scholarly journals Sign inversion in selection on ploidy

2021 ◽  
Author(s):  
Yevgeniy Raynes ◽  
Daniel M Weinreich
Keyword(s):  
Population Size ◽  
Natural World ◽  
Indirect Selection ◽  
Beneficial Mutations ◽  
Agent Based ◽  
Sign Inversion ◽  
Large Populations ◽  
A Cell ◽  
Asexual Populations ◽  
The Cost

Ploidy - the number of homologous chromosome sets in a cell - is remarkably variable across the natural world, yet the evolutionary processes that have resulted in such diversity remain poorly understood. Here we use stochastic agent-based simulations to model ploidy evolution under the influence of indirect selection, i.e., selection mediated solely by statistical associations with fitness-affecting mutations. We find that in non-equilibrium asexual populations, the sign of selection on ploidy can change with population size - a phenomenon we have previously termed sign inversion. In large populations, ploidy dynamics are dominated by indirect effects of selection on beneficial mutations, which favors haploids over diploids. However, as population size declines, selection for beneficial mutations is neutralized by random genetic drift before drift can overwhelm selection against the cost of the deleterious mutational load. As a result, in small populations indirect selection is dominated by the cost of the deleterious load, which favors diploids over haploids. Our work adds to the growing body of evidence challenging established evolutionary theory that population size can affect only the efficiency, but not the sign, of natural selection.

scholarly journals Sign of selection on mutation rate modifiers depends on population size

2018 ◽  
Vol 115 (13) ◽  
pp. 3422-3427 ◽  
Author(s):  
Yevgeniy Raynes ◽  
C. Scott Wylie ◽  
Paul D. Sniegowski ◽  
Daniel M. Weinreich
Keyword(s):  
Population Size ◽  
Mutation Rate ◽  
Genetic System ◽  
Indirect Selection ◽  
Mutation Rates ◽  
Deleterious Mutations ◽  
Fitness Effects ◽  
Sign Inversion ◽  
Large Populations ◽  
The Cost

The influence of population size (N) on natural selection acting on alleles that affect fitness has been understood for almost a century. AsNdeclines, genetic drift overwhelms selection and alleles with direct fitness effects are rendered neutral. Often, however, alleles experience so-called indirect selection, meaning they affect not the fitness of an individual but the fitness distribution of its offspring. Some of the best-studied examples of indirect selection include alleles that modify aspects of the genetic system such as recombination and mutation rates. Here, we use analytics, simulations, and experimental populations ofSaccharomyces cerevisiaeto examine the influence ofNon indirect selection acting on alleles that increase the genomic mutation rate (mutators). Mutators experience indirect selection via genomic associations with beneficial and deleterious mutations they generate. We show that, asNdeclines, indirect selection driven by linked beneficial mutations is overpowered by drift before drift can neutralize the cost of the deleterious load. As a result, mutators transition from being favored by indirect selection in large populations to being disfavored asNdeclines. This surprising phenomenon of sign inversion in selective effect demonstrates that indirect selection on mutators exhibits a profound and qualitatively distinct dependence onN.

scholarly journals Sign of selection on mutation rate modifiers depends on population size

2017 ◽  
Author(s):  
Yevgeniy Raynes ◽  
C. Scott Wylie ◽  
Paul D. Sniegowski ◽  
Daniel M. Weinreich
Keyword(s):  
Population Size ◽  
Mutation Rate ◽  
Critical Role ◽  
Genetic System ◽  
Indirect Selection ◽  
Fitness Effects ◽  
Sign Inversion ◽  
Large Populations ◽  
Laboratory Populations

SummaryThe influence of population size (N) on natural selection acting on alleles that affect fitness has been understood for over half a century1. As N declines, genetic drift overwhelms selection and alleles with direct fitness effects are rendered neutral. Often, though, alleles experience so called indirect selection, meaning they affect not the fitness of an individual but the fitness distribution of its offspring. Some of the best studied examples of indirect selection include alleles that modify aspects of the genetic system such as recombination2 and mutation3 rates. Here we use analytics, simulations and experimental populations of S. cerevisiae to show that modifiers that increase the genomic mutation rate (mutators) are favored by indirect selection in large populations but become disfavored as N declines. This surprising phenomenon of sign inversion in selective effect demonstrates that indirect selection on a mutator exhibits a qualitatively novel dependence on N. Sign inversion may help understand the relatively sporadic distribution of mutators in nature despite their frequent emergence in laboratory populations. More generally, sign inversion may be broadly applicable to other instances of indirect selection, suggesting a previously unappreciated but critical role of population size in evolution.

