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Recombination and the Nature of Bacterial Speciation

https://doi.org/10.1126/science.1127573
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Gene Transfer in Bacteria: Speciation without Species?
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The impact of homologous recombination on the generation of diversity in bacteria
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Ecology and the origin of species
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Sexual isolation in bacteria
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The relative contributions of recombination and point mutation to the diversification of bacterial clones
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Lateral gene transfer and the nature of bacterial innovation
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Fine-scale phylogenetic architecture of a complex bacterial community
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Re-evaluating prokaryotic species
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Neutral microepidemic evolution of bacterial pathogens
inferredcites →https://doi.org/10.1073/pnas.90.10.4384openalex-snapshot
How clonal are bacteria?
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Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast
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Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria
inferredcites →https://doi.org/10.1073/pnas.94.18.9786openalex-snapshot
Barriers to recombination between closely related bacteria: MutS and RecBCD inhibit recombination between Salmonella typhimurium and Salmonella typhi
inferredcites →https://doi.org/10.1073/pnas.95.6.3140openalex-snapshot
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
inferredcites →https://doi.org/10.1073/pnas.98.1.182openalex-snapshot
Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
inferredcites →https://doi.org/10.1086/285644openalex-snapshot
The Effects of Rare but Promiscuous Genetic Exchange on Evolutionary Divergence in Prokaryotes
inferredcites →https://doi.org/10.1093/genetics/112.3.441openalex-snapshot
HOMOLOGOUS RECOMBINATION IN ESCHERICHIA COLI: DEPENDENCE ON SUBSTRATE LENGTH AND HOMOLOGY
inferredcites →https://doi.org/10.1093/genetics/140.3.917openalex-snapshot
The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust.
inferredcites →https://doi.org/10.1093/genetics/148.4.1667openalex-snapshot
Rates of Spontaneous Mutation
inferredcites →https://doi.org/10.1093/genetics/153.4.1525openalex-snapshot
DNA Sequence Similarity Requirements for Interspecific Recombination in Bacillus
inferredcites →https://doi.org/10.1098/rspb.1991.0085openalex-snapshot
The population genetics of bacteria
inferredcites →https://doi.org/10.1098/rstb.2006.1917openalex-snapshot
Sequences, sequence clusters and bacterial species
inferredcites →https://doi.org/10.1098/rstb.2006.1925openalex-snapshot
Mismatch induced speciation in Salmonella : model and data
inferredcites →https://doi.org/10.1098/rstb.2006.1926openalex-snapshot
Modelling bacterial speciation
inferredcites →https://doi.org/10.1126/science.1061217openalex-snapshot
Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae
inferredcites →https://doi.org/10.1126/science.1070120openalex-snapshot
Identity and Search in Social Networks
inferredcites →https://doi.org/10.1126/science.1093857openalex-snapshot
Environmental Genome Shotgun Sequencing of the Sargasso Sea
inferredcites →https://doi.org/10.1126/science.1106028openalex-snapshot
Genotypic Diversity Within a Natural Coastal Bacterioplankton Population
inferredcites →https://doi.org/10.1128/jb.179.21.6589-6594.1997openalex-snapshot
Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges
inferredcites →https://doi.org/10.1128/jb.182.4.1016-1023.2000openalex-snapshot
Barriers to Genetic Exchange between Bacterial Species: Streptococcus pneumoniae Transformation
inferredcites →https://doi.org/10.1146/annurev.micro.56.012302.160634openalex-snapshot
What are Bacterial Species?
inferredcites →https://doi.org/10.1186/1741-7007-3-6openalex-snapshot
Fuzzy species among recombinogenic bacteria
inferredcites →https://doi.org/10.17226/11310openalex-snapshot
Systematics and the Origin of Species

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction
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A Critique of Prokaryotic Species Concepts
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The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation
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Towards a Global Perspective of the Marine Microbiome
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Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis
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Diversity of the Cyanobacteria
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Quantitative and Theoretical Microbial Population Biology
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Defining Taxonomic Ranks
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Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees
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Gene Transfer Mechanisms, Population Genetics/Genomics and the Evolution of Haloarchaea
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Populations under microevolutionary scrutiny: what will we gain?
