scholarly journals Time for spreading of compensatory mutations under gene duplication.

Genetics ◽  
1989 ◽  
Vol 123 (3) ◽  
pp. 579-584
Author(s):  
T Ohta
Keyword(s):  
Gene Duplication ◽  
Diffusion Equation ◽  
Population Size ◽  
Computer Simulations ◽  
Deleterious Mutation ◽  
Selective Constraint ◽  
Effective Population ◽  
Gene Redundancy ◽  
Tight Linkage ◽  
Compensatory Mutations

Abstract Evolution by compensatory mutations is accelerated by gene duplication because selective constraint is relaxed by gene redundancy. A mutation is called compensatory if it corrects the effect of an earlier deleterious mutation. Without duplication, Kimura has shown that the time for spreading of compensatory mutations is much reduced by tight linkage between the two chromosomal sites of mutations. In this report, the time for spreading with gene duplication was studied by using the diffusion equation method of Kimura, together with computer simulations. It was shown that, when 2Nv- is much less than unity, the time for spreading is greatly shortened by gene duplication as compared with the case of complete linkage between the two sites of mutations, where 2N is the effective population size (haploid) and v- is the rate of compensatory mutations. However, if 2Nv- greater than 1, gene duplication is not effective for accelerating the evolution by such mutations.

Evolution by gene duplication and compensatory advantageous mutations.

Genetics ◽  
1988 ◽  
Vol 120 (3) ◽  
pp. 841-847
Author(s):  
T Ohta
Keyword(s):  
Monte Carlo ◽  
Gene Duplication ◽  
Monte Carlo Simulations ◽  
Selective Constraint ◽  
Crossing Over ◽  
Compensatory Mutation ◽  
Random Genetic Drift ◽  
Selection Coefficient ◽  
Gene Redundancy ◽  
Compensatory Mutations

Abstract Relaxation of selective constraint is thought to play an important role for evolution by gene duplication, in connection with compensatory advantageous mutant substitutions. Models were investigated by incorporating gene duplication by unequal crossing over, selection, mutation and random genetic drift into Monte Carlo simulations. Compensatory advantageous mutations were introduced, and simulations were carried out with and without relaxation, when genes are redundant on chromosomes. Relaxation was introduced by assuming that deleterious mutants have no effect on fitness, so long as one or more genes free of such mutations remain in the array. Compensatory mutations are characterized by the intermediate deleterious step of their substitutions, and therefore relaxation by gene redundancy is important. Through extensive Monte Carlo simulations, it was found that compensatory mutant substitutions require relaxation in addition to gene duplication, when mutant effects are large. However when mutant effects are small, such that the product of selection coefficient and population size is around unity, evolution by compensatory mutation is enhanced by gene duplication even without relaxation.

scholarly journals Harmful mutation load in the mitochondrial genomes of cattle breeds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Genetic Diseases ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation

2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Vaishali Katju
Keyword(s):  
Gene Duplication ◽  
Population Size ◽  
Population Genetic ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Dna And Rna ◽  
Duplication Events ◽  
History Of ◽  
Theoretical Population ◽  
Novel Exon

The gene duplication process has exhibited far greater promiscuity in the creation of paralogs with novel exon-intron structures than anticipated even by Ohno. In this paper I explore the history of the field, from the neo-Darwinian synthesis through Ohno’s formulation of the canonical model for the evolution of gene duplicates and culminating in the present genomic era. I delineate the major tenets of Ohno’s model and discuss its failure to encapsulate the full complexity of the duplication process as revealed in the era of genomics. I discuss the diverse classes of paralogs originating from both DNA- and RNA-mediated duplication events and their evolutionary potential for assuming radically altered functions, as well as the degree to which they can function unconstrained from the pressure of gene conversion. Lastly, I explore theoretical population-genetic considerations of how the effective population size (Ne) of a species may influence the probability of emergence of genes with radically altered functions.

