ArticleMolecular biology and evolution2008
Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes.
Article in Molecular biology and evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- MKado: a toolkit for McDonald-Kreitman tests of natural selection.G3 (Bethesda, Md.) · 2026Article
- The Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence.Molecular biology and evolution · 2026Article
- Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2024Article
- No Evidence that Selection on Synonymous Codon Usage Affects Patterns of Protein Evolution in Bacteria.Genome biology and evolution · 2024Article
- Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genusFrontiers in plant science · 2024Article
- Correcting Bias in Allele Frequency Estimates Due to an Observation Threshold: A Markov Chain Analysis.Genome biology and evolution · 2022Article
- Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes.Scientific reports · 2021Article
- Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations.PLoS biology · 2019Article
- Allele Age Under Non-Classical Assumptions is Clarified by an Exact Computational Markov Chain Approach.Scientific reports · 2017Article
- Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in theFrontiers in microbiology · 2017Article
- Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout.BMC genomics · 2015Article
- Endosymbiont evolution: predictions from theory and surprises from genomes.Annals of the New York Academy of Sciences · 2015Review
- Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.BMC genomics · 2015Article
- ZRT1 Harbors an Excess of Nonsynonymous Polymorphism and Shows Evidence of Balancing Selection in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2013Article
- Molecular hyperdiversity and evolution in very large populations.Molecular ecology · 2013Article
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- ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes.PloS one · 2013Article
- Weak selection and protein evolution.Genetics · 2012Review
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Authors and funding
4 authors.
Funding
Abstract
Comparison of the ratio of nonsynonymous to synonymous polymorphisms within species with the ratio of nonsynonymous to synonymous substitutions between species has been widely used as a supposed indicator of positive Darwinian selection, with the ratio of these 2 ratios being designated as a neutrality index (NI). Comparison of genome-wide polymorphism within 12 species of bacteria with divergence from an outgroup species showed substantial differences in NI among taxa. A low level of nonsynonymous polymorphism at a locus was the best predictor of NI < 1, rather than a high level of nonsynonymous substitution between species. Moreover, genes with NI < 1 showed a strong tendency toward the occurrence of rare nonsynonymous polymorphisms, as expected under the action of ongoing purifying selection. Thus, our results are more consistent with the hypothesis that a high relative rate of between-species nonsynonymous substitution reflects mainly the action of purifying selection within species to eliminate slightly deleterious mutations rather than positive selection between species. This conclusion is consistent with previous results highlighting an important role of slightly deleterious variants in bacterial evolution and suggests caution in the use of the McDonald-Kreitman test and related statistics as tests of positive selection.
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