ArticleMolecular biology and evolution2012
Population genomics in bacteria: a case study of Staphylococcus aureus.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Mammaliicoccus sciuri as a sentinel for antimicrobial resistance and virulence: genomic epidemiology, transmission dynamics, and control in the one health era.Veterinary research communications · 2026Review
- Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus.Genome biology · 2026Article
- Species delimitation in theFrontiers in plant science · 2025Article
- Resistance to antibacterial antifolates in multidrug-resistant Staphylococcus aureus: prevalence estimates and genetic basis.The Journal of antimicrobial chemotherapy · 2023Article
- Understanding the Genetic Diversity ofFrontiers in genetics · 2022Article
- Phylogenomics and Biogeography ofFrontiers in plant science · 2022Article
- Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates.PloS one · 2021Article
- Impacts of local population history and ecology on the evolution of a globally dispersed pathogen.BMC genomics · 2020Article
- A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.BMC bioinformatics · 2018Article
- Genome-Wide Association Analyses in the Model RhizobiummSphere · 2018Article
- Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow.BMC genomics · 2018Article
- Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core.Heredity · 2018Article
- Coalescent framework for prokaryotes undergoing interspecific homologous recombination.Heredity · 2018Article
- Article
- Genomic divergence and cohesion in a species of pelagic freshwater bacteria.BMC genomics · 2017Article
- Inferring Local Genealogies on Closely Related Genomes.Comparative genomics : RECOMB ... International Workshop, RCG ... : revised selected papers. RECOMB-CG (Conference) · 2017Article
- Article
- Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus.PloS one · 2015Article
- Efficient inference of recombination hot regions in bacterial genomes.Molecular biology and evolution · 2014Article
- Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.Nature communications · 2014Article
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5 authors.
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Abstract
We analyzed the genome-wide pattern of single nucleotide polymorphisms (SNPs) in a sample with 12 strains of Staphylococcus aureus. Population structure of S. aureus seems to be complex, and the 12 strains were divided into five groups, named A, B, C, D, and E. We conducted a detailed analysis of the topologies of gene genealogies across the genomes and observed a high rate and frequency of tree-shape switching, indicating extensive homologous recombination. Most of the detected recombination occurred in the ancestral population of A, B, and C, whereas there are a number of small regions that exhibit evidence for homologous recombination with a distinct related species. As such regions would contain a number of novel mutations, it is suggested that homologous recombination would play a crucial role to maintain genetic variation within species. In the A-B-C ancestral population, we found multiple lines of evidence that the coalescent pattern is very similar to what is expected in a panmictic population, suggesting that this population is suitable to apply the standard population genetic theories. Our analysis showed that homologous recombination caused a dramatic decay in linkage disequilibrium (LD) and there is almost no LD between SNPs with distance more than 10 kb. Coalescent simulations demonstrated that a high rate of homologous recombination-a relative rate of 0.6 to the mutation rate with an average tract length of about 10 kb-is required to produce patterns similar to those observed in the S. aureus genomes. Our results call for more research into the evolutionary role of homologous recombination in bacterial populations.
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