scholarly journals When good mutations go bad: how population size can change the direction of natural selection

2021 ◽  
Author(s):  
Yevgeniy Raynes ◽  
Christina L Burch ◽  
Daniel M Weinreich
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Underlying Mechanism ◽  
Deleterious Mutations ◽  
Fitness Costs ◽  
Sign Inversion ◽  
Population Sizes ◽  
The Common ◽  
Fitness Benefits ◽  
The Cost

Classical evolutionary theory holds that the efficiency, but not the direction, of natural selection depends on population size. In small populations, drift overwhelms selection, rendering all fitness-affecting mutations selectively neutral. Yet, beneficial mutations never become deleterious and deleterious mutations never become beneficial. Remarkably, several mutations, including in modifiers of recombination and mutation rate, have now been shown to be favored at some population sizes but disfavored at others, challenging established theory. Previously, we have designated this phenomenon sign inversion. Here we show that, unlike selected mutations in the classical framework, mutations susceptible to sign inversion confer both fitness costs and fitness benefits, that vary among their carriers. Furthermore, all such mutations can be classified based on whether their effects differ between or within mutant lineages. Using computer simulations, we demonstrate that both between-lineage and within-lineage variability can cause sign inversion and elucidate the common underlying mechanism. Our results confirm that variability in the sign of selective effects is necessary for sign inversion, which occurs because drift overwhelms selection on carriers bearing the cost and carriers enjoying the benefit at different population sizes.

scholarly journals Beneficial Mutations, Hitchhiking and the Evolution of Mutation Rates in Sexual Populations

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1621-1631 ◽  
Author(s):  
Toby Johnson
Keyword(s):  
Mutation Rate ◽  
Indirect Selection ◽  
Mutation Rates ◽  
Deleterious Mutations ◽  
Heritable Variation ◽  
Asexual Population ◽  
Beneficial Mutations ◽  
Long Term Effect ◽  
The Cost ◽  
Substantial Change

Abstract Natural selection acts in three ways on heritable variation for mutation rates. A modifier allele that increases the mutation rate is (i) disfavored due to association with deleterious mutations, but is also favored due to (ii) association with beneficial mutations and (iii) the reduced costs of lower fidelity replication. When a unique beneficial mutation arises and sweeps to fixation, genetic hitchhiking may cause a substantial change in the frequency of a modifier of mutation rate. In previous studies of the evolution of mutation rates in sexual populations, this effect has been underestimated. This article models the long-term effect of a series of such hitchhiking events and determines the resulting strength of indirect selection on the modifier. This is compared to the indirect selection due to deleterious mutations, when both types of mutations are randomly scattered over a given genetic map. Relative to an asexual population, increased levels of recombination reduce the effects of beneficial mutations more rapidly than those of deleterious mutations. However, the role of beneficial mutations in determining the evolutionarily stable mutation rate may still be significant if the function describing the cost of high-fidelity replication has a shallow gradient.

scholarly journals Likelihoods and Simulation Methods for a Class of Nonneutral Population Genetics Models

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 853-867 ◽  
Author(s):  
Peter Donnelly ◽  
Magnus Nordborg ◽  
Paul Joyce
Keyword(s):  
Population Genetics ◽  
Population Size ◽  
Mutant Allele ◽  
Mutation Rates ◽  
Simulation Methods ◽  
Large Populations ◽  
Selection Intensities ◽  
Infinite Alleles Model

Abstract Methods for simulating samples and sample statistics, under mutation-selection-drift equilibrium for a class of nonneutral population genetics models, and for evaluating the likelihood surface, in selection and mutation parameters, are developed and applied for observed data. The methods apply to large populations in settings in which selection is weak, in the sense that selection intensities, like mutation rates, are of the order of the inverse of the population size. General diploid selection is allowed, but the approach is currently restricted to models, such as the infinite alleles model and certain K-models, in which the type of a mutant allele does not depend on the type of its progenitor allele. The simulation methods have considerable advantages over available alternatives. No other methods currently seem practicable for approximating likelihood surfaces.

