ArticleMicrobial genomics2015
Recombination produces coherent bacterial species clusters in both core and accessory genomes.
Article in Microbial genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
- Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria.iScience · 2023Article
- Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.Science advances · 2023Article
- Article
- Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen.Advances in experimental medicine and biology · 2022Article
- Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.PLoS biology · 2020Article
- Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.Nature communications · 2019Article
- PANINI: Pangenome Neighbour Identification for Bacterial Populations.Microbial genomics · 2019Article
- Fast and flexible bacterial genomic epidemiology with PopPUNK.Genome research · 2019Article
- Population genomics of bacterial host adaptation.Nature reviews. Genetics · 2018Review
- Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome.Molecular biology and evolution · 2018Article
- panX: pan-genome analysis and exploration.Nucleic acids research · 2018Article
- Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.Nature ecology & evolution · 2017Article
- Article
- Speciation trajectories in recombining bacterial species.PLoS computational biology · 2017Article
- Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.PLoS genetics · 2017Article
- Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.Molecular biology and evolution · 2017Article
- Fundamentals and Recent Developments in Approximate Bayesian Computation.Systematic biology · 2017Article
- Recombination produces coherent bacterial species clusters in both core and accessory genomes.Microbial genomics · 2015Article
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Authors and funding
5 authors.
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Abstract
backgroundPopulation samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be 'genomically coherent', even though there is no consensus on how this should be determined.
resultsWe use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates.
conclusionsThe model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.
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