substitution rate
The Problem of Counting Sites in the Estimation of the Synonymous and Nonsynonymous Substitution Rates: Implications for the Correlation Between the Synonymous Substitution Rate and Codon Usage Bias
... the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of mutations that would be ...
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The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates
... nucleotide substitution rates range from ...between substitution rate estimates in different RV genome regions are largely attributable to temporal sampling biases such that datasets containing ...
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Stochastic Demography and the Neutral Substitution Rate in Class-Structured Populations
... the rate at which a gene randomly sampled in a newborn of sex g 2 {f, m} accumulates ...neutral substitution rate under overlapping generations for diploid reproduction (Pollak 1982, equation 8) (see ...
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Explorations of Site-to-Site Synonymous Substitution Rate Variability.
... synonymous substitution rate across sites is constant and thus attributes any variation in the overall ω rate to nonsynonymous rate variation ...nonsynonymous substitution rates to vary ...
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Sojourn Times and Substitution Rate at Overdominant and Linked Neutral Loci
... the rate of accumulation of mutations, or the substitution rate, was predicted from the mean extinction time of a common overdominant ...The substitution rate calculated theoreti- cally ...
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Should We Expect Substitution Rate to Depend on Population Size?
... The rate of nucleotide substitution is generally believed to be a decreasing function of effective population size, at least for nonsynonymous ...the substitution rate to population ...
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Intracellular selection, conversion bias, and the expected substitution rate of organelle genes.
... This paper examines the expected substitution rate of new mutants by obtaining the probability that a new mutant is fixed throughout a cell, allowing for arbitrary rat[r] ...
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Genus-Specific Substitution Rate Variability among Picornaviruses
... more rate analyses of entero- viruses than of other ...enterovirus substitution rates are of serotypes and most other available substitution rates are of species, the substitution rates of an ...
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Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution
... the rate of amino acid substitution varies among different proteins and among different sites of a ...of rate variation among sites of a protein and the mean substitution rate of the ...
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Decreased Diversity but Increased Substitution Rate in Host mtDNA as a Consequence of Wolbachia Endosymbiont Infection
... elevated rate of over within the endosymbiont population, the associated mtDNA substitution, are the patterns of substitution mtDNA in a host species will be taken through an effective consistent ...
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Human Mutation/substitution Rate: Variability, Modeling And Applications
... the rate of mutation, much more than broad scale ...higher rate of transitions than transversions, which can be explained by relative ease of purine to purine or pyrimidine to pyrimidine DNA mispairing ...
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Longitudinal analysis of Plasmodium falciparum genetic variation in Turbo, Colombia: implications for malaria control and elimination
... overall substitution rate is proportional to the repeat length, that each mutation results in the gain or loss of a single repeat, and that the probability of an expansion is a decreasing linear function of ...
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Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea)
... the substitution rate per branch, a calibrated time tree was built by dating Notostraca, Cladocera and Anostraca crown groups, along with the tree root, using well-detailed and justified fossil records ...
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Phylogeography, Population Dynamics, and Molecular Evolution of European Bat Lyssaviruses
... Estimating substitution and population ...topology, substitution model, and substitution ...nucleotide substitution with parameters optimized during multiple ...the rate of population ...
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Rapid Evolution of Mammalian X-Linked Testis-Expressed Homeobox Genes
... Selection promotes the diversity of charge profile: To investigate what types of nonsynonymous substitutions are favored by selection, we counted the numbers of conservative and radical nonsynonymous substitutions on ...
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Theoretical study of near neutrality. II. Effect of subdivided population structure with local extinction and recolonization.
... In general, by increasing the population size, the substitution rate becomes lower, and the heterozygosity, higher, for nearly neutral mutations, and this prediction i[r] ...
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Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution.
... Our results show that the effect of total population size on the substitution rate is larger when 2Nus = 0.5 and 1 than when 2Nus = 0.2, indicating that the cancellation[r] ...
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Deleterious Passengers in Adapting Populations
... the substitution rate of a deleterious mutation as a function of its fi tness cost, as well as the reduction in the beneficial substitution rate due to the genetic load of the ...the rate ...
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Role of viral evolutionary rate in HIV 1 disease progression in a linked cohort
... non-synonymous/synonymous substitution rate ratio scan was performed on the com- plete genomes using a maximum likelihood estimation procedure (Figure ...
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Vanishing GC-Rich Isochores in Mammalian Genomes
... between substitution rate and GC content has been re- ...the substitution pattern observed in primate content is decreasing, one expects a positive correlation or cetartiodactyl GC-rich ...between ...
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