scholarly journals Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jacob Pieter Rutten ◽  
Paulien Hogeweg ◽  
Guillaume Beslon
Keyword(s):  
Mutation Rate ◽  
Genome Structure ◽  
Mutational Load ◽  
Bacterial Populations ◽  
Long Run ◽  
Stable Conditions ◽  
Long Time ◽  
Natural Isolates ◽  
Mean Fitness ◽  
The Mean

Abstract Background Mutators are common in bacterial populations, both in natural isolates and in the lab. The fate of these lineages, which mutation rate is increased up to 100 ×, has long been studied using population genetics models, showing that they can spread in a population following an environmental change. However in stable conditions, they suffer from the increased mutational load, hence being overcome by non-mutators. However, these results don’t take into account the fact that an elevated mutation rate can impact the genetic structure, hence changing the sensitivity of the population to mutations. Here we used Aevol, an in silico experimental evolution platform in which genomic structures are free to evolve, in order to study the fate of mutator populations evolving for a long time in constant conditions. Results Starting from wild-types that were pre-evolved for 300,000 generations, we let 100 mutator populations (point mutation rate ×100) evolve for 100,000 further generations in constant conditions. As expected all populations initially undergo a fitness loss. However, after that the mutator populations started to recover. Most populations ultimately recovered their ancestors fitness, and a significant fraction became even fitter than the non-mutator control clones that evolved in parallel. By analyzing the genomes of the mutators, we show that the fitness recovery is due to two mechanisms: i. an increase in robustness through compaction of the coding part of the mutator genomes, ii. an increase of the selection coefficient that decreases the mean-fitness of the population. Strikingly the latter is due to the accumulation of non-coding sequences in the mutators genomes. Conclusion Our results show that the mutational burden that is classically thought to be associated with mutator phenotype is escapable. On the long run mutators adapted their genomes and reshaped the distribution of mutation effects. Therewith the lineage is able to recover fitness even though the population still suffers the elevated mutation rate. Overall these results change our view of mutator dynamics: by being able to reduce the deleterious effect of the elevated mutation rate, mutator populations may be able to last for a very long time; A situation commonly observed in nature.

scholarly journals An Upper Limit on the Functional Fraction of the Human Genome

2017 ◽  
Vol 9 (7) ◽  
pp. 1880-1885 ◽  
Author(s):  
Dan Graur
Keyword(s):  
Human Genome ◽  
Human Population ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
Replacement Level ◽  
Functional Regions ◽  
Upper Limit ◽  
Constant Size ◽  
Mean Fitness ◽  
The Mean

AbstractFor the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.

Estimation of Deleterious Genomic Mutation Parameters in Natural Populations by Accounting for Variable Mutation Effects Across Loci

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1487-1500 ◽  
Author(s):  
Hong-Wen Deng ◽  
Guimin Gao ◽  
Jin-Long Li
Keyword(s):  
Statistical Method ◽  
Mutation Rate ◽  
Genetic Variance ◽  
Natural Populations ◽  
Evolutionary Genetics ◽  
Simulation Studies ◽  
Fitness Effects ◽  
Mean Fitness ◽  
The Mean ◽  
Genomic Mutation

Abstract The genomes of all organisms are subject to continuous bombardment of deleterious genomic mutations (DGM). Our ability to accurately estimate various parameters of DGM has profound significance in population and evolutionary genetics. The Deng-Lynch method can estimate the parameters of DGM in natural selfing and outcrossing populations. This method assumes constant fitness effects of DGM and hence is biased under variable fitness effects of DGM. Here, we develop a statistical method to estimate DGM parameters by considering variable mutation effects across loci. Under variable mutation effects, the mean fitness and genetic variance for fitness of parental and progeny generations across selfing/outcrossing in outcrossing/selfing populations and the covariance between mean fitness of parents and that of their progeny are functions of DGM parameters: the genomic mutation rate U, average homozygous effect s, average dominance coefficient h, and covariance of selection and dominance coefficients cov(h, s). The DGM parameters can be estimated by the algorithms we developed herein, which may yield improved estimation of DGM parameters over the Deng-Lynch method as demonstrated by our simulation studies. Importantly, this method is the first one to characterize cov(h, s) for DGM.

