ArticleMolecular biology and evolution2017
Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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114 citing papers in PubMed, 182 citations in OpenAlex.
- cgDist: Nucleotide-level distance calculation from cgMLST allelic profiles.NAR genomics and bioinformatics · 2026Article
- Recombination and accessory genome turnover shaped the rise and decline of vanA Enterococcus faecium ST80 in Denmark.Genome medicine · 2026Article
- Genomic evidence of ecological flexibility and cross-niche CRISPR spacerome targeting phage-plasmid hybrids in Latilactobacillus curvatus.BMC genomics · 2026Article
- Reduced MGE burden, virulence optimization, and acid stress tolerance shape the clonal succession of MRSA ST59.Science advances · 2026Article
- Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution inMicrobiology spectrum · 2026Article
- Natural transformation drives large-scale genome mosaicism in human gut bifidobacteria.The ISME journal · 2026Article
- Gene exchange betweenMicrobial genomics · 2026Article
- Not So Mosaic After All? The Core Genomes of IncP-1 Plasmids Evolve Predominantly Through Vertical Transmission.bioRxiv : the preprint server for biology · 2025Article
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- Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.Nature communications · 2025Article
- Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria.Molecular biology and evolution · 2025Article
- Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis.BMC microbiology · 2025Article
- Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria.Molecular biology and evolution · 2025Article
- Whole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies.Annals of clinical microbiology and antimicrobials · 2025Article
- Integrated population clustering and genomic epidemiology with PopPIPE.Microbial genomics · 2025Article
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- Whole-genome sequencing resolves biochemical misidentification ofJournal of clinical microbiology · 2024Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species.PLoS biology · 2024Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 4 institutions in 4 countries.
Funding
Abstract
Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/~pemartti/fastGEAR/ (last accessed February 6, 2017).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.