{
  "abstract": "Phylogenetic networks extend the traditional tree model to capture reticulate evolutionary processes such as gene flow and hybridization. Among available inference tools, SNaQ is a widely used quartet-based method that offers a computationally efficient, statistically grounded approach to network estimation, but is limited to level-1 networks, in which reticulation cycles do not overlap. This assumption is a statistical requirement for identifiability rather than a reflection of biological reality, as many evolutionary scenarios, particularly those involving extensive or closely spaced gene flow, are expected to produce level-2 or higher networks. How SNaQ performs when this assumption is violated remains poorly understood. Here, we systematically evaluate SNaQs performance on simulated non-level-1 networks. Because existing network comparison metrics such as hardwired cluster dissimilarity are not true distances beyond level-1, we introduce complementary measures: hybrid cluster compatibility, blob compatibility, and tree-of-blobs comparison, to more directly assess structural recovery. We find that while SNaQ does not recover the exact topology of non-level-1 networks, it reliably infers the circular order of taxa and frequently recovers a tree of blobs compatible with the true network, suggesting the level-1 constraint acts as a form of regularization against overfitting. Recovery of reticulation signal is strongly tied to inheritance proportion and the user-specified maximum number of reticulations, with SNaQ behaving as a conservative estimator that favors strong, well-supported events over finer-scale or overlapping signals. These results clarify the strengths and limits of quartet-based network inference under model misspecification and offer practical guidance for applying SNaQ to complex reticulate histories.",
  "abstract_shown": true,
  "affiliations": [
    "University of Wisconsin - Madison"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "J. A. JUSTISON"
    },
    {
      "name": "G. Ballen"
    },
    {
      "name": "R. Ceja"
    },
    {
      "affs": [
        0
      ],
      "name": "C. Solis-Lemus"
    },
    {
      "name": "C. Acosta-Cortes"
    },
    {
      "name": "R. Ceja"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9vs21q0xrp70w.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.01.748505",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748505v1.full",
  "id": "9vs21q0xrp70w",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748505v1",
  "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": "W7208729836",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748505v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9vs21q0xrp70w.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:30Z",
      "native_id": "10.64898/2026.09.01.748505",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748505v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "Assessing the robustness of SNaQ to violations induced by high-level phylogenetic networks",
  "title_text": "Assessing the robustness of SNaQ to violations induced by high-level phylogenetic networks",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:30Z",
  "url": "https://research.draconitic.com/paper/9vs21q0xrp70w",
  "venue": "bioRxiv",
  "versions": []
}