{
  "abstract": "Estimating viral substitution rates is central to evolutionary epidemiology, and recent interest in within-host evolution has sharpened the question of what such rates measure. I distinguish two classes of evolutionary rate estimand that are rarely separated in phylogenetic analysis: the virion-level substitution rate (VLSR), a molecular quantity counting mutational events along lineages, and consensus-level substitution rates (CLSRs), population-summary quantities counting allele frequency threshold crossings from below. CLSRs are indexed by the consensus-generation rule. The VLSR and CLSRs are both biologically meaningful, but not interchangeable. Because the consensus-generation rule defines a given CLSR, it should be reported routinely. This reflection should help analysts make more informed methodological choices when working with sets of virus sequences.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2605.31305",
  "author_total": 1,
  "authors": [
    {
      "name": "David J Pascall"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5cpzdx4efc6bs.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2605.31305",
  "fulltext_url": null,
  "id": "5cpzdx4efc6bs",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2605.31305",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "q-bio.PE"
    ],
    [
      "arxiv",
      "stat.ME"
    ],
    [
      "openalex",
      "1311|Evolution and Genetic Dynamics"
    ]
  ],
  "openalex": "W7162998796",
  "pdf_url": "https://arxiv.org/pdf/2605.31305",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-19",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/5cpzdx4efc6bs.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:31:01Z",
      "native_id": "2605.31305",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2605.31305"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.PE",
      "subfield": "evolutionary-biology"
    },
    {
      "field": "mathematics",
      "origin": "arxiv:stat.ME",
      "subfield": "statistics"
    }
  ],
  "title": "Consensus-level substitution rates are distinct from the virion-level rate",
  "title_text": "Consensus-level substitution rates are distinct from the virion-level rate",
  "type": "preprint",
  "updated_at": "2026-10-30T12:33:54Z",
  "url": "https://research.draconitic.com/paper/5cpzdx4efc6bs",
  "venue": "arXiv",
  "versions": []
}