Evidence That Mutation Is Universally Biased towards AT in Bacteria

• Published in: PLoS genetics Vol. 6; no. 9; p. e1001115
• Main Authors: Hershberg, Ruth, Petrov, Dmitri A.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.09.2010; Public Library of Science (PLoS)
• Subjects: Bacteria; Bacteria - genetics; Bacterial genetics; Base Composition - genetics; Bias; Computational Biology/Comparative Sequence Analysis; Computational Biology/Genomics; Confidence intervals; Evolution; Evolutionary Biology; Evolutionary Biology/Bioinformatics; Evolutionary Biology/Evolutionary and Comparative Genetics; Evolutionary Biology/Genomics; Evolutionary Biology/Microbial Evolution and Genomics; Gene mutations; Genetics and Genomics; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Comparative Genomics; Genetics and Genomics/Genomics; Genetics and Genomics/Microbial Evolution and Genomics; Genome, Bacterial - genetics; Genomes; Identification and classification; Intracellular Space - microbiology; Microbiology; Microbiology/Microbial Evolution and Genomics; Molecular Biology/Molecular Evolution; Mutation; Mutation - genetics; Natural selection; Nucleotides - genetics; Phylogenetics; Phylogeny; Sequence Analysis, DNA; Single nucleotide polymorphisms; United States
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1001115

Mutation is the engine that drives evolution and adaptation forward in that it generates the variation on which natural selection acts. Mutation is a random process that nevertheless occurs according to certain biases. Elucidating mutational biases and the way they vary across species and within genomes is crucial to understanding evolution and adaptation. Here we demonstrate that clonal pathogens that evolve under severely relaxed selection are uniquely suitable for studying mutational biases in bacteria. We estimate mutational patterns using sequence datasets from five such clonal pathogens belonging to four diverse bacterial clades that span most of the range of genomic nucleotide content. We demonstrate that across different types of sites and in all four clades mutation is consistently biased towards AT. This is true even in clades that have high genomic GC content. In all studied cases the mutational bias towards AT is primarily due to the high rate of C/G to T/A transitions. These results suggest that bacterial mutational biases are far less variable than previously thought. They further demonstrate that variation in nucleotide content cannot stem entirely from variation in mutational biases and that natural selection and/or a natural selection-like process such as biased gene conversion strongly affect nucleotide content.