{
  "abstract": "Selective pressures can vary across both sites and evolutionary lineages; however, most codon models accommodate heterogeneity along only one of these dimensions and require the number of selective regimes to be specified in advance. Here, we introduce OmegaSwitch, a Bayesian phylogenetic software framework for inferring changes in the nonsynonymous-to-synonymous substitution-rate ratio (dN/dS) across sites and through evolutionary time. We implement a Markov-modulated codon model in which lineages transition among discrete dN/dS regimes and use reversible-jump Markov chain Monte Carlo to infer the number of regimes simultaneously. We further develop a Dirichlet-process mixture extension that allows the parameters governing these time-heterogeneous processes to vary among sites. Ancestral sampling produces joint posterior distributions of dN/dS across sites and nodes of the phylogeny, enabling lineage- and site-specific summaries with quantified uncertainty. Simulation analyses showed that both the posterior intervals for dN/dS and the number of evolutionary regimes were well calibrated under both models. We demonstrate OmegaSwitch using vertebrate alpha- and beta-globins. OmegaSwitch therefore provides a flexible Bayesian framework for investigating how selective pressures vary across protein-coding sequences and phylogenetic history.",
  "abstract_shown": true,
  "affiliations": [
    "University of Maryland at College Park"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "W. C. DeMontigny"
    },
    {
      "name": "C. F. Delwiche"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ew451cae2m1cd.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.14.744968",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.14.744968v2.full",
  "id": "ew451cae2m1cd",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.14.744968v2",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "evolutionary biology"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7203753671",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.14.744968v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/ew451cae2m1cd.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:34Z",
      "native_id": "10.64898/2026.08.14.744968",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.14.744968v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "OmegaSwitch: Bayesian Markov-Modulated Codon Models for Estimating dN/dS",
  "title_text": "OmegaSwitch: Bayesian Markov-Modulated Codon Models for Estimating dN/dS",
  "type": "preprint",
  "updated_at": "2026-10-30T12:22:34Z",
  "url": "https://research.draconitic.com/paper/ew451cae2m1cd",
  "venue": "bioRxiv",
  "versions": []
}