ArticleMolecular biology and evolution2020
Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- The effects of hitchhiking and repulsion of deleterious alleles on linkage disequilibrium during a selective sweep.bioRxiv : the preprint server for biology · 2026Article
- Put your money where your mouth is: surveillance of antibiotic resistance within the commensalMicrobiology spectrum · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- Put your money where your mouth is: Surveillance of antibiotic resistance within the commensalbioRxiv : the preprint server for biology · 2026Article
- Article
- Genetic surveillance of first- and second-line drug-resistant isolates of Mycobacterium tuberculosis in Peru.PloS one · 2026Article
- CommensalAnnual review of microbiology · 2025Review
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Article
- Detecting co-selection through excess linkage disequilibrium in bacterial genomes.NAR genomics and bioinformatics · 2024Article
- Rolling the evolutionary dice:Microbiology spectrum · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- Empirical Evidence That Complexity Limits Horizontal Gene Transfer.Genome biology and evolution · 2023Article
- Review
- Demographic Expansions and the Emergence of Host Specialization in Genetically Distinct Ecotypes of the Tick-Transmitted Bacterium Anaplasma phagocytophilum.Applied and environmental microbiology · 2022Article
- Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations.mSystems · 2022Article
- Article
- Linkage disequilibrium between rare mutations.Genetics · 2022Article
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
- Comparative Population Genetics in the Human Gut Microbiome.Genome biology and evolution · 2022Article
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Authors and funding
7 authors.
Funding
Abstract
Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.
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