{
  "abstract": "The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often declines with the sequence divergence between strains, but the mechanisms responsible for this broad empirical trend are still debated. Existing models have primarily focused on de novo mutations, overlooking the older genetic variants that are continually introduced through horizontal gene transfer and recombination. Here we introduce a phenomenological model of dN/dS in recombining populations of bacteria, which allows us to disentangle the effects of recombination among pairs of closely related strains. We find that clonally inherited regions of the genome exhibit consistently higher dN/dS ratios, and that the accumulation of recombined segments can quantitatively explain the majority of the decline in dN/dS. We use these observations to re-examine models of purifying selection and adaptive reversion in human gut bacteria, and uncover evidence for widespread weak selection at a large fraction of protein-coding sites. Our findings show that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint, and raise new questions about the effectiveness of natural selection in complex bacterial populations.\n\nThe ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about selection pressures. This study develops a model of dN/dS in recombining populations of bacteria, revealing that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Applied Physics, Stanford University, Stanford, California, United States of America.",
    "Department of Biology, Stanford University, Stanford, California, United States of America.",
    "Biohub, San Francisco, California, United States of America."
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Zhiru Liu"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Benjamin H Good",
      "orcid": "0000-0002-7757-3347"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b6r9f2rcrn8dn.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pbio.3004052",
  "fulltext_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004052",
  "id": "b6r9f2rcrn8dn",
  "issns": [
    "1545-7885",
    "1544-9173"
  ],
  "landing_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004052",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
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    ],
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      "openalex",
      "1311|Evolution and Genetic Dynamics"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA recombination"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA recombination/Homologous recombination"
    ],
    [
      "plos",
      "/Biology and life sciences/Evolutionary biology/Evolutionary processes/Natural selection"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/DNA/DNA recombination"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/DNA/DNA recombination/Homologous recombination"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Microbial genomics/Bacterial genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Microbial genetics/Bacterial genetics/Bacterial genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Mutation/Nonsense mutation"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Bacteriology/Bacterial genetics/Bacterial genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Microbial genomics/Bacterial genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Gut bacteria"
    ],
    [
      "plos",
      "/Physical sciences/Mathematics/Probability theory/Markov models/Hidden Markov models"
    ]
  ],
  "openalex": "W7221559247",
  "pdf_url": "https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3004052&type=printable",
  "pmcid": "PMC13690274",
  "pmid": "42862870",
  "published": "2026-10-12",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/b6r9f2rcrn8dn.ris",
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    {
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      "native_id": "10.1371/journal.pbio.3004052",
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  "subjects": [
    {
      "field": "biology",
      "origin": "plos:genetics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria",
  "title_text": "Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria",
  "type": "peer-reviewed",
  "updated_at": "2026-10-31T14:22:28Z",
  "url": "https://research.draconitic.com/paper/b6r9f2rcrn8dn",
  "venue": "PLOS Biology",
  "versions": []
}