scholarly journals The apparent selection on neutral marker loci in partially inbreeding populations

1991 ◽  
Vol 57 (2) ◽  
pp. 159-175 ◽  
Author(s):  
D. Charlesworth
Keyword(s):  
Inbreeding Depression ◽  
Relative Fitness ◽  
Heterozygote Advantage ◽  
Neutral Locus ◽  
Fitness Value ◽  
Marker Loci ◽  
Neutral Marker ◽  
Computer Calculations

SummaryDeterministic computer calculations were used to investigate the effects on the fitnesses of genotypes at neutral loci that are caused by associations with several linked or unlinked selected loci, in partially self fertilizing populations. Both mutation to partially recessive alleles and heterozygote advantage at the selected loci were studied. In the heterozygote advantage models, either arbitrary linkage between all loci was modelled, with a single neutral locus, or many unlinked selected and neutral loci were modelled. Large apparent overdominance could be generated in all types of model studied. As has previously been suggested, these types of effect can explain the observed associations between fitness and heterozygosity in partially inbreeding populations. There were also apparent fitness differences between the genotypes at the neutral locus among the progeny produced by selfing, especially with linkage between the neutral and selected loci. There is thus no genotype-independent fitness value for these progeny. Marker based methods for estimating the relative fitness of selfed and outcrossed progeny assume equality of these fitnesses, and will therefore be inaccurate (with in most cases a bias towards overestimating the degree of inbreeding depression) when there is linkage between the neutral marker loci and loci determining fitness.

scholarly journals Associative overdominance caused by linked detrimental mutations

1971 ◽  
Vol 18 (3) ◽  
pp. 277-286 ◽  
Author(s):  
Tomoko Ohta
Keyword(s):  
Blood Group ◽  
Inbreeding Depression ◽  
Recombination Fraction ◽  
Abo Blood Group ◽  
Deleterious Mutations ◽  
Method Of Moment ◽  
Moment Equations ◽  
Neutral Locus ◽  
Neutral Marker ◽  
Image Position

SUMMARYAssociative overdominance due to linked detrimental mutations was investigated using the method of moment equations based on diffusion models. The expectation of the apparent selective value at the marker (neutral) locus has been evaluated. Assume two linked loci, at one of which the steady flux equilibrium is reached under constant mutational input of deleterious mutations (with rate v) having disadvantages hs in heterozygote and s in homozygotes. At another locus, the neutral alleles are segregating with frequencies near 0·5. Let Ne be the effective size of the population and c be the recombination fraction between the two loci. Then the coefficient of associative overdominance at the neutral locus can be obtained by taking the expectation with respect to chromosome frequencies at steady flux equilibrium. It becomes approximatelywhere (LI−L0) is the inbreeding depression caused by deleterious mutations under complete inbreeding, and Nehs ≫ l and hs ≫ v are assumed. More generally, if the inbreeding depression of a chromosome segment with a length of recombination fraction C is (LI−L0) then s′ at the neutral marker at the edge of the segment iswhere hs is the average heterozygote disadvantage of detrimentals.The significance of the associative overdominance is discussed in relation to actual observations. It is proposed that the most of the observed heterozygote superiority including inversion chromosomes of Drosophila, isozyme alleles in Avena and ABO blood group genes in man could be explained by the associated detrimentals.

scholarly journals The effect of selected linked locus on heterozygosity of neutral alleles (the hitch-hiking effect)

1975 ◽  
Vol 25 (3) ◽  
pp. 313-325 ◽  
Author(s):  
Tomoko Ohta ◽  
Motoo Kimura
Keyword(s):  
Monte Carlo ◽  
Natural Selection ◽  
Mathematical Theory ◽  
Recombination Fraction ◽  
Small Populations ◽  
Selection Coefficient ◽  
Monte Carlo Experiments ◽  
Neutral Locus ◽  
Marker Loci ◽  
Neutral Marker

SUMMARYA diffusion model was developed to investigate the effect of a mutant substitution by natural selection on heterozygosity at a linked neutral locus. Using this theory, we made extensive numerical analyses to compute the expected total heterozygosity (i.e. the sum of the fraction of heterozygotes over all generations until fixation or loss) at the neutral locus. It was shown that the hitch-hiking effect is generally unimportant as a mechanism for reducing heterozygosity. The effect becomes significant only when the recombination fraction between the selected and the neutral marker loci is smaller than the selection coefficient. In order to check the validity of the mathematical theory, Monte Carlo experiments were performed, and the results were in agreement. It has been suggested that linkage is important only in transient small populations such as at the time of speciation.

scholarly journals Resolving the conflict between associative overdominance and background selection

