ArticleProceedings of the National Academy of Sciences of the United States of America2017
Disentangling the effects of selection and loss bias on gene dynamics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- A generative model for bipartite gene-sharing networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Eukaryotic domestication of a bacterial immune protein following horizontal transfer.bioRxiv : the preprint server for biology · 2026Article
- The paradox of immune systems conservation between prokaryotes and eukaryotes.Nature reviews. Microbiology · 2026Article
- Bacteriophages mobilize bacterial defense systems via lateral transduction.Science advances · 2026Article
- Functional Coupling and Evolutionary Relationships Between Toxin-Antitoxin Systems and CRISPR-Cas Systems.Toxins · 2025Review
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- Laboratory evolution of the bacterial genome structure through insertion sequence activation.Nucleic acids research · 2025Article
- Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.Genome research · 2025Article
- The contribution of antimicrobials and antimicrobial resistance to climate change and a possible way to reverse it whilst still offering high quality healthcare-a conceptual analysis.Frontiers in public health · 2025Review
- The fitness connection of antibiotic resistance.Frontiers in microbiology · 2025Article
- The population genetics of prokaryotic pangenomes.Nature ecology & evolution · 2024Article
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.Genome biology · 2023Article
- Associate toxin-antitoxin with CRISPR-Cas to kill multidrug-resistant pathogens.Nature communications · 2023Article
- Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution.The ISME journal · 2022Article
- Thermodynamics of evolution and the origin of life.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Toward a theory of evolution as multilevel learning.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes.Frontiers in molecular biosciences · 2022Review
- Towards the biogeography of prokaryotic genes.Nature · 2022Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes.
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