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Microbiology and the species problem
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On the need for integrative phylogenomics, and some steps toward its creation
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Relaxed natural selection alone does not permit transposable element expansion within 4,000 generations in Escherichia coli
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The fitness effects of a point mutation in Escherichia coli change with founding population density
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Evolving Concepts of Bacterial Species
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Molecular phylogenetic and biochemical characterization of Staphylococcus aureus isolates from non-sterile pharmaceutical cough formulations: An insight into genetic diversity
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Development of a species-specific PCR assay for identification and detection of Dickeya solani
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Genetic relatedness and novel sequence types of clinical Aeromonas dhakensis from Malaysia
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Multilocus Sequence Typing of Pathogens
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Multilocus Sequence Typing of Pathogens
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Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?
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Population genomics meets the taxonomy of cyanobacteria
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Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems
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DNA Sequence Alignment by Microhomology Sampling during Homologous Recombination
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Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae
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Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids
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Prokaryotic Sex: Eukaryote-like Qualities of Recombination in an Archaean Lineage
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Differences in genetic flux in invasive Streptococcus pneumoniae associated with bacteraemia and meningitis
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Population genetics and evolution of the pan-genome of Streptococcus pneumoniae
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Population genomics and morphological data bridge the centuries of cyanobacterial taxonomy along the continuum of Microcoleus species
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Distribution, virulence-associated genes and antimicrobial resistance of Aeromonas isolates from diarrheal patients and water, China
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The impact of host metapopulation structure on the population genetics of colonizing bacteria
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Pherotypes of pneumococcal strains co-existing in healthy children
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Highlights on molecular identification of closely related species
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Homologous recombination is facilitated in starving populations of Pseudomonas putida by phenol stress and affected by chromosomal location of the recombination target
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Characterization of an archaeal recombinase paralog that exhibits novel anti-recombinase activity
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Tracking microbial biodiversity through molecular and genomic ecology
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Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis
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Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community
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Strong functional stability of soil microbial communities under semiarid Mediterranean conditions and subjected to long-term shifts in baseline precipitation
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Evaluation of the use of multilocus sequence analysis (MLSA) to resolve taxonomic conflicts within the genus Marichromatium
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Multilocus phylogenetic analysis of the genus Aeromonas
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Horizontal gene transfer and the evolution of bacterial and archaeal population structure
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Looking for Darwin's footprints in the microbial world
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Impact of recombination on bacterial evolution
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A species concept for bacteria based on adaptive divergence
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Ordering microbial diversity into ecologically and genetically cohesive units
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Genome Surfing As Driver of Microbial Genomic Diversity
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The Biology of Reproduction
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Preface
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Introduction
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Introductory Concepts
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Reproduction and Life Cycle
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The Natural History of Reproduction
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Parental Investment in Sexual Reproduction
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Genetics and Cytogenetics of Reproduction
inferred← citeshttps://doi.org/10.1017/9781108758970.008openalex-snapshot
Determination of Sex and Mating Type
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Reproduction: a Taxonomic Survey
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Coda
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A Classification of Living Organisms
