scholarly journals Hidden genetic variance contributes to increase the short-term adaptive potential of selfing populations

2019 ◽  
Author(s):  
Josselin Clo ◽  
Joëlle Ronfort ◽  
Diala Abu Awad
Keyword(s):  
Genetic Variation ◽  
Mutation Rate ◽  
Genetic Variance ◽  
Purifying Selection ◽  
Stabilizing Selection ◽  
Genetic Associations ◽  
Adaptive Potential ◽  
Short Term ◽  
Additive Variance ◽  
Standing Variation

Standing genetic variation is considered a major contributor to the adaptive potential of species. The low heritable genetic variation observed in self-fertilising populations has led to the hypothesis that species with this mating system would be less likely to adapt. However, a non-negligible amount of cryptic genetic variation for polygenic traits, accumulated through negative linkage disequilibrium, could prove to be an important source of standing variation in self-fertilising species. To test this hypothesis we simulated populations under stabilizing selection subjected to an environmental change. We demonstrate that, when the mutation rate is high (but realistic), selfing populations are better able to store genetic variance than outcrossing populations through genetic associations, notably due to the reduced effective recombination rate associated with predominant selfing. Following an environmental shift, this diversity can be partially remobilized, which increases the additive variance and adaptive potential of predominantly (but not completely) selfing populations. In such conditions, despite initially lower observed genetic variance, selfing populations adapt as readily as outcrossing ones within a few generations. For low mutation rates, purifying selection impedes the storage of diversity through genetic associations, in which case, as previously predicted, the lower genetic variance of selfing populations results in lower adaptability compared to their outcrossing counterparts. The population size and the mutation rate are the main parameters to consider, as they are the best predictors of the amount of stored diversity in selfing populations. Our results and their impact on our knowledge of adaptation under high selfing rates are discussed.

Short-term Changes in the Variance: 1. Changes in the Additive Variance

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Linkage Disequilibrium ◽  
Assortative Mating ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Allele Frequencies ◽  
Disruptive Selection ◽  
Stabilizing Selection ◽  
Short Term ◽  
Additive Variance ◽  
The Mean

Selection changes the additive-genetic variance (and hence the response in the mean) by both changing allele frequencies and by generating correlations among alleles at different loci (linkage disequilibrium). Such selection-induced correlations can be generated even between unlinked loci, and (generally) are negative, such that alleles increasing trait values tend to become increasingly negative correlated under direction or stabilizing selection, and positively correlated under disruptive selection. Such changes in the additive-genetic variance from disequilibrium is called the Bulmer effects. For a large number of loci, the amount of change can be predicted from the Bulmer equation, the analog of the breeder's equation, but now for the change in the variance. Upon cessation of selection, any disequilibrium decays away, and the variances revert back to their additive-genic variances (the additive variance in the absence of disequilibrium). Assortative mating also generates such disequilibrium.

scholarly journals Variance components of fitness under stabilizing selection

1988 ◽  
Vol 51 (1) ◽  
pp. 47-53 ◽  
Author(s):  
Hidenori Tachida ◽  
C. Clark Cockerham
Keyword(s):  
Mutation Rate ◽  
Variance Components ◽  
Present Method ◽  
Gaussian Approximation ◽  
Stabilizing Selection ◽  
Additive Variance ◽  
Gene Effects ◽  
Selection Scheme ◽  
House Of Cards ◽  
Gaussian Case

SummaryVariance components of fitness under the stabilizing selection scheme of Wright (1935) for metric characters are calculated, extending his original analysis to the case with any number of alleles and multiple characters assuming additivity of gene effects. They are calculated in terms of the moments of the effects of alleles at individual loci for the metric characters. From these formulas, the variance components of fitness are evaluated at the mutation–selection equilibria predicted by the ‘Gaussian’ approximation (Lande, 1976), which is applicable if the per locus mutation rate is high, and the ‘House of Cards’ approximation (Turelli, 1984), which is applicable if the per locus mutation rate is low. It is found that the additive variance of fitness is small compared to non-additive variance in the ‘Gaussian’ case, whereas the additive variance is larger than non-additive variance in the ‘House of Cards’ case if the number of loci per character and the number of characters affected by each locus are not too large. With the assumption that a significant portion of fitness is due to this type of stabilizing selection, it is suggested that the real parameters are in the range where the ‘House of Cards’ approximation is applicable, since available data on variance components of fitness components in Drosophila show that the additive variance is far larger than the non-additive variance. It is noted that the present method does not discriminate the two approximations if the average values of the metric characters deviate from the optimum values. Other limitations of the present method are also discussed.

scholarly journals Deleterious mutations, apparent stabilizing selection and the maintenance of quantitative variation.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 603-618 ◽  
Author(s):  
A S Kondrashov ◽  
M Turelli
Keyword(s):  
Quantitative Trait ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Pleiotropic Effects ◽  
Direct Selection ◽  
Selection Function ◽  
Stabilizing Selection ◽  
Deleterious Mutations ◽  
Additive Variance ◽  
Deleterious Alleles

