ArticleProceedings of the National Academy of Sciences of the United States of America2009
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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83 citing papers in PubMed.
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- Understanding the evolution of immune genes in jawed vertebrates.Journal of evolutionary biology · 2023Review
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- Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes.Medical review (2021) · 2022Review
- Variation of natural selection in the Amoebozoa reveals heterogeneity across the phylogeny and adaptive evolution in diverse lineages.Frontiers in ecology and evolution · 2022Article
- Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus.Microorganisms · 2021Article
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- A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards.Journal of molecular evolution · 2021Article
- Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.Molecular biology and evolution · 2020Article
- Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids.BMC genomics · 2019Article
- Evolutionary patterns of chimeric retrogenes in Oryza species.Scientific reports · 2019Article
- A Single Adaptive Mutation in Sodium Taurocholate Cotransporting Polypeptide Induced by Hepadnaviruses Determines Virus Species Specificity.Journal of virology · 2019Article
- Contrasting patterns of molecular evolution in metazoan germ line genes.BMC evolutionary biology · 2019Article
- Multinucleotide mutations cause false inferences of lineage-specific positive selection.Nature ecology & evolution · 2018Article
- Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms.Molecular biology and evolution · 2017Article
- Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection.Molecular phylogenetics and evolution · 2017Article
- Selection on the mitochondrial ATP synthase 6 and the NADH dehydrogenase 2 genes in hares (Lepus capensis L., 1758) from a steep ecological gradient in North Africa.BMC evolutionary biology · 2017Article
- Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference.BMC evolutionary biology · 2016Article
23 more citing papers are in PubMed but not listed here.
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Abstract
Natural selection operating in protein-coding genes is often studied by examining the ratio (omega) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved is often very small, we conducted a computer simulation to examine the reliability of BSM in comparison with the small-sample method (SSM) based on Fisher's exact test. The results indicate that BSM often generates false positives compared with SSM when the number of nucleotide substitutions is approximately 80 or smaller. Because the omega value is also used for predicting positively selected sites, we examined the reliabilities of the site-prediction methods, using nucleotide sequence data for the dim-light and color vision genes in vertebrates. The results showed that the site-prediction methods have a low probability of identifying functional changes of amino acids experimentally determined and often falsely identify other sites where amino acid substitutions are unlikely to be important. This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high omega values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high omega value. To understand adaptive evolution, some form of experimental confirmation is necessary.
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