2016 ◽  
Author(s):  
Lei Zhao ◽  
Brian Charlesworth
Keyword(s):  
Selective Advantage ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Effective Population ◽  
Infinite Population ◽  
Recessive Mutations ◽  
Neutral Locus ◽  
Large Populations ◽  
Marker Loci ◽  
Shed Light

In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance), and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical and simulation studies that shed light on the conditions under which retardation versus acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection, with no linkage disequilibrium. With mutation and selection, retardation only occurs when S, the product of twice the effective population size and the selection coefficient, is of order one. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, there is nearly always a retardation of loss of variability. The results shed light on experiments on the loss of variability at marker loci in laboratory populations, and on the results of computer simulations of the effects of multiple selected loci on neutral variability.

scholarly journals Multilocus models of inbreeding depression with synergistic selection and partial self-fertilization

1991 ◽  
Vol 57 (2) ◽  
pp. 177-194 ◽  
Author(s):  
B. Charlesworth ◽  
M. T. Morgan ◽  
D. Charlesworth
Keyword(s):  
Inbreeding Depression ◽  
Mutation Rate ◽  
Approximate Expression ◽  
Heterozygote Advantage ◽  
Selfing Rate ◽  
Deleterious Alleles ◽  
Plausible Model ◽  
Computer Calculations ◽  
Mean Fitness ◽  
The Mean

SummaryMean fitness and inbreeding depression values in multi-locus models of the control of fitness were studied, using both a model of mutation to deleterious alleles, and a model of heterozygote advantage. Synergistic fitness interactions between loci were assumed, to find out if this more biologically plausible model altered the conclusions we obtained previously using a model of multiplicative interactions. Systems of unlinked loci were assumed. We used deterministic computer calculations, and approximations based on normal or Poisson theory. These approximations gave good agreement with the exact results for some regions of the parameter space. In the mutational model, we found that the effect of synergism was to lower the number of mutant alleles per individual, and thus to increase the mean fitness, compared with the multiplicative case. Inbreeding depression, however, was increased. Similar effects on mean fitness and inbreeding depression were found for the case of heterozygote advantage. For that model, the results were qualitatively similar to those previously obtained assuming multiplicativity. With the mutational load model, however, the mean fitness sometimes decreased, and the inbreeding depression increased, at high selfing rates, after declining as the selfing rate increased from zero. We also studied the behaviour of modifier alleles that changed the selfing rate, introduced into equilibrium populations. In general, the results were similar to those with the multiplicative model, but in some cases an ESS selfing rate, with selfing slightly below one, existed. Finally, we derive an approximate expression for the inbreeding depression in completely selfing populations. This depends only on the mutation rate and the dominance coefficient and can therefore be used to obtain estimates of the mutation rate to mildly deleterious alleles for plant species.

Inbreeding reduces reproductive fitness

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Natural Selection ◽  
Inbreeding Depression ◽  
Reproductive Fitness ◽  
Heterozygote Advantage ◽  
Small Populations ◽  
Population Bottlenecks ◽  
Risk Of Extinction ◽  
Survival And Reproduction

The harmful impacts of inbreeding are generally greater in species that naturally outbreed compared to those in inbreeding species, greater in stressful than benign environments, greater for fitness than peripheral traits, and greater for total fitness compared to its individual components. Inbreeding reduces survival and reproduction (i.e., it causes inbreeding depression), and thereby increases the risk of extinction. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Natural selection may remove (purge) the alleles that cause inbreeding depression, especially following inbreeding or population bottlenecks, but it has limited effects in small populations and usually does not completely eliminate inbreeding depression. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies.

scholarly journals LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Saurin Bipin Parikh ◽  
Nelson Castilho Coelho ◽  
Anne-Ruxandra Carvunis
Keyword(s):  
Linear Interpolation ◽  
Colony Growth ◽  
Relative Fitness ◽  
Environment Interaction ◽  
Nutrient Distribution ◽  
Underlying Distribution ◽  
Fitness Effects ◽  
Fitness Value ◽  
Genetic Perturbations ◽  
Surface Irregularities

Abstract Microbial growth characteristics have long been used to investigate fundamental questions of biology. Colony-based high-throughput screens enable parallel fitness estimation of thousands of individual strains using colony growth as a proxy for fitness. However, fitness estimation is complicated by spatial biases affecting colony growth, including uneven nutrient distribution, agar surface irregularities, and batch effects. Analytical methods that have been developed to correct for these spatial biases rely on the following assumptions: (1) that fitness effects are normally distributed, and (2) that most genetic perturbations lead to minor changes in fitness. Although reasonable for many applications, these assumptions are not always warranted and can limit the ability to detect small fitness effects. Beneficial fitness effects, in particular, are notoriously difficult to detect under these assumptions. Here, we developed the linear interpolation-based detector (LI Detector) framework to enable sensitive colony-based screening without making prior assumptions about the underlying distribution of fitness effects. The LI Detector uses a grid of reference colonies to assign a relative fitness value to every colony on the plate. We show that the LI Detector is effective in correcting for spatial biases and equally sensitive toward increase and decrease in fitness. LI Detector offers a tunable system that allows the user to identify small fitness effects with unprecedented sensitivity and specificity. LI Detector can be utilized to develop and refine gene–gene and gene–environment interaction networks of colony-forming organisms, including yeast, by increasing the range of fitness effects that can be reliably detected.

