{
  "abstract": "Inferring ancestral states--determining, at each polymorphic site, which allele is ancestral and which derived--underpins many downstream population-genetic analyses, from selection scans and the unfolded site-frequency spectrum to demographic inference. However, no existing tool uniformly supports the full range of relevant inputs: plain variant data or ancestral recombination graphs (ARGs), with or without outgroups, while accommodating poly-allelic and recurrently-mutated sites. Here we present Ancestree, a likelihood-based engine that unifies these inputs within a single framework and returns full posteriors over the four nucleotide states at every site. It runs in three modes: a fixed-tree mode that assumes a single topology across sites and co-infers the per-branch substitution rates by maximum likelihood; an ARG mode that reads a different local tree at each site directly from a supplied ancestral recombination graph; and a local-tree mode that instead samples those local trees from the genotype data via a pairwise-coalescent HMM, needing no pre-existing ARG. On simulated data, the genealogy-based modes (ARG and local-tree) are more accurate and scale better, and remain robust under outgroup configurations that violate the fixed-tree assumption. Outgroups themselves remain difficult to replace: per-site inference accuracy on ingroup-polymorphic sites is markedly limited without them, and improves substantially with a single outgroup. The hardest sites are those fixed for the derived allele within the ingroup, which carry no within-ingroup signal and so need several sufficiently deep outgroups to recover, yet these are also highly informative downstream, carrying the high-frequency divergence signal on which selection and adaptation analyses often depend. Ancestree is available at github.com/Sendrowski/Ancestree.",
  "abstract_shown": true,
  "affiliations": [
    "Aarhus University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "J. Sendrowski"
    },
    {
      "name": "T. Bataillon"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6cfq6dcpqwazv.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.11.750934",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750934v1.full",
  "id": "6cfq6dcpqwazv",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750934v1",
  "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": "W7212443006",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750934v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-11",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6cfq6dcpqwazv.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:51Z",
      "native_id": "10.64898/2026.09.11.750934",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750934v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "Ancestree: unified likelihood inference of ancestral alleles under supplied or inferred genealogies",
  "title_text": "Ancestree: unified likelihood inference of ancestral alleles under supplied or inferred genealogies",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:51Z",
  "url": "https://research.draconitic.com/paper/6cfq6dcpqwazv",
  "venue": "bioRxiv",
  "versions": []
}