{
  "abstract": "Homologous recombination and horizontal gene transfer assemble mosaic chromosomes across divergent lineages. Reticulate evolution violates bifurcating trees, yet existing detectors enforce a stark trade-off: phylogenetic changepoint models optimize partitioned topologies at exponential computational cost, whereas sequence triplet heuristics evaluate rapidly but suffer from severe combinatorial event overcounting. We introduce RhizAeon, an open-source platform that deconvolves reticulate evolution through continuous trajectory mechanics across metric embeddings in linear time (O(N K L)). Projecting aligned sequences into canonical metric coordinates and routing lineage-specific rate variation into an unpolarized root sink, the engine iteratively scrubs mosaic tracts and verifies breakpoints through Brownian-bridge statistics, dyadic matched filters, and maximum-likelihood polishing. Across canonical coalescent benchmarks and a continuous parameter sweep of 1,000,000 whole genomes, RhizAeon bounds false-positive rates well below the 5.0% nominal ceiling (0.58% on 1,200 rate-variation nulls and 1.01% across 333,334 continuous sweep nulls). Leave-one-in verification and bidirectional overlap clustering collapse co-recombinant clades into single ancestral reticulations. Empirical analyses across wildlife sarbecovirus Spike chimeras, multidrug-resistant Streptococcus pneumoniae chromosomes (2.22 Mb), and 379 primate HLA Class I alleles reconstruct complex whole-genome mosaicism, cassette exchanges, and micro-conversions in seconds. The core engine compiles to WebAssembly for interactive execution within standard web browsers.",
  "abstract_shown": true,
  "affiliations": [
    "Temple University Institute for Genomics and Evolutionary Medicine"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "S. L. Kosakovsky Pond"
    },
    {
      "name": "D. Callan"
    },
    {
      "name": "S. Weaver"
    },
    {
      "name": "H. Verdonk"
    },
    {
      "name": "J. Zehr"
    },
    {
      "name": "A. Nekrutenko"
    },
    {
      "name": "T. K. Paisie"
    },
    {
      "name": "D. P. Martin"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/e0kh8xw4rsze5.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.19.760237",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.19.760237v1.full",
  "id": "e0kh8xw4rsze5",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.19.760237v1",
  "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": "W7223683645",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.19.760237v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-19",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/e0kh8xw4rsze5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:24Z",
      "native_id": "10.64898/2026.10.19.760237",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.19.760237v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds",
  "title_text": "Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:24Z",
  "url": "https://research.draconitic.com/paper/e0kh8xw4rsze5",
  "venue": "bioRxiv",
  "versions": []
}