scholarly journals Polygenic adaptation to an environmental shift: temporal dynamics of variation under Gaussian stabilizing selection and additive effects on a single trait

2018 ◽  
Author(s):  
Kevin R. Thornton
Keyword(s):  
Temporal Dynamics ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
Standing Variation ◽  
Polygenic Adaptation ◽  
Standard Models ◽  
The Times ◽  
General Populations ◽  
Mutational Variance ◽  
New Mutations

AbstractPredictions about the effect of natural selection on patterns of linked neutral variation are largely based on models involving the rapid fixation of unconditionally beneficial mutations. However, when phenotypes adapt to a new optimum trait value, the strength of selection on individual mutations decreases as the population adapts. Here, I use explicit forward simulations of a single trait with additive-effect mutations adapting to an optimum shift. Detectable “hitch-hiking” patterns are only apparent if i. the optimum shifts are large with respect to equilibrium variation for the trait, ii. mutation rates to large-effect mutations are low, and iii., large-effect mutations rapidly increase in frequency and eventually reach fixation, which typically occurs after the population reaches the new optimum. For the parameters simulated here, partial sweeps do not appreciably affect patterns of linked variation, even when the mutations are strongly selected. The contribution of new mutations versus standing variation to fixation depends on the mutation rate affecting trait values. Given the fixation of a strongly-selected variant, patterns of hitch-hiking are similar on average for the two classes of sweeps because sweeps from standing variation involving large-effect mutations are rare when the optimum shifts. The distribution of effect sizes of new mutations has little effect on the time to reach the new optimum, but reducing the mutational variance increases the magnitude of hitch-hiking patterns. In general, populations reach the new optimum prior to the completion of any sweeps, and the times to fixation are longer for this model than for standard models of directional selection. The long fixation times are due to a combination of declining selection pressures during adaptation and the possibility of interference among weakly selected sites for traits with high mutation rates.

scholarly journals Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1513-1530 ◽  
Author(s):  
Kevin R. Thornton
Keyword(s):  
Temporal Dynamics ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
Standing Variation ◽  
Polygenic Adaptation ◽  
Standard Models ◽  
The Times ◽  
General Populations ◽  
Mutational Variance ◽  
New Mutations

Predictions about the effect of natural selection on patterns of linked neutral variation are largely based on models involving the rapid fixation of unconditionally beneficial mutations. However, when phenotypes adapt to a new optimum trait value, the strength of selection on individual mutations decreases as the population adapts. Here, I use explicit forward simulations of a single trait with additive-effect mutations adapting to an “optimum shift.” Detectable “hitchhiking” patterns are only apparent if (i) the optimum shifts are large with respect to equilibrium variation for the trait, (ii) mutation rates to large-effect mutations are low, and (iii) large-effect mutations rapidly increase in frequency and eventually reach fixation, which typically occurs after the population reaches the new optimum. For the parameters simulated here, partial sweeps do not appreciably affect patterns of linked variation, even when the mutations are strongly selected. The contribution of new mutations vs. standing variation to fixation depends on the mutation rate affecting trait values. Given the fixation of a strongly selected variant, patterns of hitchhiking are similar on average for the two classes of sweeps because sweeps from standing variation involving large-effect mutations are rare when the optimum shifts. The distribution of effect sizes of new mutations has little effect on the time to reach the new optimum, but reducing the mutational variance increases the magnitude of hitchhiking patterns. In general, populations reach the new optimum prior to the completion of any sweeps, and the times to fixation are longer for this model than for standard models of directional selection. The long fixation times are due to a combination of declining selection pressures during adaptation and the possibility of interference among weakly selected sites for traits with high mutation rates.

scholarly journals Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

2018 ◽  
Author(s):  
Markus G Stetter ◽  
Kevin Thornton ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Stabilizing Selection ◽  
Relative Importance ◽  
Selective Sweeps ◽  
Weak Selection ◽  
Standing Variation ◽  
Polygenic Adaptation ◽  
Maize Domestication ◽  
New Mutations

ABSTRACTUnderstanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our understanding of the process of polygenic adaptation is still limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters in determining a number of aspects of the process of adaptation including the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then compare our results to two traits under selection during maize domestication, showing that our simulations qualitatively recapitulate differences between them. Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models, but provide a glimpse into the factors that drive this complexity and the potential of these approaches for understanding polygenic adaptation.Author summaryMany traits are controlled by a large number of genes, and environmental changes can lead to shifts in trait optima. How populations adapt to these shifts depends on a number of parameters including the genetic basis of the trait as well as population demography. We simulate a number of trait architectures and population histories to study the genetics of adaptation to distant trait optima. We find that selective sweeps occur even in traits under relatively weak selection and our machine learning analyses find that demography and the effect sizes of mutations have the largest influence on genetic variation after adaptation. Maize domestication is a well suited model for trait adaptation accompanied by demographic changes. We show how two example traits under a maize specific demography adapt to a distant optimum and demonstrate that polygenic adaptation is a well suited model for crop domestication even for traits with major effect loci.

