{
  "abstract": "The contraction of the plant-cell-wall-degrading enzyme (PCWDE) repertoire in ectomycorrhizal (ECM) fungi is among the most reproducible results in fungal comparative genomics, and it is routinely read as a loss of decay capacity - a statement about the genes that persist, which counts cannot make. We addressed that question in 183 fungal genomes at two levels and reached opposite conclusions. Gene loss is measurable. On a 182-tip species tree, ECM genomes carry 0.367 times the PCWDE complement of free-living decomposers (phylogenetic generalized least squares; 95% CI 0.295-0.457; P = 1.3 x 10^-15; Pagel's {lambda} = 0.92); the ECM coefficient is not absorbed into the phylogenetic covariance term. The selective regime of the copies that remain is not measurable with the standard branch-partitioned test, and this version retracts the relaxed-selection claims we made for GH6, GH7 and GH28 in version 1. Four independent controls support the retraction. (i) Calibration: applying the identical design to single-copy orthologues, which have no reason to experience a change of selective regime specific to ECM lineages, the relaxation test rejected the null for 35.8% of loci at = 0.05 (29 of 81; 43.9% of the 66 returning an interpretable statistic), against a nominal 5%. (ii) Non-convergence: in 46 of 410 fits the likelihood-ratio statistic was negative, an outcome that cannot occur if the optimisation has converged. (iii) Non-reproducibility: across 80 pairs of fits sharing alignment, tree and branch labels, none recovered its own log-likelihood to within 0.01 units, while the nested model fits computed inside the same runs agreed to within 1.99 units. (iv) Resolution: with 81 to 82 null replicates the smallest attainable empirical P value is about 0.012, against a Bonferroni threshold of 0.0125 for the four families tested here - a margin we had not computed, and one that any expansion of the family set removes. No family-level statement about selective regime is supported by these data. We emphasise the symmetry: we do not claim that these genes are maintained either. The pattern of gene loss described by previous work stands, and is strengthened by phylogenetic correction; what does not stand is the inference from that pattern to the functional state of the genes that remain.",
  "abstract_shown": true,
  "affiliations": [
    "Kyungpook National University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "K. MinSeo"
    },
    {
      "name": "J.-H. Shin"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/68mwyyp2tnqpk.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.07.20.739482",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.07.20.739482v2.full",
  "id": "68mwyyp2tnqpk",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.07.20.739482v2",
  "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",
      "1110|Mycorrhizal Fungi and Plant Interactions"
    ]
  ],
  "openalex": "W7170034951",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.07.20.739482v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-07-20",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/68mwyyp2tnqpk.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:19Z",
      "native_id": "10.64898/2026.07.20.739482",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.07.20.739482v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "Gene loss is measurable, relaxed selection on the genes that remain is not: a retraction and recalibration of branch-specific selection tests in ectomycorrhizal fungi",
  "title_text": "Gene loss is measurable, relaxed selection on the genes that remain is not: a retraction and recalibration of branch-specific selection tests in ectomycorrhizal fungi",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:19Z",
  "url": "https://research.draconitic.com/paper/68mwyyp2tnqpk",
  "venue": "bioRxiv",
  "versions": []
}