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References
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Taxonomic Index
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Subject Index
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The poverty of the protists
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Biogeography of prokaryotes
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Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives
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Single-Cell Microfluidics to Study the Effects of Genome Deletion on Bacterial Growth Behavior
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A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome
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Genomic patterns of recombination, clonal divergence and environment in marine microbial populations
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Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter
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Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution
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Widespread homologous recombination within and between Streptomyces species
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Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
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Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea
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Competitive strategies differentiate closely related species of marine actinobacteria
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Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas
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Predicting microbial traits with phylogenies
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Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages
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Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
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Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus
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Diversification of bacterial genome content through distinct mechanisms over different timescales
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Explaining microbial population genomics through phage predation
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A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains
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Microbial diversity and the genetic nature of microbial species
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The rise and fall of bacterial clones: Streptococcus pneumoniae
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Explaining microbial population genomics through phage predation
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Explaining microbial genomic diversity in light of evolutionary ecology
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Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa
inferred← citeshttps://doi.org/10.1038/s41396-018-0199-5openalex-snapshot
Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence
inferred← citeshttps://doi.org/10.1038/s41396-019-0423-yopenalex-snapshot
Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa
inferred← citeshttps://doi.org/10.1038/s41396-019-0481-1openalex-snapshot
Coherence of Microcystis species revealed through population genomics
inferred← citeshttps://doi.org/10.1038/s41396-020-00743-7openalex-snapshot
Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites
inferred← citeshttps://doi.org/10.1038/s41396-020-00867-wopenalex-snapshot
Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures
inferred← citeshttps://doi.org/10.1038/s41396-021-01039-0openalex-snapshot
Modeling host-associating microbes under selection
inferred← citeshttps://doi.org/10.1038/s41396-023-01531-9openalex-snapshot
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts
inferred← citeshttps://doi.org/10.1038/s41437-017-0034-1openalex-snapshot
Coalescent framework for prokaryotes undergoing interspecific homologous recombination
inferred← citeshttps://doi.org/10.1038/s41467-017-02209-5openalex-snapshot
Strain profiling and epidemiology of bacterial species from metagenomic sequencing
inferred← citeshttps://doi.org/10.1038/s41467-019-13429-2openalex-snapshot
Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence
inferred← citeshttps://doi.org/10.1038/s41467-024-46459-6openalex-snapshot
The global speciation continuum of the cyanobacterium Microcoleus
inferred← citeshttps://doi.org/10.1038/s41467-024-53787-0openalex-snapshot
Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination
inferred← citeshttps://doi.org/10.1038/s41467-026-71231-3openalex-snapshot
Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans
inferred← citeshttps://doi.org/10.1038/s41564-022-01300-yopenalex-snapshot
Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome
inferred← citeshttps://doi.org/10.1038/s41576-018-0032-zopenalex-snapshot
Population genomics of bacterial host adaptation
inferred← citeshttps://doi.org/10.1038/s41579-020-0368-1openalex-snapshot
Diversity within species: interpreting strains in microbiomes
inferred← citeshttps://doi.org/10.1038/s41586-026-10476-wopenalex-snapshot
Genome-wide sweeps create ecological units in the human gut microbiome
inferred← citeshttps://doi.org/10.1038/s41592-018-0293-7openalex-snapshot
Inferring bacterial recombination rates from large-scale sequencing datasets
inferred← citeshttps://doi.org/10.1038/s41598-017-02845-3openalex-snapshot
Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations
inferred← citeshttps://doi.org/10.1038/s41598-017-02955-yopenalex-snapshot
Geographic variation in pneumococcal vaccine efficacy estimated from dynamic modeling of epidemiological data post-PCV7
inferred← citeshttps://doi.org/10.1038/s41598-019-40842-wopenalex-snapshot
Proteotyping as alternate typing method to differentiate Campylobacter coli clades
