ArticleGenetics2000
Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions.
Article in Genetics, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- dJournal of molecular evolution · 2022Article
- Why Do Some Vertebrates Have Microchromosomes?Cells · 2021Review
- Are Synonymous Sites in Primates and Rodents Functionally Constrained?Journal of molecular evolution · 2016Article
- Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?Evolution, medicine, and public health · 2015Article
- Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae.Genetics and molecular biology · 2012Article
- Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.Genome biology and evolution · 2009Article
- Clinical, agricultural, and evolutionary biology of myostatin: a comparative review.Endocrine reviews · 2008Review
- Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage.Genome research · 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
- Comparative genomics and diversifying selection of the clustered vertebrate protocadherin genes.Genetics · 2005Article
- Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.Genome research · 2005Article
- Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences.Journal of molecular evolution · 2004Article
- 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
- Article
- Diversifying selection in a parasitoid's symbiotic virus among genes involved in inhibiting host immunity.Immunogenetics · 2003Article
- Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes.Genome research · 2003Article
- Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content.Nucleic acids research · 2002Article
- The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes.Genetics · 2001Article
- Substitution rates in Drosophila nuclear genes: implications for translational selection.Genetics · 2001Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Rates and patterns of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous sites. Previous studies of mammalian nuclear genes largely employed approximate methods to estimate rates of nonsynonymous and synonymous substitutions. Because these methods did not account for major features of DNA sequence evolution such as transition/transversion rate bias and unequal codon usage, they might not have produced reliable results. To evaluate the impact of the estimation method, we analyzed a sample of 82 nuclear genes from the mammalian orders Artiodactyla, Primates, and Rodentia using both approximate and maximum-likelihood methods. Maximum-likelihood analysis indicated that synonymous substitution rates were positively correlated with GC content at the third codon positions, but independent of nonsynonymous substitution rates. Approximate methods, however, indicated that synonymous substitution rates were independent of GC content at the third codon positions, but were positively correlated with nonsynonymous rates. Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates.
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