Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

2015 ◽  
Vol 25 (1) ◽  
pp. 79-88 ◽  
Author(s):  
Wolfgang Stephan
Keyword(s):  
Positive Selection ◽  
Allele Frequency ◽  
Selective Sweeps ◽  
Polygenic Adaptation ◽  
Frequency Changes

scholarly journals Distinct patterns of selective sweep and polygenic adaptation

2019 ◽  
Author(s):  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Allele Frequency ◽  
Computer Simulations ◽  
Selective Sweep ◽  
Empirical Work ◽  
Selective Sweeps ◽  
Adaptive Architectures ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Independent Effects ◽  
Distinct Features

AbstractThe central paradigm of molecular population genetics is selective sweeps, where targets of selection have independent effects on the phenotype and quickly rise to fixation. In quantitative genetics, many loci contribute epistatically to adaptation and subtle frequency changes occur at many loci. Since both paradigms could result in a sweep-like genomic signature, additional criteria are needed to distinguish them. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles under both paradigms. We identify several distinct patterns of selective sweeps and polygenic adaptation in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two paradigms.Author’s summaryThe selective sweep model assumes an independent frequency increase of favorable alleles and has been the basis of many tests for selection. While, polygenic adaptation is typically modelled by small frequency shifts in many loci. Recently, some theoretical and empirical work demonstrated that polygenic adaptation, similar to sweep, could also results in pronounced allele frequency changes. These results suggest that other distinct features need to be identified. Using computer simulations, we identified distinctive features for each paradigm that can be used to differentiate the sweep model from polygenic adaptation. Features such as allele frequency trajectories, time-series fitness, distribution of selected alleles on haplotypes, and parallelism among replicates can be used for development of suitable tests to distinguish between different adaptive architectures. These features provide the basis for theoretical modeling, design of selection experiments and data analysis.

scholarly journals Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation

2019 ◽  
Author(s):  
Eirini Christodoulaki ◽  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Allele Frequency ◽  
Ad Hoc ◽  
Time Series Data ◽  
Series Data ◽  
Data Sets ◽  
Multiple Time ◽  
Adaptive Architecture ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Multiple Time Points

AbstractPolygenic adaptation is frequently associated with small allele frequency changes of many loci. Recent works suggest, that large allele frequency changes can be also expected. Laboratory natural selection (LNS) experiments provide an excellent experimental framework to study the adaptive architecture under controlled laboratory conditions: time series data in replicate populations evolving independently to the same trait optimum can be used to identify selected loci. Nevertheless, the choice of the new trait optimum in the laboratory is typically an ad hoc decision without consideration of the distance of the starting population to the new optimum. Here, we used forward-simulations to study the selection signatures of polygenic adaptation in populations evolving to different trait optima. Mimicking LNS experiments we analyzed allele frequencies of the selected alleles and population fitness at multiple time points. We demonstrate that the inferred adaptive architecture strongly depends on the choice of the new trait optimum in the laboratory and the significance cut-off used for identification of selected loci. Our results not only have a major impact on the design of future Evolve and Resequence (E&R) studies, but also on the interpretation of current E&R data sets.

scholarly journals Detection of human adaptation during the past 2,000 years

2016 ◽  
Author(s):  
Yair Field ◽  
Evan A Boyle ◽  
Natalie Telis ◽  
Ziyue Gao ◽  
Kyle J. Gaulton ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Complex Traits ◽  
Frequency Shifts ◽  
The Past ◽  
Polygenic Adaptation ◽  
Selection For ◽  
Frequency Changes ◽  
Long Timescales ◽  
Blue Eyes ◽  
New Evidence

AbstractDetection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

scholarly journals Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

2020 ◽  
Author(s):  
Alan Garcia-Elfring ◽  
Antoine Paccard ◽  
Timothy J. Thurman ◽  
Ben A. Wasserman ◽  
Eric P. Palkovacs ◽  
...  
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Calcium Binding ◽  
Gasterosteus Aculeatus ◽  
Environmental Changes ◽  
Threespine Stickleback ◽  
Functional Enrichment ◽  
Genomic Changes ◽  
Parallel Selection ◽  
Frequency Changes

AbstractParallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection in action under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele frequency changes in these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.

