Synonymous and nonsynonymous rate variation in nuclear genes of mammals

@article{Yang2009SynonymousAN,
  title={Synonymous and nonsynonymous rate variation in nuclear genes of mammals},
  author={Ziheng Yang and Rasmus Nielsen},
  journal={Journal of Molecular Evolution},
  year={2009},
  volume={46},
  pages={409-418}
}
A maximum likelihood approach was used to estimate the synonymous and nonsynonymous substitution rates in 48 nuclear genes from primates, artiodactyls, and rodents. A codon-substitution model was assumed, which accounts for the genetic code structure, transition/transversion bias, and base frequency biases at codon positions. Likelihood ratio tests were applied to test the constancy of nonsynonymous to synonymous rate ratios among branches (evolutionary lineages). It is found that at 22 of the… 
Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence Comparisons
TLDR
A Bayesian method is implemented to estimate ω and t in pairwise sequence comparisons of genome-scale comparisons of protein-coding gene sequences and it is shown that the Bayesian estimates have better statistical properties than the ML estimates.
2 MARKOV MODEL OF CODON SUBSTITUTION
TLDR
This chapter reviews statistical methods for detecting adaptive molecular evolution by comparing synonymous and nonsynonymous substitution rates in protein-coding DNA sequences and discusses the limitations of current methods.
Mammalian nonsynonymous sites are not overdispersed: comparative genomic analysis of index of dispersion of mammalian proteins.
TLDR
It is found that the mean index of dispersion for nonsynonymous sites of mammalian proteins is not significantly different from 1.0, and patterns of lineage-specific selective constraint are consistent with the nearly neutral model of molecular evolution.
Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins.
TLDR
Results and analyses of real data indicate that synonymous substitutions are very informative and substantially improve evolutionary inference, even when the sequences are highly divergent, and that amino acid models should be adopted only after carefully investigating and discarding the possibility that synonymous substitution can reveal important evolutionary information.
Investigations into the relationship between evolutionary rate variation, protein structure and codon usage
TLDR
Results show that different secondary structures in E. coli K12 and Homo sapiens are under different evolutionary pressures, and shows that preferred codons experience different selective constraints to unpreferred codons.
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model
TLDR
The use of a mutation–selection framework that includes a Dirichlet process approach to account for across-codon-site variation in amino acid fitness profiles as a null model for the detection of adaptation is studied.
Variation of the adaptive substitution rate between species and within genomes
TLDR
A comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species is delivered.
The positive correlation between dN/dS and dS in mammals is due to runs of adjacent substitutions.
TLDR
It is shown that the correlation between ω and dS is reduced when genes that are high quality in sequence, annotation, and alignment are used, and that estimates of ω are biased when levels of divergence are low.
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
TLDR
This study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size, and illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.
...
...

References

SHOWING 1-10 OF 26 REFERENCES
Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory
TLDR
The rate and pattern found here are consistent with the nearly neutral theory, such that the relative contributions of drift and selection differ between the two types of substitutions, and are also consistent with Gillespie's episodic selection theory.
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
TLDR
Simulations help confirm previous suggestions that silent sites are saturated, leaving no evidence of heterogeneity in synonymous substitution rates, and confirm previous findings that substitution rates in the chloroplast genome are subject to both lineage-specific and locus-specific effects.
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
TLDR
A new method that gives unbiased estimates is proposed and an application of the new and the old method to 14 pairs of mouse and rat genes shows that the new method gives aKS value very close to the number of substitutions per fourfold degenerate site whereas the oldmethod gives a value 30% higher.
Pattern of synonymous and nonsynonymous substitutions: An indicator of mechanisms of molecular evolution
  • Y. Ina
  • Biology
    Journal of Genetics
  • 2008
TLDR
When the transition/transversion bias at the mutation level is strong, the numbers of synonymous and nonsynonymous substitutions are estimated more accurately by the PBL and Ina methods than by the NG, MY and LWL methods.
A method for estimating the numbers of synonymous and nonsynonymous substitutions per site
TLDR
Computer simulations indicate that the method presented gives more accurate Ks and Ka estimates than the aforementioned methods, and the obtention of confidence intervals for divergence estimates by computer simulation is proposed.
Correlated rates of synonymous site evolution across plant genomes.
TLDR
It is shown that grasses evolve more rapidly than palms at synonymous sites in a mitochondrial, a nuclear, and a plastid gene, and that the relative rates of synonymous substitution between grasses and palms are similar at the three loci.
Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral.
TLDR
It is shown that substitution rates at fourfold-degenerate sites and at sites in noncoding regions do not vary between the primate and rodent lineages, implying mutation-rate uniformity, and that this difference in substitution-rate pattern between the two types of site is incompatible with neutral theory.
Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application
TLDR
It is suggested that, in the coding regions surrounding the splicing points of intervening sequences ofβ-globin genes, there exist rigid secondary structures that show the slowing down of evolutionary rates of both synonymous and amino acid substitutions in the primate line.
Adaptive protein evolution at the Adh locus in Drosophila
TLDR
A simple statistical test of the neutral protein evolution hypothesis is proposed based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus, finding that there are more fixed replacement differences between species than expected.
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
  • M. Kimura
  • Biology
    Journal of Molecular Evolution
  • 2005
TLDR
Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
...
...