ArticleeLife2021
Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
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- Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak.Genome biology and evolution · 2026Article
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- Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.Microorganisms · 2026Article
- Article
- Persistent trade-offs balance competition and colonization across centuries.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Exploring clonality ofMicrobiology spectrum · 2026Article
- Linkage of nucleotide and functional diversity varies across gut bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- Article
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.eLife · 2025Article
- Persistent trade-offs balance competition and colonization across centuries.bioRxiv : the preprint server for biology · 2025Article
- Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025Article
- Article
- High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli.PLoS genetics · 2025Article
- Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria.Molecular biology and evolution · 2025Article
- Intraspecies associations from strain-rich metagenome samples.Cell reports · 2025Article
- Unraveling the tempo and mode of horizontal gene transfer in bacteria.Trends in microbiology · 2025Review
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.bioRxiv : the preprint server for biology · 2025Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Although recombination is accepted to be common in bacteria, for many species robust phylogenies with well-resolved branches can be reconstructed from whole genome alignments of strains, and these are generally interpreted to reflect clonal relationships. Using new methods based on the statistics of single-nucleotide polymorphism (SNP) splits, we show that this interpretation is incorrect. For many species, each locus has recombined many times along its line of descent, and instead of many loci supporting a common phylogeny, the phylogeny changes many thousands of times along the genome alignment. Analysis of the patterns of allele sharing among strains shows that bacterial populations cannot be approximated as either clonal or freely recombining but are structured such that recombination rates between lineages vary over several orders of magnitude, with a unique pattern of rates for each lineage. Thus, rather than reflecting clonal ancestry, whole genome phylogenies reflect distributions of recombination rates.
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