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.

The Problem of Identifying and Modeling the Relationship between Monetary Factor and Inflation in the Russian Economy

2008 ◽  
pp. 61-76
Author(s):  
A. Porshakov ◽  
A. Ponomarenko
Keyword(s):  
Money Supply ◽  
Money Demand ◽  
Russian Economy ◽  
Long Run ◽  
Complex Approach ◽  
Wide Range ◽  
Long Time ◽  
The Relationship ◽  
Supply Side Factors

The role of monetary factor in generating inflationary processes in Russia has stimulated various debates in social and scientific circles for a relatively long time. The authors show that identification of the specificity of relationship between money and inflation requires a complex approach based on statistical modeling and involving a wide range of indicators relevant for the price changes in the economy. As a result a model of inflation for Russia implying the decomposition of inflation dynamics into demand-side and supply-side factors is suggested. The main conclusion drawn is that during the recent years the volume of inflationary pressures in the Russian economy has been determined by the deviation of money supply from money demand, rather than by money supply alone. At the same time, monetary factor has a long-run spread over time impact on inflation.

COUNTING TOTAL BACTERIA IN LAND ORGANIC WASTE HOUSEHOLD AND LAND INORGANIC WITH TOTAL PLATE COUNT METHOD (TPC)

2017 ◽  
Vol 4 (2) ◽  
pp. 87-91
Author(s):  
Ekamaida Ekamaida
Keyword(s):  
Soil Fertility ◽  
Bacterial Population ◽  
Organic Soil ◽  
Biological Properties ◽  
Plate Count ◽  
Bacterial Populations ◽  
Fertility Data ◽  
Plate Count Method ◽  
The Mean ◽  
Total Bacteria

The soil fertility aspect is characterized by the good biological properties of the soil. One important element of the soil biological properties is the bacterial population present in it. This research was conducted in the laboratory of Microbiology University of Malikussaleh in the May until June 2016. This study aims to determine the number of bacterial populations in soil organic and inorganic so that can be used as an indicator to know the level of soil fertility. Data analysis was done by T-Test that is by comparing the mean of observation parameter to each soil sample. The sampling method used is a composite method, which combines 9 of soil samples taken from 9 sample points on the same plot diagonally both on organic soil and inorganic soil. The results showed the highest bacterial population was found in total organic soil cfu 180500000 and total inorganic soil cfu 62.500.000

scholarly journals GENETIC LOAD IN NATURAL POPULATIONS: IS IT COMPATIBLE WITH THE HYPOTHESIS THAT MANY POLYMORPHISMS ARE MAINTAINED BY NATURAL SELECTION?

Genetics ◽  
1974 ◽  
Vol 77 (3) ◽  
pp. 569-589
Author(s):  
Martin L Tracey ◽  
Francisco J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Natural Population ◽  
Natural Populations ◽  
Genetic Load ◽  
Structural Genes ◽  
Invertebrate Species ◽  
Average Proportion ◽  
Mean Fitness ◽  
The Mean

ABSTRACT Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster.

scholarly journals The mutation load under tetrasomic inheritance and its consequences for the evolution of the selfing rate in autotetraploid species

1999 ◽  
Vol 74 (1) ◽  
pp. 31-42 ◽  
Author(s):  
J. RONFORT
Keyword(s):  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Stable State ◽  
Approximate Solutions ◽  
Balance Model ◽  
Deleterious Mutations ◽  
Selfing Rate ◽  
Mutation Load ◽  
Mean Fitness ◽  
The Mean

