ArticleGenome biology and evolution2013
Gene frequency distributions reject a neutral model of genome evolution.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 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
- Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution inMicrobiology spectrum · 2026Article
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- Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.Molecular biology and evolution · 2025Article
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centricMicrobial genomics · 2023Article
- Dynamics of nucleic acid mobility.Genetics · 2023Article
- Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.BMC ecology and evolution · 2022Article
- Core genes can have higher recombination rates than accessory genes within global microbial populations.eLife · 2022Article
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
- Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs.Genome biology · 2021Article
- Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century.Trends in microbiology · 2021Review
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- Deciphering functional redundancy in the human microbiome.Nature communications · 2020Article
- Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.Nucleic acids research · 2020Article
- Global Organization and Proposed Megataxonomy of the Virus World.Microbiology and molecular biology reviews : MMBR · 2020Review
- Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.The ISME journal · 2020Article
- PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.PLoS computational biology · 2020Article
- MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.Briefings in bioinformatics · 2019Article
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3 authors.
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Abstract
Evolution of prokaryotes involves extensive loss and gain of genes, which lead to substantial differences in the gene repertoires even among closely related organisms. Through a wide range of phylogenetic depths, gene frequency distributions in prokaryotic pangenomes bear a characteristic, asymmetrical U-shape, with a core of (nearly) universal genes, a "shell" of moderately common genes, and a "cloud" of rare genes. We employ mathematical modeling to investigate evolutionary processes that might underlie this universal pattern. Gene frequency distributions for almost 400 groups of 10 bacterial or archaeal species each over a broad range of evolutionary distances were fit to steady-state, infinite allele models based on the distribution of gene replacement rates and the phylogenetic tree relating the species in each group. The fits of the theoretical frequency distributions to the empirical ones yield model parameters and estimates of the goodness of fit. Using the Akaike Information Criterion, we show that the neutral model of genome evolution, with the same replacement rate for all genes, can be confidently rejected. Of the three tested models with purifying selection, the one in which the distribution of replacement rates is derived from a stochastic population model with additive per-gene fitness yields the best fits to the data. The selection strength estimated from the fits declines with evolutionary divergence while staying well outside the neutral regime. These findings indicate that, unlike some other universal distributions of genomic variables, for example, the distribution of paralogous gene family membership, the gene frequency distribution is substantially affected by selection.
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