ArticleGenetics1999
The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents.
Article in Genetics, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Genomic insights into positive selection during barley domestication.BMC plant biology · 2022Article
- Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.Genome biology and evolution · 2021Article
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.Genome research · 2011Article
- Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.Genome biology and evolution · 2009Article
- Widespread positive selection in synonymous sites of mammalian genes.Molecular biology and evolution · 2007Article
- Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation.Genome biology · 2007Article
- Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals.Journal of molecular evolution · 2006Article
- Further understanding human disease genes by comparing with housekeeping genes and other genes.BMC genomics · 2006Article
- Enhanced synonymous site divergence in positively selected vertebrate antimicrobial peptide genes.Journal of molecular evolution · 2005Article
- Selection on codon usage for error minimization at the protein level.Journal of molecular evolution · 2004Article
- Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile.Genome research · 2004Article
- Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome.PLoS biology · 2004Review
- The signature of selection mediated by expression on human genes.Genome research · 2003Article
- Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication.Plant physiology · 2003Article
- Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content.Nucleic acids research · 2002Article
- Estimation of genetic distances from human and mouse introns.Genome biology · 2002Article
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2 authors.
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Abstract
Nonsynonymous substitutions in DNA cause amino acid substitutions while synonymous substitutions in DNA leave amino acids unchanged. The cause of the correlation between the substitution rates at nonsynonymous (K(A)) and synonymous (K(S)) sites in mammals is a contentious issue, and one that impacts on many aspects of molecular evolution. Here we use a large set of orthologous mammalian genes to investigate the causes of the K(A)-K(S) correlation in rodents. The strength of the K(A)-K(S) correlation exceeds the neutral theory expectation when substitution rates are estimated using algorithmic methods, but not when substitution rates are estimated by maximum likelihood. Irrespective of this methodological uncertainty the strength of the K(A)-K(S) correlation appears mostly due to tandem substitutions, an excess of which is generated by substitutional nonindependence. Doublet mutations cannot explain the excess of tandem synonymous-nonsynonymous substitutions, and substitution patterns indicate that selection on silent sites is the likely cause. We find no evidence for selection on codon usage. The nature of the relationship between synonymous divergence and base composition is unclear because we find a significant correlation if we use maximum-likelihood methods but not if we use algorithmic methods. Finally, we find that K(S) is reduced at the start of genes, which suggests that selection for RNA structure may affect silent sites in mammalian protein-coding genes.
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