scholarly journals A simple expression for the strength of selection on recombination generated by interference among mutations

2021 ◽  
Vol 118 (19) ◽  
pp. e2022805118
Author(s):  
Denis Roze
Keyword(s):  
Genetic Recombination ◽  
Quantitative Estimation ◽  
Theoretical Work ◽  
Selective Advantage ◽  
Indirect Selection ◽  
Simple Expression ◽  
Rate Variation ◽  
Effective Population ◽  
Deleterious Alleles ◽  
Recombination Rate Variation

One of the most widely cited hypotheses to explain the evolutionary maintenance of genetic recombination states that the reshuffling of genotypes at meiosis increases the efficiency of natural selection by reducing interference among selected loci. However, and despite several decades of theoretical work, a quantitative estimation of the possible selective advantage of a mutant allele increasing chromosomal map length (the average number of cross-overs at meiosis) remains difficult. This article derives a simple expression for the strength of selection acting on a modifier gene affecting the genetic map length of a whole chromosome or genome undergoing recurrent mutation. In particular, it shows that indirect selection for recombination caused by interference among mutations is proportional to NeU2/NeR3, where Ne is the effective population size, U is the deleterious mutation rate per chromosome, and R is the chromosome map length. Indirect selection is relatively insensitive to the fitness effects of deleterious alleles, epistasis, or the genetic architecture of recombination rate variation and may compensate for substantial costs associated with recombination when linkage is tight. However, its effect generally stays weak in large, highly recombining populations.

scholarly journals The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals a pronounced effect of linked selection

2018 ◽  
Author(s):  
Ahmed R. Hasan ◽  
Rob W. Ness
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Gc Content ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Entire Genome ◽  
Recombination Rate Variation ◽  
Linked Selection

AbstractRecombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations and facilitating selection. Here, we use genome-wide patterns of LD to infer fine-scale recombination rate variation in the genome of the model green alga Chlamydomonas reinhardtii and estimate rates of LD decay across the entire genome. We observe recombination rate variation of up to two orders of magnitude, finding evidence of recombination hotspots playing a role in the genome. Recombination rate is highest just upstream of genic regions, suggesting the preferential targeting of recombination breakpoints in promoter regions. Furthermore, we observe a positive correlation between GC content and recombination rate, suggesting a role for GC-biased gene conversion or selection on base composition within the GC-rich genome of C. reinhardtii. We also find a positive relationship between nucleotide diversity and recombination, consistent with widespread influence of linked selection in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations of this important model microbe, estimating a sexual cycle roughly every 770 generations. We argue that the relatively infrequent rate of sex and large effective population size creates an population genetic environment that increases the influence of linked selection on the genome.

scholarly journals Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii

2020 ◽  
Vol 12 (4) ◽  
pp. 370-380 ◽  
Author(s):  
Ahmed R Hasan ◽  
Rob W Ness
Keyword(s):  
Linkage Disequilibrium ◽  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Effective Rate ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

scholarly journals Connecting theory and data to understand recombination rate evolution

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160469 ◽  
Author(s):  
Amy L. Dapper ◽  
Bret A. Payseur
Keyword(s):  
Recombination Rate ◽  
Empirical Studies ◽  
Theoretical Work ◽  
Rate Variation ◽  
Recombination Rates ◽  
Theoretical Approaches ◽  
Evolutionary Advantage ◽  
New Directions ◽  
The Rich ◽  
Recombination Rate Variation

Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 395-411 ◽  
Author(s):  
Toby Johnson ◽  
Nick H Barton
Keyword(s):  
Selective Sweep ◽  
Deleterious Mutation ◽  
Short Interval ◽  
Selective Advantage ◽  
Asexual Population ◽  
Restrictive Assumption ◽  
Deleterious Alleles ◽  
Fixation Probabilities ◽  
Asexual Populations ◽  
Beneficial Allele

Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

scholarly journals Recombination Can Evolve in Large Finite Populations Given Selection on Sufficient Loci

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2249-2258 ◽  
Author(s):  
Mark M Iles ◽  
Kevin Walters ◽  
Chris Cannings
Keyword(s):  
Experimental Evidence ◽  
Genetic Drift ◽  
Finite Population ◽  
Selective Advantage ◽  
Indirect Selection ◽  
Small Populations ◽  
Finite Populations ◽  
Population Sizes ◽  
Population Recombination

AbstractIt is well known that an allele causing increased recombination is expected to proliferate as a result of genetic drift in a finite population undergoing selection, without requiring other mechanisms. This is supported by recent simulations apparently demonstrating that, in small populations, drift is more important than epistasis in increasing recombination, with this effect disappearing in larger finite populations. However, recent experimental evidence finds a greater advantage for recombination in larger populations. These results are reconciled by demonstrating through simulation without epistasis that for m loci recombination has an appreciable selective advantage over a range of population sizes (am, bm). bm increases steadily with m while am remains fairly static. Thus, however large the finite population, if selection acts on sufficiently many loci, an allele that increases recombination is selected for. We show that as selection acts on our finite population, recombination increases the variance in expected log fitness, causing indirect selection on a recombination-modifying locus. This effect is enhanced in those populations with more loci because the variance in phenotypic fitnesses in relation to the possible range will be smaller. Thus fixation of a particular haplotype is less likely to occur, increasing the advantage of recombination.

scholarly journals Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 581-588
Author(s):  
Mohamed A F Noor ◽  
Aimee L Cunningham ◽  
John C Larkin
Keyword(s):  
Quantitative Trait Locus ◽  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Recombination Rate ◽  
Genome Project ◽  
Gene Density ◽  
Rate Variation ◽  
Trait Locus ◽  
Recombination Rate Variation

Abstract We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the “small X-effect” that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

scholarly journals Sexual Selection Does Not Increase the Rate of Compensatory Adaptation to a Mutation Influencing a Secondary Sexual Trait in Drosophila melanogaster

2020 ◽  
Vol 10 (5) ◽  
pp. 1541-1551
Author(s):  
Christopher H. Chandler ◽  
Anna Mammel ◽  
Ian Dworkin
Keyword(s):  
Drosophila Melanogaster ◽  
Sexual Selection ◽  
Natural Selection ◽  
Spontaneous Mutation ◽  
Phenotypic Expression ◽  
Theoretical Work ◽  
Phenotypic Suppression ◽  
Compensatory Adaptation ◽  
Deleterious Alleles ◽  
Sex Comb

Theoretical work predicts that sexual selection can enhance natural selection, increasing the rate of adaptation to new environments and helping purge harmful mutations. While some experiments support these predictions, remarkably little work has addressed the role of sexual selection on compensatory adaptation—populations’ ability to compensate for the costs of deleterious alleles that are already present. We tested whether sexual selection, as well as the degree of standing genetic variation, affect the rate of compensatory evolution via phenotypic suppression in experimental populations of Drosophila melanogaster. These populations were fixed for a spontaneous mutation causing mild abnormalities in the male sex comb, a structure important for mating success. We fine-mapped this mutation to an ∼85 kb region on the X chromosome containing three candidate genes, showed that the mutation is deleterious, and that its phenotypic expression and penetrance vary by genetic background. We then performed experimental evolution, including a treatment where opportunity for mate choice was limited by experimentally enforced monogamy. Although evolved populations did show some phenotypic suppression of the morphological abnormalities in the sex comb, the amount of suppression did not depend on the opportunity for sexual selection. Sexual selection, therefore, may not always enhance natural selection; instead, the interaction between these two forces may depend on additional factors.

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