Single-locus equilibrium frequencies of a partially recessive deleterious mutation under the mutation–selection balance model are derived for partially selfing autotetraploid populations. Assuming multiplicative fitness interactions among loci, approximate solutions for the mean fitness and inbreeding depression values are also derived for the multiple locus case and compared with expectations for the diploid model. As in diploids, purging of deleterious mutations through consanguineous matings occurs in autotetraploid populations, i.e. the equilibrium mutation load is a decreasing function of the selfing rate. However, the variation of inbreeding depression with the selfing rate depends strongly on the dominance coefficients associated with the three heterozygous genotypes. Inbreeding depression can either increase or decrease with the selfing rate, and does not always vary monotonically. Expected issues for the evolution of the selfing rate consequently differ depending on the dominance coefficients. In some cases, expectations for the evolution of the selfing rate resemble expectations in diploids; but particular sets of dominance coefficients can be found that lead to either complete selfing or intermediate selfing rates as unique evolutionary stable state.

Relationship between temporal and spatial averages in grid turbulence

2013 ◽  
Vol 730 ◽  
pp. 593-606 ◽  
Author(s):  
L. Djenidi ◽  
S. F. Tardu ◽  
R. A. Antonia
Keyword(s):  
Strong Support ◽  
Statistical Properties ◽  
Grid Turbulence ◽  
Mean Flow ◽  
Lateral Direction ◽  
Ergodic Hypothesis ◽  
Long Time ◽  
The Mean ◽  
Temporal And Spatial ◽  
Boltzmann Method

AbstractA long-time direct numerical simulation (DNS) based on the lattice Boltzmann method is carried out for grid turbulence with the view to compare spatially averaged statistical properties in planes perpendicular to the mean flow with their temporal counterparts. The results show that the two averages become equal a short distance downstream of the grid. This equality indicates that the flow has become homogeneous in a plane perpendicular to the mean flow. This is an important result, since it confirms that hot-wire measurements are appropriate for testing theoretical results based on spatially averaged statistics. It is equally important in the context of DNS of grid turbulence, since it justifies the use of spatial averaging along a lateral direction and over several realizations for determining various statistical properties. Finally, the very good agreement between temporal and spatial averages validates the comparison between temporal (experiments) and spatial (DNS) statistical properties. The results are also interesting because, since the flow is stationary in time and spatially homogeneous along lateral directions, the equality between the two types of averaging provides strong support for the ergodic hypothesis in grid turbulence in planes perpendicular to the mean flow.

scholarly journals Selection, Load and Inbreeding Depression in a Large Metapopulation

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1191-1202 ◽  
Author(s):  
Michael C Whitlock
Keyword(s):  
Population Structure ◽  
Inbreeding Depression ◽  
Population Subdivision ◽  
Response To Selection ◽  
Mutation Load ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Soft Selection ◽  
Mean Fitness ◽  
The Mean

Abstract The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

Justice and Inclusion Mutually Cause Each Other

2021 ◽  
pp. 194855062110297
Author(s):  
Chris C. Martin ◽  
Michael J. Zyphur
Keyword(s):  
Work Experience ◽  
Social Exchanges ◽  
Panel Models ◽  
Reciprocal Influence ◽  
Entrepreneurial Teams ◽  
Overall Justice ◽  
Random Intercept ◽  
Long Run ◽  
The Mean ◽  
Robustness Check

Justice should increase inclusion because just treatment conveys acceptance and enables social exchanges that build cohesion. Inclusion should increase justice because people can use inclusion as a convenient fairness cue. Prior research touches on these causal associations but relies on a thin conception of inclusion and neglects within-person effects. We analyze whether justice causes inclusion at the within-person level. Five waves of data were gathered from 235 college students in 38 entrepreneurial teams. Teams were similar in size, work experience, deadlines, and goals. General cross-lagged panel models indicated that justice and inclusion had a reciprocal influence on each other. A robustness check with random-intercept cross-lagged models supported the results. In the long run, reversion to the mean occurred after an effect decayed, suggesting that virtuous or vicious cycles are unlikely. The results imply that maintaining overall justice at the peer-to-peer level may lead to inclusion.

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