scholarly journals Properties of spontaneous mutations affecting quantitative traits

1999 ◽  
Vol 74 (3) ◽  
pp. 341-350 ◽  
Author(s):  
A. GARCÍA-DORADO ◽  
C. LÓPEZ-FANJUL ◽  
A. CABALLERO
Keyword(s):  
Deleterious Mutation ◽  
Natural Populations ◽  
Detectable Effect ◽  
Environment Interaction ◽  
Fitness Component ◽  
Standing Variation ◽  
Genotype Environment Interaction ◽  
Component Traits ◽  
Mutational Variance ◽  
New Mutations

Recent mutation accumulation results from invertebrate species suggest that mild deleterious mutation is far less frequent than previously thought, implying smaller expressed mutational loads. Although the rate (λ) and effect (s) of very slight deleterious mutation remain unknown, most mutational fitness decline would come from moderately deleterious mutation (s ≈ 0·2, λ ≈ 0·03), and this situation would not qualitatively change in harsh environments. Estimates of the average coefficient of dominance (h¯) of non-severe deleterious mutations are controversial. The typical value of h¯ = 0·4 can be questioned, and a lower estimate (about 0·1) is suggested. Estimated mutational parameters are remarkably alike for morphological and fitness component traits (excluding lethals), indicating low mutation rates and moderate mutational effects, with a distribution generally showing strong negative asymmetry and little leptokurtosis. New mutations showed considerable genotype–environment interaction. However, the mutational variance of fitness-component traits due to non-severe detrimental mutations did not increase with environmental harshness. For morphological traits, a class of predominantly additive mutations with no detectable effect on fitness and relatively small effect on the trait was identified. This should be close to that responsible for standing variation in natural populations.

scholarly journals Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161785 ◽  
Author(s):  
Long Wang ◽  
Yanchun Zhang ◽  
Chao Qin ◽  
Dacheng Tian ◽  
Sihai Yang ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Recombination Rate ◽  
Mutation Rates ◽  
Recombination Rates ◽  
Rate Analysis ◽  
A Genome ◽  
Break Points ◽  
New Mutations

Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent–offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination–heterozygozity correlation in peach, we caution against such an interpretation.

scholarly journals Distinct Patterns of Selective Sweep and Polygenic Adaptation in Evolve and Resequence Studies

2020 ◽  
Vol 12 (6) ◽  
pp. 890-904 ◽  
Author(s):  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Experimental Evolution ◽  
Selective Sweep ◽  
Time Series Data ◽  
Empirical Studies ◽  
Series Data ◽  
Stabilizing Selection ◽  
Selection Signatures ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Optimum Model

Abstract In molecular population genetics, adaptation is typically thought to occur via selective sweeps, where targets of selection have independent effects on the phenotype and rise to fixation, whereas in quantitative genetics, many loci contribute to the phenotype and subtle frequency changes occur at many loci during polygenic adaptation. The sweep model makes specific predictions about frequency changes of beneficial alleles and many test statistics have been developed to detect such selection signatures. Despite polygenic adaptation is probably the prevalent mode of adaptation, because of the traditional focus on the phenotype, we are lacking a solid understanding of the similarities and differences of selection signatures under the two models. Recent theoretical and empirical studies have shown that both selective sweep and polygenic adaptation models could result in a sweep-like genomic signature; therefore, additional criteria are needed to distinguish the two models. With replicated populations and time series data, experimental evolution studies have the potential to identify the underlying model of adaptation. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles for two models: 1) adaptation of a trait via independent beneficial mutations that are conditioned for fixation, that is, selective sweep model and 2) trait optimum model (polygenic adaptation), that is adaptation of a quantitative trait under stabilizing selection after a sudden shift in trait optimum. We identify several distinct patterns of selective sweep and trait optimum models in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two models.

Maintenance of genetic variability by mutation–selection balance: a child's guide through the jungle

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 761-767 ◽  
Author(s):  
M. G. Bulmer
Keyword(s):  
Genetic Variability ◽  
Theoretical Work ◽  
Complex Problem ◽  
Recurrent Mutation ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
House Of Cards ◽  
Model Account ◽  
Optimal Value ◽  
Selection For

Metric characters closely connected with fitness have little additive genetic variability, presumably because it is quickly exhausted under continuous directional selection on fitness. Other metric characters have substantial additive genetic variability with a typical heritability of about 0.5. A popular model is that the second class of characters is subject to weak stabilizing selection for an optimal value, which depletes genetic variability, while recurrent mutation tends to restore it. Can this model account for the variability observed, given the evidence available about the strength of selection and mutation rates? Much theoretical work has been done on this complex problem. This work is reviewed, with the intention of simplifying it as much as possible.Key words: mutation–selection balance, genetic variability, continuum-of-alleles model, house-of-cards approximation.