Genetic and statistical analyses of strong selection on polygenic traits: what, me normal?

Genetics ◽  
1994 ◽  
Vol 138 (3) ◽  
pp. 913-941 ◽  
Author(s):  
M Turelli ◽  
N H Barton
Keyword(s):  
Allele Frequency ◽  
Genetic Variance ◽  
Gaussian Approximation ◽  
Selection Response ◽  
Disruptive Selection ◽  
Breeding Values ◽  
Central Moments ◽  
Linkage Disequilibria ◽  
The Mean ◽  
Frequency Changes

Abstract We develop a general population genetic framework for analyzing selection on many loci, and apply it to strong truncation and disruptive selection on an additive polygenic trait. We first present statistical methods for analyzing the infinitesimal model, in which offspring breeding values are normally distributed around the mean of the parents, with fixed variance. These show that the usual assumption of a Gaussian distribution of breeding values in the population gives remarkably accurate predictions for the mean and the variance, even when disruptive selection generates substantial deviations from normality. We then set out a general genetic analysis of selection and recombination. The population is represented by multilocus cumulants describing the distribution of haploid genotypes, and selection is described by the relation between mean fitness and these cumulants. We provide exact recursions in terms of generating functions for the effects of selection on non-central moments. The effects of recombination are simply calculated as a weighted sum over all the permutations produced by meiosis. Finally, the new cumulants that describe the next generation are computed from the non-central moments. Although this scheme is applied here in detail only to selection on an additive trait, it is quite general. For arbitrary epistasis and linkage, we describe a consistent infinitesimal limit in which the short-term selection response is dominated by infinitesimal allele frequency changes and linkage disequilibria. Numerical multilocus results show that the standard Gaussian approximation gives accurate predictions for the dynamics of the mean and genetic variance in this limit. Even with intense truncation selection, linkage disequilibria of order three and higher never cause much deviation from normality. Thus, the empirical deviations frequently found between predicted and observed responses to artificial selection are not caused by linkage-disequilibrium-induced departures from normality. Disruptive selection can generate substantial four-way disequilibria, and hence kurtosis; but even then, the Gaussian assumption predicts the variance accurately. In contrast to the apparent simplicity of the infinitesimal limit, data suggest that changes in genetic variance after 10 or more generations of selection are likely to be dominated by allele frequency dynamics that depend on genetic details.

scholarly journals Mutation Rate Model Used in the DNA VIEW Program

2020 ◽  
Vol 10 (10) ◽  
pp. 3585 ◽  
Author(s):  
Tomasz Krajka
Keyword(s):  
Computer Simulation ◽  
Allele Frequency ◽  
Mutation Rate ◽  
Allele Frequencies ◽  
Rate Model ◽  
Dna Database ◽  
Mutation Model ◽  
Population Allele Frequency ◽  
Frequency Changes

The first problem considered in this paper is the problem of correctness of a mutation model used in the DNA VIEW program. To this end, we theoretically predict population allele frequency changes in time according to this and similar models (we determine the limit frequencies of alleles—they are uniformly distributed). Furthermore, we evaluate the speed of the above changes using computer simulation applied to our DNA database. Comparing uniformly distributed allele frequencies with these existing in the population (for example, using entropy), we conclude that this mutation model is not correct. The evolution does not follow this direction (direction of uniformly distributed frequencies). The second problem relates to the determination of the extent to which an incorrect mutation model can disturb DNA VIEW program results. We show that in typical computations (simple paternity testing without maternal mutation) this influence is negligible, but in the case of maternal mutation, this should be taken into account. Furthermore, we show that this model is inconsistent from a theoretical viewpoint. Equivalent methods result in different error levels.