Letter To The Editor

PEDIATRICS ◽  
1996 ◽  
Vol 98 (4) ◽  
pp. 795-795
Author(s):  
Sanford Schneider
Keyword(s):  
Virus Vaccine ◽  
Limited Resources ◽  
Single Product ◽  
Live Virus ◽  
Polio Virus ◽  
Live Virus Vaccine ◽  
Letter To The Editor ◽  
Large Populations ◽  
The Cost ◽  
Cost Of Protection

The pro and con commentaries by Drs Judelsohn and Katz (Pediatrics 1996;98:115-117) do not mention projected costs. In these days of limited resources, the greatest bang for the buck is important and perhaps is becoming the most important factor of delivery of medical services to large populations. Developing a single product multi-vaccine containing inactivated polio virus, to be followed by oral live virus vaccine, will unquestionably add to the cost of protection. Also, Dr Katz does not seem to address the problem of compliance.

Prescreening in large populations as a tool for identifying elevated CO2-responsive genotypes in plants

2019 ◽  
Vol 46 (1) ◽  
pp. 1 ◽  
Author(s):  
Hiroyuki Shimono ◽  
Graham Farquhar ◽  
Matthew Brookhouse ◽  
Florian A. Busch ◽  
Anthony O'Grady ◽  
...  
Keyword(s):  
Genetic Selection ◽  
Co2 Concentration ◽  
Elevated Atmospheric Co2 ◽  
High Performing ◽  
Active Selection ◽  
Wide Range ◽  
Large Populations ◽  
Increase Productivity ◽  
The Cost ◽  
Selection Of

Elevated atmospheric CO2 concentration (e[CO2]) can stimulate the photosynthesis and productivity of C3 species including food and forest crops. Intraspecific variation in responsiveness to e[CO2] can be exploited to increase productivity under e[CO2]. However, active selection of genotypes to increase productivity under e[CO2] is rarely performed across a wide range of germplasm, because of constraints of space and the cost of CO2 fumigation facilities. If we are to capitalise on recent advances in whole genome sequencing, approaches are required to help overcome these issues of space and cost. Here, we discuss the advantage of applying prescreening as a tool in large genome×e[CO2] experiments, where a surrogate for e[CO2] was used to select cultivars for more detailed analysis under e[CO2] conditions. We discuss why phenotypic prescreening in population-wide screening for e[CO2] responsiveness is necessary, what approaches could be used for prescreening for e[CO2] responsiveness, and how the data can be used to improve genetic selection of high-performing cultivars. We do this within the framework of understanding the strengths and limitations of genotype–phenotype mapping.

scholarly journals Loving Nature in João Guimarães Rosa: The Non-human as 'amável'

2020 ◽  
Vol 5 (2) ◽  
pp. 55-74
Author(s):  
Ashley Brock
Keyword(s):  
Present Article ◽  
Natural World ◽  
Critical Discourse ◽  
Political Debates ◽  
Emotional Relationships ◽  
Joao Guimaraes Rosa ◽  
Human World ◽  
Human Capacity ◽  
A Site ◽  
The Cost

In the present article, I locate an implicit environmentalism JoãoGuimarães Rosa’s writing from the 1950s and 1960s. This sensibility is easy tomiss, in part because it transposes political debates on damage inflicted in thename of development and progress onto the affective-ethical plane; however, itdoes so in a way that resists sentimentality or projecting a misplaced innocenceonto the non-human world. Focusing on emotional relationships between humansand non-humans, I read “As margens da alegria” and “Os cimos” as expressingan eco-critical discourse that was already latent in Grande sertão: veredas.Recasting the natural world as a site of both unfathomable otherness and relationsof tenderness, Guimarães Rosa presents the emotional hold that nature has onhumans and the cost of cleaving oneself from it—a cost that includes diminishingthe human capacity for delight, wonder, and eros.

Agent Support for Design of Aircraft Parts

1998 ◽  
Author(s):  
Krishna N. Jha ◽  
Andrea Morris ◽  
Ed Mytych ◽  
Judith Spering
Keyword(s):  
Preliminary Design ◽  
Formal Representation ◽  
Web Based ◽  
Agent Based ◽  
Multi Agent ◽  
High Level ◽  
Legacy Applications ◽  
The Cost ◽  
And Control ◽  
Task Structures

Abstract Designing aircraft parts requires extensive coordination among multiple distributed design groups. Achieving such a coordination is time-consuming and expensive, but the cost of ignoring or minimizing it is much higher in terms of delayed and inferior quality products. We have built a multi-agent-based system to provide the desired coordination among the design groups, the legacy applications, and other resources during the preliminary design (PD) process. A variety of agents are used to model the various design and control functionalities. The agent-representation includes a formal representation of the task-structures. A web-based user-interface provides high-level interface to the users. The agents collaborate to achieve the design goals.

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