inferred← citeshttps://doi.org/10.1038/s42003-024-06069-wopenalex-snapshot
Genetic barriers more than environmental associations explain Serratia marcescens population structure
inferred← citeshttps://doi.org/10.1042/bst20190713openalex-snapshot
Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis
inferred← citeshttps://doi.org/10.1051/ebr:2008014openalex-snapshot
Risks from GMOs due to Horizontal Gene Transfer
inferred← citeshttps://doi.org/10.1073/pnas.0706358104openalex-snapshot
Searching for species in haloarchaea
inferred← citeshttps://doi.org/10.1073/pnas.1001291107openalex-snapshot
Phylogenetic incongruence arising from fragmented speciation in enteric bacteria
inferred← citeshttps://doi.org/10.1073/pnas.1015622108openalex-snapshot
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
inferred← citeshttps://doi.org/10.1073/pnas.1120436109openalex-snapshot
Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
inferred← citeshttps://doi.org/10.1073/pnas.1212452109openalex-snapshot
Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa
inferred← citeshttps://doi.org/10.1073/pnas.1307090110openalex-snapshot
High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake
inferred← citeshttps://doi.org/10.1073/pnas.1315278110openalex-snapshot
Bacterial natural transformation by highly fragmented and damaged DNA
inferred← citeshttps://doi.org/10.1073/pnas.1510839112openalex-snapshot
Recombinant transfer in the basic genome of Escherichia coli
inferred← citeshttps://doi.org/10.1073/pnas.1603257113openalex-snapshot
Regulation of genetic flux between bacteria by restriction–modification systems
inferred← citeshttps://doi.org/10.1073/pnas.1900056116openalex-snapshot
Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria
inferred← citeshttps://doi.org/10.1073/pnas.2104378118openalex-snapshot
Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups
inferred← citeshttps://doi.org/10.1073/pnas.2313367121openalex-snapshot
Modeling the mosaic structure of bacterial genomes to infer their evolutionary history
inferred← citeshttps://doi.org/10.1073/pnas.2521012123openalex-snapshot
Linkage of nucleotide and functional diversity varies across gut bacteria
inferred← citeshttps://doi.org/10.1080/2159256x.2015.1137380openalex-snapshot
Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome
inferred← citeshttps://doi.org/10.1080/21645515.2015.1021521openalex-snapshot
Genetic diversity of the Pneumococcal CbpA: Implications for next-generation vaccine development
inferred← citeshttps://doi.org/10.1086/693564openalex-snapshot
Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life
inferred← citeshttps://doi.org/10.1086/720002openalex-snapshot
Moving beyond the “Diversity Paradox”: The Limitations of Competition-Based Frameworks in Understanding Species Diversity
inferred← citeshttps://doi.org/10.1089/cmb.2016.0051openalex-snapshot
Recombination Processes and Nonlinear Markov Chains
inferred← citeshttps://doi.org/10.1089/cmb.2018.0083openalex-snapshot
Large-Scale Simulations of Bacterial Populations Over Complex Networks
inferred← citeshttps://doi.org/10.1089/fpd.2009.0342openalex-snapshot
Multilocus Sequence Typing of Outbreak-Associated Listeria monocytogenes Isolates to Identify Epidemic Clones
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.001.0001openalex-snapshot
Evolution in Health and Disease
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.002.0004openalex-snapshot
Preface to the Second Edition
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.002.0006openalex-snapshot
Contributors
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0001openalex-snapshot
Introducing Evolutionary Thinking For Medicine
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0002openalex-snapshot
Global spatial patterns of infectious diseases and human evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0003openalex-snapshot
Medically relevant variation in the human genome
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0004openalex-snapshot
Health consequences of ecogenetic variation
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0005openalex-snapshot
Human genetic variation of medical significance
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0006openalex-snapshot
Intimate relations: Evolutionary conflicts of pregnancy and childhood
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0007openalex-snapshot
How hormones mediate trade-offs in human health and disease
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0008openalex-snapshot
Functional significance of MHC variation in mate choice, reproductive outcome, and disease risk
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0009openalex-snapshot
Perspectives on human health and disease from evolutionary and behavioral ecology
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0010openalex-snapshot
The ecology and evolution of antibiotic-resistant bacteria
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0011openalex-snapshot
Pathogen evolution in a vaccinated world
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0012openalex-snapshot
The evolution and expression of virulence
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0013openalex-snapshot
Evolutionary origins of diversity in human viruses
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0014openalex-snapshot
The population structure of pathogenic bacteria
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0015openalex-snapshot
Whole-genome analysis of pathogen evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0016openalex-snapshot
Emergence of new infectious diseases
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0017openalex-snapshot
Evolution of parasites
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0018openalex-snapshot
Evolutionary biology as a foundation for studying aging and aging-related disease
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199207466.003.0019openalex-snapshot
Evolution, developmental plasticity, and metabolic disease
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