scholarly journals Harmful Mutation Load in the Mitochondrial Genomes of Cattle Breeds 

2021 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract ObjectiveDomestication of wild animals results in a reduction in the effective population size and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to accumulation deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 252 animals belonging to 15 cattle breeds of the world. ResultsOur analysis revealed more than fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the neutral heterozygosity and the ratio of amino acid changing diversity to silent diversity. This suggests a proportionally higher amino acid changing variants in breeds with low diversity. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals Background selection theory overestimates effective population size for high mutation rates

2022 ◽  
Author(s):  
Joseph D Matheson ◽  
Joanna Masel
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Deleterious Mutation ◽  
Neutral Theory ◽  
Mutation Rates ◽  
Background Selection ◽  
Effective Population ◽  
Selection Theory ◽  
Linkage Disequilibria ◽  
Genome Wide

Simple models from the neutral theory of molecular evolution are claimed to be flexible enough to incorporate the complex effects of background selection against linked deleterious mutations. Complexities are collapsed into an "effective" population size that specifies neutral genetic diversity. To achieve this, current background selection theory assumes linkage equilibrium among deleterious variants. Data do not support this assumption, nor do theoretical considerations when the genome-wide deleterious mutation is realistically high. We simulate genomes evolving under background selection, allowing the emergence of linkage disequilibria. With realistically high deleterious mutation rates, neutral diversity is much lower than predicted from previous analytical theory.

scholarly journals Relative precision of the sibship and LD methods for estimating effective population size with genomics-scale datasets

2021 ◽  
Author(s):  
Robin S Waples
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Computer Simulations ◽  
Sibling Relationships ◽  
Single Sample ◽  
Effective Population ◽  
Model Species ◽  
Relative Precision ◽  
Combining Information

Computer simulations were used to compare relative precision of two widely-used single-sample methods for estimating effective population size (Ne)--the sibship method and the linkage-disequilibrium (LD) method. Emphasis is on performance when thousands of gene loci are used, which now can easily be achieved even for non-model species. Results show that unless Ne is very small, if at least 500-2000 diallelic loci are used, precision of the LD method is higher than the maximum possible precision for the sibship method, which occurs when all sibling relationships have been correctly identified. Results also show that when precision is high for both methods, their estimates of effective population size are high and positively correlated, which limits additional gains in precision that might be obtained by combining information from the two estimators

scholarly journals The interaction between effective population size and linkage intensity under artificial selection

1966 ◽  
Vol 7 (3) ◽  
pp. 313-323 ◽  
Author(s):  
B. D. H. Latter
Keyword(s):  
Population Size ◽  
Finite Population ◽  
Low Frequency ◽  
Selection Response ◽  
Appreciable Effect ◽  
Effective Population ◽  
Mean Waiting Time ◽  
Tight Linkage ◽  
The Mean ◽  
Total Selection

The effects of tight linkage on the total response due to pairs of identical additive loci, segregating in a population initially in linkage equilibrium, have been studied both algebraically and by means of computer simulation. Particular attention has been given to the effects of finite population size on the probabilities of (a) the elimination from the population of the gamete carrying both ‘plus’ alleles; (b) the joint preservation of the two types of repulsion gametes; (c) the recovery of the desired combination of plus alleles through crossing-over; and (d) the fixation of the gamete in the population following its recovery.The study is restricted to situations in which linkage is known to have an appreciable effect on total selection response, i.e. to the case of genes of large effect initially at low frequency. A comparison of regimes with the same expected response under free recombination has shown the probability of (a) to be high, and the probability of (b) to be very nearly the same for all regimes tested. Provided that the recovery of the gamete carrying both plus alleles is an unlikely event at any given point in time, the probability of the fixation of the gamete, once reconstituted, is expected to be independent of population size for genes of large effect. In this context, approximate algebraic expressions have been derived for the probability of effective recovery of the required gamete, and for the mean waiting time involved.

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