ArticleBMC genomics2020
Impact of homologous recombination on core genome phylogenies.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of theMicrobial genomics · 2022Pooled it
- Comparative Pan- and Phylo-Genomic Analysis of Ideonella and Thermobifida Strains: Dissemination of Biodegradation Potential and Genomic Divergence.Biochemical genetics · 2026Article
- Expanding the molecular epidemiology of melioidosis in North Central Vietnam.PLoS neglected tropical diseases · 2026Article
- Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.PloS one · 2025Article
- Comparative genomic analysis of food-animal-derived and human-derivedFrontiers in microbiology · 2025Article
- Comparative genomics reveal a novel phylotaxonomic order in the genus Fusobacterium.Communications biology · 2024Article
- Comment on Shah et al. Genetic Characteristics and Phylogeographic Dynamics of Lagoviruses, 1988-2021.Viruses · 2024Article
- Article
- Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria.ISME communications · 2024Article
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.Genome biology · 2023Article
- Genome-wide phylodynamic approach reveals the epidemic dynamics of the mainMicrobial genomics · 2023Article
- Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.BMC genomics · 2023Article
- Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains.Genome medicine · 2023Article
- A long-awaited taxogenomic investigation of the familyFrontiers in microbiology · 2023Article
- Profiling of the intestinal community ofMicrobiome research reports · 2023Article
- Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes.Microbiology spectrum · 2022Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Phylogenomic analysis of the genusFrontiers in microbiology · 2022Article
- Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.Molecular biology and evolution · 2021Article
- Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.eLife · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundCore genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.
resultsIn this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts.
conclusionsOverall, these results have important implications for the application of core genome phylogenies in prokaryotes.
Indexed as
Identifiers
What OpenQuestion holds
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.