Selection on Codon Bias. Annu Rev Genet. 2008; 42:287-99. doi: 10.1146/ annurev.genet.42.110807.091442 PMID: 18983258Hershberg R,Petrov DA.Selection on codon bias. Annual Review of Genetics . 2008Hershberg R,Petrov DA.Selection on codon bias. Annual Review of Genetics . 2008...
Population genetic studies have shown that synonymous sites are under weak selection and that codon bias is maintained by a balance between selection, mutation, and genetic drift. It appears that the major cause for selection on codon bias is that certain preferred codons are translated more ...
Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature 428, 942–945 (2004); see also communication from Nielsen et al.; Chen et al.; Plotkin et al. reply The idea that natural selection on genes might be detected using only a single genome ha
and Fop, as the latter is well known to be correlated with the intensity of selection on codon usage bias (reviewed inHershberg and Petrov, 2008;Zeng and Charlesworth, 2009). Considering the large variance of theFestimators and the dearth of SNPs in individual genes, we grouped the genes in...
Selection intensity is notoriously hard to measure107,108,109,110, however, based on estimates for codon bias111, we consider sp/ν− = 10 and sp/ν− = 100 in case of weak and strong selection, respectively. Finally, we assume that sr < sp for a typical target gene,...
Again, this seems like a natural result rather than bias, as it is harder to envisage coherence at a suite of codon sites within orders if the sequences do not group together in the tree: the same branch-site model was still preferred among orthogroups that lacked order-monophyly....
摘要: Codon usage bias has been observed in various organisms. In this study, the correlation between SHH genes expression in some tissues and codon usage features was analyzed by bioinformatics. We found that translational selection may act on compositional features of this set of genes....
[89], later referred as M3-Dual, and implemented in HYPHY [90]. Hypotheses concerning selection, codon bias, and rate variability were tested using likelihood ratio tests (LRTs). For a review about the application of codon models, see Anisimova and Kosiol [91]. Models combining coding and ...
The selection-mutation-drift theory of synonymous codon usage. Genetics 129, 897–907 (1991). CAS PubMed PubMed Central Google Scholar Hershberg, R. & Petrov, D. A. Selection on codon bias. Annu. Rev. Genet. 42, 287–299 (2008). Article CAS PubMed Google Scholar Gouy, M. & ...
gossypii. Relationships of GC contents (estimated by GC3s: GC content at the third site of each codon) and codon usage bias (measured by Nc: effective number of codons which is a parameter measuring overall gene codon bias) on further analysis in all studies species show us that the higher...