scholarly journals Estimating the genome-wide contribution of selection to temporal allele frequency change

2019 ◽  
Author(s):  
Vince Buffalo ◽  
Graham Coop
Keyword(s):  
Allele Frequency ◽  
Genetic Drift ◽  
Genomic Data ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Standing Variation ◽  
Genome Wide ◽  
Selection Experiments ◽  
Frequency Changes ◽  
Linked Selection

AbstractRapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult, since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data, e.g. evolve-and-resequence studies. These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one timepoint to be predictive of the changes at later timepoints, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time-points and across replicates. We estimate that at least 17% to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.Significance StatementA long-standing problem in evolutionary biology is to understand the processes that shape the genetic composition of populations. In a population without migration, the two processes that change allele frequencies are selection, which increases beneficial alleles and removes deleterious ones, and genetic drift which randomly changes frequencies as some parents contribute more or less alleles to the next generation. Previous efforts to disentangle these processes have used genomic samples from a single timepoint and models of how selection affects neighboring sites (linked selection). Here, we use genomic data taken through time to quantify the contributions of selection and drift to genome-wide frequency changes. We show selection acts over short timescales in three evolve-and-resequence studies and has a sizable genome-wide impact.

scholarly journals Estimating the genome-wide contribution of selection to temporal allele frequency change

2020 ◽  
Vol 117 (34) ◽  
pp. 20672-20680
Author(s):  
Vince Buffalo ◽  
Graham Coop
Keyword(s):  
Allele Frequency ◽  
Genetic Drift ◽  
Time Course ◽  
Frequency Change ◽  
Time Points ◽  
Standing Variation ◽  
Genome Wide ◽  
Selection Experiments ◽  
Frequency Changes ◽  
Linked Selection

Rapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data (e.g., evolve-and-resequence studies). These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one time point to be predictive of the changes at later time points, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time points and across replicates. We estimate that at least 17 to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances, we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.

scholarly journals The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data

2019 ◽  
Author(s):  
Vince Buffalo ◽  
Graham Coop
Keyword(s):  
Genetic Variation ◽  
Allele Frequency ◽  
Genomic Data ◽  
Frequency Change ◽  
Rapid Adaptation ◽  
Effective Population ◽  
Additive Genetic Variation ◽  
Analytic Expressions ◽  
Frequency Changes ◽  
Linked Selection

AbstractPopulations can adapt over short, ecological timescales via standing genetic variation. Genomic data collected over tens of generations in both natural and lab populations is increasingly used to find selected loci underpinning such rapid adaptation. Although selection on large effect loci may be detectable in such data, often the fitness differences between individuals have a polygenic architecture, such that selection at any one locus leads to allele frequency changes that are too subtle to distinguish from genetic drift. However, one promising signal comes from the fact that selection on polygenic traits leads to heritable fitness backgrounds that neutral alleles can become stochastically associated with. These associations perturb neutral allele frequency trajectories, creating autocovariance across generations that can be directly measured from temporal genomic data. We develop theory that predicts the magnitude of these temporal autocovariances, showing that it is determined by the level of additive genetic variation, recombination, and linkage disequilibria in a region. Furthermore, by using analytic expressions for the temporal variances and autocovariances in allele frequency, we demonstrate one can estimate the additive genetic variation for fitness and the drift-effective population size from temporal genomic data. Finally, we also show how the proportion of total variation in allele frequency change due to linked selection can be estimated from temporal data. Temporal genomic data offers strong opportunities to identify the role linked selection has on genome-wide diversity over short timescales, and can help bridge population genetic and quantitative genetic studies of adaptation.

scholarly journals The promise and deceit of genomic selection component analyses

2021 ◽  
Vol 288 (1961) ◽  
Author(s):  
John K. Kelly
Keyword(s):  
Allele Frequency ◽  
Statistical Power ◽  
Field Experiments ◽  
Whole Genome Sequence ◽  
Frequency Change ◽  
Genome Wide ◽  
Pooled Sequencing ◽  
Frequency Changes ◽  
Selection Intensities ◽  
Combine Information

Selection component analyses (SCA) relate individual genotype to fitness components such as viability, fecundity and mating success. SCA are based on population genetic models and yield selection estimates directly in terms of predicted allele frequency change. This paper explores the statistical properties of gSCA: experiments that apply SCA to genome-wide scoring of SNPs in field sampled individuals. Computer simulations indicate that gSCA involving a few thousand genotyped samples can detect allele frequency changes of the magnitude that has been documented in field experiments on diverse taxa. To detect selection, imprecise genotyping from low-level sequencing of large samples of individuals provides much greater power than precise genotyping of smaller samples. The simulations also demonstrate the efficacy of ‘haplotype matching’, a method to combine information from a limited collection of whole genome sequence (the reference panel) with the much larger sample of field individuals that are measured for fitness. Pooled sequencing is demonstrated as another way to increase statistical power. Finally, I discuss the interpretation of selection estimates in relation to the Beavis effect, the overestimation of selection intensities at significant loci.

scholarly journals Allele frequency dynamics in a pedigreed natural population

2018 ◽  
Vol 116 (6) ◽  
pp. 2158-2164 ◽  
Author(s):  
Nancy Chen ◽  
Ivan Juric ◽  
Elissa J. Cosgrove ◽  
Reed Bowman ◽  
John W. Fitzpatrick ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Success ◽  
Allele Frequency ◽  
Natural Population ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Short Term ◽  
Individual Survival ◽  
Frequency Changes ◽  
Genetic Contributions

