportunities for mutations than defectors. Thus, the allele encoding cooperation has a greater probability of hitchhiking with alleles conferring stress adaptation. We label this probabilistic enhancement the "Hankshaw effect" after the character Sissy Hankshaw, whose anomalously large thumbs made her a singularly effective hitchhiker. Using an agent-based model, we demonstrate that there exists a broad set of conditions allowing the evolution of cooperation through the Hankshaw effect. We discuss the feasibility of our theoretical assumptions for natural systems, not only for the case of cooperation, but also for other costly social behaviors such as spite. The primary elements of our model, including genetic hitchhiking and population structure, have been discussed separately in previous models exploring the evolution of cooperation. However, the combination of these elements has not been appreciated as a solution to the problem of cooperation.

Posted Content
TL;DR: In this paper, the authors studied the genetic signature left by a selective sweep induced by recurrent mutations at a given locus from an allele A to an allele a, depending on the mutation frequency.
Abstract: Recurrent mutations are a common phenomenon in population genetics. They may be at the origin of the fixation of a new genotype, if they give a phenotypic advantage to the carriers of the new mutation. In this paper, we are interested in the genetic signature left by a selective sweep induced by recurrent mutations at a given locus from an allele A to an allele a, depending on the mutation frequency. We distinguish three possible scales for the mutation probability per reproductive event, which entail distinct genetic signatures. Besides, we study the hydrodynamic limit of the A- and a-population size dynamics when mutations are frequent, and find non trivial equilibria leading to several possible patterns of polymorphism.

Posted ContentDOI
22 May 2015-bioRxiv
TL;DR: An analytical investigation of a model in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation finds that in general, adaptation from a uniquely derived standing variant will be difficult to detect on the basis of genetic polymorphism data alone.
Abstract: The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical ``hard sweep'' hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways, and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep, and multiple mutation soft sweeps. We find that in general, adaptation from a uniquely derived standing variant will be difficult to detect on the basis of genetic polymorphism data alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps.


Posted Content
TL;DR: It is proved that the stochasticity of the population size has a major impact on this genealogy and the derivation of the linkage disequilibrium between neutral loci is applied, a statistic which is frequently used to detect recent se-lection on genetic data.
Abstract: We study the impact of a hard selective sweep on the genealogy of partially linked neu-tral loci in the vicinity of the positively selected allele. We consider a sexual population of varying size and, focusing on two neighboring loci, derive an approximate formula for the neutral geneal-ogy of a sample of individuals taken at the end of the sweep. We prove that the stochasticity of the population size has a major impact on this genealogy and apply our results to the derivation of the linkage disequilibrium between neutral loci, a statistic which is frequently used to detect recent se-lection on genetic data. Furthermore, we provide a deeper insight into the dynamics of the mutant and wild type population during the different stages of a selective sweep.

Journal Article
TL;DR: The hitchhiking effects in the advanced wild soybean chromosome segment substitution lines with selection under100-seed weight conditions were analyzed by scanning multiple molecular loci and segregation distortion of allelic genes was reduced but the degree of segregation distortion increased.
Abstract: The hitchhiking effects in the advanced wild soybean chromosome segment substitution lines with selection under100-seed weight conditions were analyzed by scanning multiple molecular loci. The lociare connected with 100-seed weight and their response in selection condition were analysized. 28. 10% of the loci in random population were detected with segregation distortion( P 0. 05),after selection in view of 100-seed weight,the segregation distortion of allelic genes was reduced but the degree of segregation distortion increased. The segregation distortion ratio reduced to 4. 13% and 23. 14%,the variation of chi-square reduced to 0-166. 67 and 0. 01-81. 30. Twelve putative 100-seed weight related loci were obtained using chi-square test( P 0. 05) by comparison of the introgressive frequency of alleles between random population and selected population.

Posted ContentDOI
06 Aug 2015-bioRxiv
TL;DR: The existing theory on the evolution of mutation rates, which was thought to be limited to asexual populations, is extended, with possibly far-reaching consequences concerning invasiveness and the rate at which species can adapt to novel environmental conditions.
Abstract: The evolution of dispersal during range expansion increases invasion speed, provided that a species can adapt sufficiently fast to novel local conditions. Iterated founder effects during range expansion, however, cause low levels of local genetic diversity at these range margins. Mutation rates can evolve, too, under conditions that favor an increased rate of local adaptation, but this has thus far only been associated with asexual populations. As selection acts on the mutation that occurs at a gene under selection and not on the rate with which such mutations occur, the evolution of mutation rates is the result of indirect selection. The establishment of a particular mutation rate is thus restricted to genetic hitchhiking, which is highly sensitive to recombination. However, under conditions of genetic similarity, typical for expanding range margins, the evolution of mutation rates in sexual populations might be possible. Using an individual-based model we show that natural selection leads to co-evolution of dispersal rates and mutation rates in sexual populations due to spatial sorting. The evolution of mutation rate is adaptive and clearly advances range expansion both through its effect on the evolution of dispersal rate, and the evolution of local adaptation. By this we extend the existing theory on the evolution of mutation rates, which was thought to be limited to asexual populations, with possibly far-reaching consequences concerning invasiveness and the rate at which species can adapt to novel environmental conditions.