ArticlePLoS computational biology2014
Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 44 citations in OpenAlex.
- Independent, ongoing clade-specific expansions of ISMicrobial genomics · 2026Article
- Bioenergetic Model of Retrotransposon Activity in Cancer Cells.Life (Basel, Switzerland) · 2025Article
- Influence of Different Transposon Families on Genomic Stability of Shewanella oneidensis MR1.Microbial biotechnology · 2025Article
- Laboratory evolution of the bacterial genome structure through insertion sequence activation.Nucleic acids research · 2025Article
- Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.Nature ecology & evolution · 2024Article
- Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle.mSystems · 2024Article
- Detection of drug resistance inFrontiers in veterinary science · 2024Article
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.Genome biology · 2023Article
- Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources.Life (Basel, Switzerland) · 2021Article
- Bacterial Adaptation by a Transposition Burst of an Invading IS Element.Genome biology and evolution · 2021Article
- Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria.Clinical microbiology reviews · 2021Article
- Impact of insertion sequences on convergent evolution of Shigella species.PLoS genetics · 2020Article
- The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach.Frontiers in microbiology · 2019Review
- On the networked architecture of genotype spaces and its critical effects on molecular evolution.Open biology · 2018Review
- Article
- Disentangling the effects of selection and loss bias on gene dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers.BMC bioinformatics · 2017Article
- Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Inevitability of Genetic Parasites.Genome biology and evolution · 2016Article
- Evidence of horizontal gene transfer between obligate leaf nodule symbionts.The ISME journal · 2016Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.
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