synonymous and nonsynonymous substitution rates
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
... different substitution rate to ...different rates while the number of tially that of Li (1993) and Pamilo and Bianchi (1993) sites is calculated assuming that transitions and transver- but with one small ...
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Evolutionary Rates and Expression Level in Chlamydomonas
... the synonymous and nonsynonymous substitution rates among the ...The synonymous substitution divergence across the genes studied here is at least as large as the among-gene ...
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Explorations of Site-to-Site Synonymous Substitution Rate Variability.
... the synonymous substitution rate across sites is constant and thus attributes any variation in the overall ω rate to nonsynonymous rate variation ...the synonymous and nonsynonymous ...
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Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution: Approximate and Maximum-Likelihood Methods Lead to Different Conclusions
... of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous ...estimate ...
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The Effect of Tandem Substitutions on the Correlation Between Synonymous and Nonsynonymous Rates in Rodents
... Simulated substitution sequences were generated under the tein-coding sequence available in a single GenBank/EMBL assumption of independent ...and nonsynonymous substitution rates of the real ...
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CODON SUBSTITUTION IN EVOLUTION AND THE "SATURATION" OF SYNONYMOUS CHANGES
... Synonymous and nonsynonymous changes under equal mutation rates: T o examine the accuracy of the PCD method under the mutation scheme with equal mu- tation rates (t[r] ...
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Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes
... in substitution patterns between parts of the tree were, in fact, the cause of the observed discrepancies, we would expect that incorporating these differences into a model for the nucleotide frequency dynamics ...
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γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
... estimate nonsynonymous and synonymous substitution rates for interrogating sequence dynamics and constructing phylogenetic ...per nonsynonymous and synonymous site, respectively, ...
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Genome-Wide Patterns of Nucleotide Substitution Reveal Stringent Functional Constraints on the Protein Sequences of Thermophiles
... more deleterious in a thermophile than in a nonthermo- phile. On this hypothesis, the especially deleterious na- ture of mutation in thermophiles would have favored the evolutionary fixation of modifiers that ...
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Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guanche
... of nonsynonymous and synonymous changes are beneath the branches of the Adh -Twain ...the rates of amino acid substitution, but not synonymous substitutions, relative to the ancestral ...
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Molecular Clocks and the Puzzle of RNA Virus Origins
... of substitution rates in a wider array of RNA ...of rates of viral replication in ...replication rates are also associated with low substitution rates, as this is perhaps the ...
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Mutations as Missing Data: Inferences on the Ages and Distributions of Nonsynonymous and Synonymous Mutations
... any function of the distribution of mutations on a gene genealogy. There are already several methods available for estimating population genetical parameters using MCMC and related simulation methods (e.g., Griffiths and ...
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Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test
... While there is clearly a genome-wide increase in nonsynonymous substitution rate in the grass lineage (Table 1 ) , rejec- tion of the nonsynonymous relative ratio test is[r] ...
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Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses
... associated synonymous substitution rates, and greatest degrees of complementary coevolution between paired nucleotides are shown using arcs in cyan and magenta (to distinguish the two complementary ...
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Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response
... either synonymous or non-synonymous, and the highest virus diversity, evalu- ated by genetic distance, were found in patients with sustained virological responses ...
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The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory
... test, and it is able to distinguish between hypotheses of balancing selection and selection on deleterious muta- tions. It should therefore provide additional informa- tion regarding selection coefficients when applied ...
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The Correlation Between Synonymous and Nonsynonymous Substitutions in Drosophila: Mutation, Selection or Relaxed Constraints?
... in the analyses. The sequences were aligned after translation expected to lead to a relative excess of codons with both using CLUSTAL W ( Thompson et al. 1994) with minor manual synonymous and nonsynonymous ...
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Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection
... For each gene, the relative frequencies for each co- conjectured (Debry and Marzluff 1994). However, don were calculated with respect to the other codons the fact that these two correlations disappear when the that ...
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Patterns of Synonymous Codon Usage in Drosophila melanogaster Genes With Sex-Biased Expression
... greater expression in males than in females were classified as been reported (Nurminsky et al. 1998; Ting et al. 1998; male biased, genes with twofold or greater expression in fe- Parsch et al. 2001; Betra´n and Long ...
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Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
... “To my knowledge, no one has yet performed deep mutational scanning on an unstructured protein domain. But once such experiments are done, as the reviewer sug- gests, it would be very interesting to test whether such ...
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