Polygenic adaptation: a unifying framework to understand positive selection

2020 ◽  
Vol 21 (12) ◽  
pp. 769-781 ◽  
Author(s):  
Neda Barghi ◽  
Joachim Hermisson ◽  
Christian Schlötterer
Keyword(s):  
Positive Selection ◽  
Polygenic Adaptation

scholarly journals Unique Genomic and Phenotypic Responses to Extreme and Variable pH Conditions in Purple Urchin Larvae

2020 ◽  
Vol 60 (2) ◽  
pp. 318-331
Author(s):  
April D Garrett ◽  
Reid S Brennan ◽  
Anya L Steinhart ◽  
Aubrey M Pelletier ◽  
Melissa H Pespeni
Keyword(s):  
Genetic Variation ◽  
Allele Frequency ◽  
Sea Urchin ◽  
Genetic Basis ◽  
Adaptive Genetic Variation ◽  
Protein Coding ◽  
Purple Sea Urchin ◽  
Ph Conditions ◽  
Frequency Changes ◽  
Genetic Responses

Synopsis Environmental variation experienced by a species across space and time can promote the maintenance of genetic diversity that may be adaptive in future global change conditions. Selection experiments have shown that purple sea urchin, Strongylocentrotus purpuratus, populations have adaptive genetic variation for surviving pH conditions at the “edge” (pH 7.5) of conditions experienced in nature. However, little is known about whether populations have genetic variation for surviving low-pH events beyond those currently experienced in nature or how variation in pH conditions affects organismal and genetic responses. Here, we quantified survival, growth, and allele frequency shifts in experimentally selected developing purple sea urchin larvae in static and variable conditions at three pH levels: pH 8.1 (control), pH 7.5 (edge-of-range), and pH 7.0 (extreme). Variable treatments recovered body size relative to static treatments, but resulted in higher mortality, suggesting a potential tradeoff between survival and growth under pH stress. However, within each pH level, allele frequency changes were overlapping between static and variable conditions, suggesting a shared genetic basis underlying survival to mean pH regardless of variability. In contrast, genetic responses to pH 7.5 (edge) versus pH 7.0 (extreme) conditions were distinct, indicating a unique genetic basis of survival. In addition, loci under selection were more likely to be in exonic regions than regulatory, indicating that selection targeted protein-coding variation. Loci under selection in variable pH 7.5 conditions, more similar to conditions periodically experienced in nature, performed functions related to lipid biosynthesis and metabolism, while loci under selection in static pH 7.0 conditions performed functions related to transmembrane and mitochondrial processes. While these results are promising in that purple sea urchin populations possess genetic variation for surviving extreme pH conditions not currently experienced in nature, they caution that increased acidification does not result in a linear response but elicits unique physiological stresses and survival mechanisms.

scholarly journals Coat colour in mouse populations selected for weight gain: support for hitchhiking, not pleiotropy

2013 ◽  
Vol 95 (1) ◽  
pp. 4-13 ◽  
Author(s):  
PHILIP W. HEDRICK
Keyword(s):  
Weight Gain ◽  
Allele Frequency ◽  
High Weight ◽  
Coat Colour ◽  
Correlated Response ◽  
Term Selection ◽  
Low Weight ◽  
High Weight Gain ◽  
Frequency Changes ◽  
Positive Correlations

SummaryWith many molecular markers in many species, research efforts in quantitative genetics have focused on dissecting these traits and understanding the importance of factors such as correlated response due to hitchhiking or pleiotropy. Here, in an examination of long-term selection experiments in mice, the evidence strongly supports the primary importance of hitchhiking on the coat colour loci brown and dilute in mice selected for high weight gain. First, the amount of observed change in coat colour allele frequency could not be explained by genetic drift alone, implying that selection was of high importance. Second, the allele frequency changes included reversals in the direction change, but there were still positive correlations in the early generations with differences in weight gain between the phenotypes. Third, the correlation between the change in allele frequencies and phenotypic difference in weight gain declined over time, consistent with the decay expected from linkage associations. Fourth, the changes at both loci in a short-term selection experiment for low weight gain were in the opposite direction than the changes in the contemporaneous related population selected for high weight gain.

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