ArticleGenome research2012
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
87 citing papers in PubMed, 154 citations in OpenAlex.
- Canonical fact versus hypothesis testing to decipher transmission of non-tuberculous and tuberculous mycobacteria: a comparative review.Clinical microbiology reviews · 2025Review
- Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex.Nature reviews. Microbiology · 2025Review
- Dinucleotide codon substitutions as a signature of diversifying selection inFrontiers in molecular biosciences · 2025Article
- Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry.Nature microbiology · 2024Article
- Evolution and emergence of Mycobacterium tuberculosis.FEMS microbiology reviews · 2024Review
- Population genetic analysis of clinicalFrontiers in cellular and infection microbiology · 2024Article
- Phylogenetically Informative Mutations in Drug Resistance Genes of Human-InfectingTransboundary and emerging diseases · 2024Article
- The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions.The Journal of clinical investigation · 2023Review
- Host microbiome in tuberculosis: disease, treatment, and immunity perspectives.Frontiers in microbiology · 2023Review
- The rate and role of pseudogenes of theMicrobial genomics · 2022Article
- Inhibition of the Niemann-Pick C1 protein is a conserved feature of multiple strains of pathogenic mycobacteria.Nature communications · 2022Article
- Promising Antimycobacterial Activities of Flavonoids againstMolecules (Basel, Switzerland) · 2022Review
- A critical evaluation ofMicrobial genomics · 2022Article
- The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis.G3 (Bethesda, Md.) · 2022Article
- The evolving biology ofFrontiers in cellular and infection microbiology · 2022Review
- Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis.Scientific reports · 2021Article
- A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China.BMC infectious diseases · 2021Article
- ESX-1-Independent Horizontal Gene Transfer by Mycobacterium tuberculosis Complex Strains.mBio · 2021Article
- In-host population dynamics ofeLife · 2021Article
- Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.eLife · 2021Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 4 countries.
Funding
Abstract
Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.
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Registered trials
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.