Abstract Apparent stabilizing selection on a quantitative trait that is not causally connected to fitness can result from the pleiotropic effects of unconditionally deleterious mutations, because as N. Barton noted, "...individuals with extreme values of the trait will tend to carry more deleterious alleles...." We use a simple model to investigate the dependence of this apparent selection on the genomic deleterious mutation rate, U; the equilibrium distribution of K, the number of deleterious mutations per genome; and the parameters describing directional selection against deleterious mutations. Unlike previous analyses, we allow for epistatic selection against deleterious alleles. For various selection functions and realistic parameter values, the distribution of K, the distribution of breeding values for a pleiotropically affected trait, and the apparent stabilizing selection function are all nearly Gaussian. The additive genetic variance for the quantitative trait is kQa2, where k is the average number of deleterious mutations per genome, Q is the proportion of deleterious mutations that affect the trait, and a2 is the variance of pleiotropic effects for individual mutations that do affect the trait. In contrast, when the trait is measured in units of its additive standard deviation, the apparent fitness function is essentially independent of Q and a2; and beta, the intensity of selection, measured as the ratio of additive genetic variance to the "variance" of the fitness curve, is very close to s = U/k, the selection coefficient against individual deleterious mutations at equilibrium. Therefore, this model predicts appreciable apparent stabilizing selection if s exceeds about 0.03, which is consistent with various data. However, the model also predicts that beta must equal Vm/VG, the ratio of new additive variance for the trait introduced each generation by mutation to the standing additive variance. Most, although not all, estimates of this ratio imply apparent stabilizing selection weaker than generally observed. A qualitative argument suggests that even when direct selection is responsible for most of the selection observed on a character, it may be essentially irrelevant to the maintenance of variation for the character by mutation-selection balance. Simple experiments can indicate the fraction of observed stabilizing selection attributable to the pleiotropic effects of deleterious mutations.

scholarly journals Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection

2021 ◽  
Author(s):  
Chao Zhang ◽  
Anurag Verma ◽  
Yuanqing Feng ◽  
Marcelo C. R. Melo ◽  
Michael McQuillan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Positive Selection ◽  
Low Frequency ◽  
Purifying Selection ◽  
Upper Respiratory Tract ◽  
Genetic Associations ◽  
Hunter Gatherers ◽  
Clinical Phenotypes ◽  
Global Patterns ◽  
Coding Variants

The COVID-19 pandemic caused by SARS-COV-2 has had a devastating impact on population health. We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans, 15,997 individuals of European (7,061) and African (8,916) ancestry recruited by the Penn Medicine BioBank (PMBB), and comparative data from 2,504 individuals from the 1000 Genomes project. At ACE2 we identified 41 non-synonymous variants, found to be at low frequency in most populations. However, three non-synonymous variants were frequent among Central African hunter-gatherers (CAHG) from Cameroon, and signatures of positive selection could be detected on haplotypes encompassing those variants. We also detected signatures of positive selection for variants at regulatory regions upstream of ACE2 in diverse African populations. At TMPRSS2, we identified 48 non-synonymous variants, several of which are common in global populations, and 13 amino acid changes that are fixed in the human lineage after divergence from Chimpanzee. At DPP4 and LY6E most variants were rare in global populations indicating that purifying selection is acting at these loci. At all four loci, we identified common non-coding variants associated with gene expression that vary in frequency across global populations. By analyzing electronic health records from the PMBB we discovered genetic associations with clinical phenotypes, such as respiratory failure with ACE2 and upper respiratory tract infection with DPP4. Our study provides new insights into global variation at genes potentially affecting susceptibility to SARS-CoV-2 infection.

scholarly journals Joint Effects of Pleiotropic Selection and Stabilizing Selection on the Maintenance of Quantitative Genetic Variation at Mutation-Selection Balance

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 459-471 ◽  
Author(s):  
Xu-Sheng Zhang ◽  
William G Hill
Keyword(s):  
Genetic Variation ◽  
Genetic Variance ◽  
Stabilizing Selection ◽  
Limited Impact ◽  
Quantitative Genetic ◽  
High Heritability ◽  
Selection For ◽  
Selection Parameters ◽  
Mutation And Selection ◽  
Polygenic Variation

AbstractIn quantitative genetics, there are two basic “conflicting” observations: abundant polygenic variation and strong stabilizing selection that should rapidly deplete that variation. This conflict, although having attracted much theoretical attention, still stands open. Two classes of model have been proposed: real stabilizing selection directly on the metric trait under study and apparent stabilizing selection caused solely by the deleterious pleiotropic side effects of mutations on fitness. Here these models are combined and the total stabilizing selection observed is assumed to derive simultaneously through these two different mechanisms. Mutations have effects on a metric trait and on fitness, and both effects vary continuously. The genetic variance (VG) and the observed strength of total stabilizing selection (Vs,t) are analyzed with a rare-alleles model. Both kinds of selection reduce VG but their roles in depleting it are not independent: The magnitude of pleiotropic selection depends on real stabilizing selection and such dependence is subject to the shape of the distributions of mutational effects. The genetic variation maintained thus depends on the kurtosis as well as the variance of mutational effects: All else being equal, VG increases with increasing leptokurtosis of mutational effects on fitness, while for a given distribution of mutational effects on fitness, VG decreases with increasing leptokurtosis of mutational effects on the trait. The VG and Vs,t are determined primarily by real stabilizing selection while pleiotropic effects, which can be large, have only a limited impact. This finding provides some promise that a high heritability can be explained under strong total stabilizing selection for what are regarded as typical values of mutation and selection parameters.

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