Evidence That Mutation Is Universally Biased towards AT in Bacteria
| Autor: | Hershberg, Ruth, Petrov, Dmitri A. |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2010 |
| Předmět: |
Evolutionary Biology
Base Composition Microbiology/Microbial Evolution and Genomics Evolutionary Biology/Evolutionary and Comparative Genetics Bacteria Nucleotides Evolutionary Biology/Bioinformatics Intracellular Space Genetics and Genomics Molecular Biology/Molecular Evolution Computational Biology/Comparative Sequence Analysis Sequence Analysis DNA Genetics and Genomics/Bioinformatics Genetics and Genomics/Microbial Evolution and Genomics Microbiology Evolutionary Biology/Microbial Evolution and Genomics Bias Mutation Genetics and Genomics/Comparative Genomics Genetics and Genomics/Genomics Evolutionary Biology/Genomics Genome Bacterial Phylogeny Research Article Computational Biology/Genomics |
| Zdroj: | PLoS Genetics |
| ISSN: | 1553-7404 1553-7390 |
| Popis: | 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. Author Summary Natural selection sorts through the variability generated by mutation and biases evolution toward fitter outcomes. However, because mutation is itself not entirely random it can also bias the direction of evolution independently of selection. For instance, it is often assumed that the extreme variation observed in nucleotide content among bacteria (from ∼20% to ∼80% GC) is predominantly driven by extreme differences in mutational biases towards or away from GC. Here, we show that bacterial lineages that recently developed clonal, pathogenic lifestyles evolve under weak selection and that polymorphisms in these bacteria can be used as a fair proxy for mutational spectra. We analyze large sequence datasets from five clonal pathogens in four diverse bacterial clades spanning most of the range of genomic nucleotide content. We find that, surprisingly, mutation is AT-biased in every case to a very similar degree and in each case it is dominated by transitions from C/G to T/A. This demonstrates that mutational biases are far les variable than previously assumed and that variation in bacterial nucleotide content is not due entirely to mutational biases. Rather natural selection or a selection like process such as biased gene conversion strongly affect nucleotide content in bacteria. |
| Databáze: | OpenAIRE |
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