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes—variation in individual survival, reproductive success, and movement—are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

scholarly journals Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed population

2021 ◽  
Author(s):  
Rose M.H. Driscoll ◽  
Felix E.G. Beaudry ◽  
Elissa J Cosgrove ◽  
Reed Bowman ◽  
John W Fitzpatrick ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Evolutionary Dynamics ◽  
Z Chromosome ◽  
Frequency Change ◽  
Effective Population ◽  
Genome Wide ◽  
Males And Females ◽  
Frequency Changes ◽  
Genetic Contributions ◽  
The Impact

Sex-biased demography, including sex-biased survival or migration, can impact allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females have similar contributions to autosomal allele frequency change, but males have higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in accounting for genome-wide allele frequency change in wild populations.

scholarly journals Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

2019 ◽  
Author(s):  
Seth M. Rudman ◽  
Sharon Greenblum ◽  
Rachel C. Hughes ◽  
Subhash Rajpurohit ◽  
Ozan Kiratli ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Rapid Evolution ◽  
Natural Populations ◽  
Genomic Data ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Microbiome Composition ◽  
Population Genomic ◽  
Genome Wide ◽  
Microbial Group

AbstractPopulation genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging - it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host-microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Manipulation of the microbiome altered population dynamics and increased divergence between treatments in allele frequencies genome-wide, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.Significance statementNatural selection can drive evolution over short timescales. However, there is little understanding of which ecological factors are capable of driving rapid evolution and how this rapid evolution alters allele frequencies across the genome. Here we combine a field experiment with population genomic data from natural populations across a latitudinal gradient to assess whether and how microbiome composition drives rapid genomic evolution of host populations. We find that differences in microbiome composition cause divergence in allele frequencies genome-wide, including in genes previously associated with local adaptation. Moreover, we observed concordance between experimental and natural populations in terms of the direction of allele frequency change, suggesting that microbiome composition may be an agent of selection that drives adaptation in the wild.

scholarly journals Allele frequency dynamics in a pedigreed natural population

2018 ◽  
Author(s):  
Nancy Chen ◽  
Ivan Juric ◽  
Elissa J. Cosgrove ◽  
Reed Bowman ◽  
John W. Fitzpatrick ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Success ◽  
Allele Frequency ◽  
Natural Population ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Short Term ◽  
Individual Survival ◽  
Frequency Changes ◽  
Genetic Contributions

ABSTRACTA central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes - variation in individual survival, reproductive success, and movement - are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

scholarly journals Distinguishing among modes of convergent adaptation using population genomic data

2017 ◽  
Author(s):  
Kristin M. Lee ◽  
Graham Coop
Keyword(s):  
Gene Flow ◽  
Fundulus Heteroclitus ◽  
Copper Toxicity ◽  
Genomic Data ◽  
Composite Likelihood ◽  
Allele Frequencies ◽  
Standing Variation ◽  
Genome Wide ◽  
Genetic Level ◽  
The Impact

AbstractGeographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower, Mimulus guttatus. We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish, Fundulus heteroclitus, that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species’ range.

scholarly journals Genome-Wide Detection of Allele Frequency Change and Quantitative Trait Loci for Respiratory Disease and Immune-Related Traits in Landrace Pigs Selected for Mycoplasmal Pneumonia of Swine Resistance

2021 ◽  
Author(s):  
Yoshinobu Uemoto ◽  
Kasumi Ichinoseki ◽  
Toshimi Matsumoto ◽  
Nozomi Oka ◽  
Hironori Takamori ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Allele Frequency ◽  
Respiratory Disease ◽  
Quantitative Trait ◽  
Association Studies ◽  
Frequency Change ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Mycoplasmal Pneumonia ◽  
Frequency Changes

Abstract Background: The genetic improvement of disease resistance in pig has been well-received. Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for understanding the genomic background of disease resistance and to apply marker-assisted selection. The objective of this study was to understand the influence of genomic factors on respiratory disease and immune-related traits in MPS-selected pigs.Results: A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip, and were then used for genomic analyses. First, we performed genome-wide association studies (GWAS) to detect a novel QTL for a total of 22 performance, respiratory disease, and immune-related traits using additive and nonadditive genetic effects. Second, we evaluated the changes in allele frequency due to selection for MPS resistance and compared the putative selected regions with the detected QTL. GWAS detected a total of 11 genome-wide significant single nucleotide polymorphisms (SNPs) with an additive effect in five traits and a total of three significant SNPs with a nonadditive effect in three traits. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic region among traits, only five of these detected QTL regions overlapped among traits. Changes in allele frequencies at the many putative selected regions were spread across the whole genome and overlapped with the detected QTL. Some of these selected regions were the ones that contained the detected QTL for MPS score and other traits.Conclusion: These results suggest that a closed-line breeding population is a useful target population to refine and confirm QTL regions by integrating the results of GWAS and allele frequency changes. The study provides new insights into the genomic factors that affect respiratory disease and immune-related traits in pigs.

scholarly journals Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila

2021 ◽  
Author(s):  
Jason Bertram
Keyword(s):  
Allele Frequency ◽  
Evolutionary Biology ◽  
Polymorphic Locus ◽  
Purifying Selection ◽  
Allele Frequencies ◽  
Intermediate Allele ◽  
Genome Wide ◽  
Signature Of Selection ◽  
Basic Objective ◽  
Genomic Regions

Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally-resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantial at intermediate allele frequencies, which we argue is most parsimoniously explained by positive --- not purifying --- selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as a purging of deleterious mutations.

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