scholarly journals Evidence for the partial dominance of viability genes contributing to inbreeding depression in Mimulus guttatus.

Genetics ◽  
1994 ◽  
Vol 136 (1) ◽  
pp. 323-331
Author(s):  
Y B Fu ◽  
K Ritland
Keyword(s):  
Inbreeding Depression ◽  
Wild Plant ◽  
Mimulus Guttatus ◽  
Selfed Progeny ◽  
Partial Dominance ◽  
Complete Dominance ◽  
Model Free ◽  
Segregation Ratios ◽  
Marker Loci ◽  
In The Wild

Abstract The relative importance of different modes of gene expression of viability genes contributing to inbreeding depression was investigated in the wild plant, Mimulus guttatus. Viability genes were identified by self-fertilizing 31 outbred plants, each heterozygous for three to nine unlinked allozyme markers, and analyzing segregation ratios of selfed progeny at maturity for deviations from 1:2:1 ratios. In this study, 24 linkages of viability genes to marker loci were detected. To infer the nature of gene action for these viability genes, a "model-free" graphical method was developed that examines the "space" of segregation ratios allowed by each of seven selection models (i.e., overdominance, complete recessivity, partial recessivity, additivity, partial dominance, complete dominance and underdominance). Using this method, we found that, of 24 linkages detected, 18 were consistent with either partial dominance, complete dominance or underdominance. Six were consistent with either partial recessivity, complete recessivity or overdominance. This finding indicates that, in these chromosomal segments identified by allozyme markers, partial dominance plays the predominant role in inbreeding depression. This is inconsistent with either the dominance or overdominance hypotheses proposed to account for inbreeding depression.

Inbreeding and loss of genetic diversity increase extinction risk

2019 ◽  
pp. 31-48
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Raw Material ◽  
Heterozygote Advantage ◽  
Isolated Populations ◽  
Survival And Reproduction ◽  
Loss Of Genetic Diversity ◽  
Harmful Effects

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

scholarly journals Inbreeding depresses sperm competitiveness, but not fertilization or mating success in male Tribolium castaneum

2010 ◽  
Vol 277 (1699) ◽  
pp. 3483-3491 ◽  
Author(s):  
Łukasz Michalczyk ◽  
Oliver Y. Martin ◽  
Anna L. Millard ◽  
Brent C. Emerson ◽  
Matthew J. G. Gage
Keyword(s):  
Sperm Competition ◽  
Inbreeding Depression ◽  
Tribolium Castaneum ◽  
Mating Behaviour ◽  
Fertilization Success ◽  
Heterozygote Advantage ◽  
Length Variation ◽  
Sperm Length ◽  
Mating Pattern ◽  
Normal Fertilization

As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male–male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P 2 ‘offence’ role in sperm competition was significantly more depressed under inbreeding than sperm ‘defence’ (P 1 ). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.

An Improved Adaptive Evolutionary Algorithm for Multi-Objective Optimization

2013 ◽  
Vol 303-306 ◽  
pp. 1494-1500
Author(s):  
Jian Wei Wang ◽  
Jian Ming Zhang
Keyword(s):  
Evolutionary Algorithm ◽  
Optimal Solution ◽  
Optimization Methods ◽  
Relative Fitness ◽  
Multi Objective Optimization ◽  
Multi Objective ◽  
Fitness Value ◽  
Crossover Probability ◽  
Optimal Solution Set ◽  
Adaptive Evolutionary Algorithms

Aiming at effectively overcoming the disadvantages of traditional evolutionary algorithm which converge slowly and easily run into local extremism, an improved adaptive evolutionary algorithms is proposed. Firstly, in order to choose the optimal objective fitness value from the population in every generation, the absolute and relative fitness are defined. Secondly, fuzzy technique is adopted to adjust the weights of objective functions, crossover probability, mutation probability, crossover positions and mutation positions during the iterative process. Finally, three classical test functions are given to illustrate the validity of improved adaptive evolutionary algorithm, simulation results show that the diversity and practicability of the optimal solution set are better by using the proposed method than other multi-objective optimization methods.

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