scholarly journals Fly wing evolution explained by a neutral model with mutational pleiotropy

2020 ◽  
Author(s):  
Daohan Jiang ◽  
Jianzhi Zhang
Keyword(s):  
Linear Correlation ◽  
Evolutionary Biology ◽  
Stabilizing Selection ◽  
Evolutionary Divergence ◽  
Phenotypic Evolution ◽  
Central Question ◽  
Evolutionary Patterns ◽  
Strong Linear Correlation ◽  
Mutational Variance

ABSTRACTTo what extent the speed of mutational production of phenotypic variation determines the rate of long-term phenotypic evolution is a central question in evolutionary biology. In a recent study, Houle et al. addressed this question by studying the mutational variation, microevolution, and macroevolution of locations of vein intersections on fly wings, reporting very slow phenotypic evolution relative to the rates of mutational input, high phylogenetic signals of these traits, and a strong, linear correlation between the mutational variance of a trait and its rate of evolution. Houle et al. examined multiple models of phenotypic evolution but found none consistent with all these observations. Here we demonstrate that the purported linear correlation between mutational variance and evolutionary divergence is an artifact. More importantly, patterns of fly wing evolution are explainable by a simple model in which the wing traits are neutral or neutral within a range of phenotypic values but their evolutionary rates are reduced because most mutations affecting these traits are purged owing to their pleiotropic effects on other traits that are under stabilizing selection. We conclude that the evolutionary patterns of fly wing morphologies are explainable under the existing theoretical framework of phenotypic evolution.

scholarly journals Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada

mSphere ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Calvin P. Sjaarda ◽  
Jennifer L. Guthrie ◽  
Samira Mubareka ◽  
Jared T. Simpson ◽  
Bettina Hamelin ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Viral Genome ◽  
Temporal Dynamics ◽  
Viral Transmission ◽  
Mutation Rates ◽  
Protein Mutation ◽  
Rate Of Spread ◽  
Viral Mutation ◽  
Genome Wide ◽  
Control And Prevention

ABSTRACT Genome-wide variation in SARS-CoV-2 reveals evolution and transmission dynamics which are critical considerations for disease control and prevention decisions. Here, we review estimates of the genome-wide viral mutation rates, summarize current COVID-19 case load in the province of Ontario, Canada (5 January 2021), and analyze published SARS-CoV-2 genomes from Ontario (collected prior to 24 November 2020) to test for more infectious genetic variants or lineages. The reported mutation rate (∼10−6 nucleotide [nt]−1 cycle−1) for SARS-CoV-2 is typical for coronaviruses. Analysis of published SARS-CoV-2 genomes revealed that the G614 spike protein mutation has dominated infections in Ontario and that SARS-CoV-2 lineages present in Ontario have not differed significantly in their rate of spread. These results suggest that the SARS-CoV-2 population circulating in Ontario has not changed significantly to date. However, ongoing genome monitoring is essential for identification of new variants and lineages that may contribute to increased viral transmission.

scholarly journals Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates

2014 ◽  
Author(s):  
Chuan-Chao Wang ◽  
Li Hui
Keyword(s):  
Sequence Data ◽  
Mutation Rates ◽  
Str Markers ◽  
Time Estimates ◽  
The Times

We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R. In addition, genealogical rates lead to more plausible time estimates for Neolithic coalescent sublineages compared with sequence-based dating.

scholarly journals Selection constrains high rates of satellite DNA mutation in Daphnia pulex

2017 ◽  
Author(s):  
Jullien M. Flynn ◽  
Ian Caldas ◽  
Melania E. Cristescu ◽  
Andrew G. Clark
Keyword(s):  
Satellite Dna ◽  
Related Species ◽  
Rapid Evolution ◽  
Daphnia Pulex ◽  
Selective Constraint ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
Closely Related Species ◽  
Dna Mutation ◽  
Evolutionary Forces

AbstractA long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated satellite DNA whose composition varies greatly among even closely related species. To elucidate the evolutionary forces governing satellite dynamics, quantification of the rates and patterns of mutations in satellite DNA copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of satellite sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual satellite sequence “kmers” were both high and highly variable, ranging from additions/deletions of 0.29 – 105 copies per generation (reflecting changes of 0.12 - 0.80 percent per generation). Our results also provide evidence that new kmer sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33 % lower variation in kmer abundance on average than the MA lines, although the level of selective constraint was not evenly distributed across all kmers. The changes between many pairs of kmers were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that kmer sequences can experience extremely rapid evolution in abundance, which can lead to high levels of divergence in genome-wide satellite DNA composition between closely related species.

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