ArticleMolecular biology and evolution2013
Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Not So Mosaic After All? The Core Genomes of IncP-1 Plasmids Evolve Predominantly Through Vertical Transmission.bioRxiv : the preprint server for biology · 2025Article
- Enhancing plasmid typing with MOB-typer: resolving IncP and other incompatibility group misclassifications inMicrobial genomics · 2025Article
- Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost.Molecular biology and evolution · 2025Article
- Birmingham-group IncP-1Microbial genomics · 2025Article
- Distribution Patterns ofInternational journal of molecular sciences · 2024Article
- Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost.bioRxiv : the preprint server for biology · 2024Article
- Evolution End Classification ofInternational journal of molecular sciences · 2023Article
- The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids.Nucleic acids research · 2022Article
- Lysis-Hi-C as a method to study polymicrobial communities and eDNA.Molecular ecology resources · 2022Article
- Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.Environmental microbiology · 2022Article
- Long-Range PCR Reveals the Genetic Cargo of IncP-1 Plasmids in the Complex Microbial Community of an On-Farm Biopurification System Treating Pesticide-Contaminated Wastewater.Applied and environmental microbiology · 2022Article
- Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria.Frontiers in microbiology · 2021Article
- Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids.Nature communications · 2020Article
- Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches.BMC bioinformatics · 2020Article
- Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology.Frontiers in microbiology · 2020Article
- Differentially Marked IncP-1β R751 Plasmids for Cloning via Recombineering and Conjugation.Polish journal of microbiology · 2019Article
- Assessing genetic diversity and similarity of 435 KPC-carrying plasmids.Scientific reports · 2019Article
- Mobile Genetic Elements Associated with Antimicrobial Resistance.Clinical microbiology reviews · 2018Review
- Novel Self-Transmissible and Broad-Host-Range Plasmids Exogenously Captured From Anaerobic Granules or Cow Manure.Frontiers in microbiology · 2018Article
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4 authors.
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Abstract
Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history.
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