{
  "citation": "Specimen Registry v0.0.7 (2026). Maintained by Michael Gonzalez with AI assistance. https://specimenregistry.org. Data licensed under CC BY 4.0.",
  "license": "https://specimenregistry.org/license",
  "version": "0.0.12-neon",
  "specimen": {
    "id": "denisova-3",
    "site_id": "denisova-cave",
    "common_name": "Denisova 3",
    "community_name": null,
    "catalog_number": "(not stated in abstract — pull from paper Methods or Reich 2010 SI)",
    "catalog_number_source_quote": null,
    "material_type": "phalanx (distal manual phalanx)",
    "taxonomic_assignment": "Denisovan",
    "taxonomic_assignment_source_quote": "Using a single-stranded library preparation method, Meyer et al. ... provide a detailed analysis of a high-quality Denisovan genome.",
    "assignment_method": "aDNA-nuclear",
    "assignment_publication": "10.1038/nature09710",
    "provenance_publication": null,
    "stratigraphic_context": {
      "raw": "East Gallery, Denisova Cave (layer needs cross-check with Reich 2010 / Douka 2019)"
    },
    "stratigraphic_context_source_quote": null,
    "current_custody": "Institute of Archaeology and Ethnography, SB RAS, Novosibirsk (standard)",
    "inferred_fields": null,
    "disputed_assignment": false,
    "verification_state": "pending-verification",
    "verification_notes": "\n\nEditorial pass 2026-07-26: source-locked quote attached from ingest; ready for founder eyeball review against paper PDF.",
    "fts_tsv": "'3':2A 'archaeolog':10C 'denisova':1A 'denisovan':3B 'distal':5C 'ethnographi':12C 'institut':8C 'manual':6C 'novosibirsk':15C 'phalanx':4C,7C 'ras':14C 'sb':13C 'standard':16C",
    "created_at": "2026-07-26T18:01:51.160Z",
    "updated_at": "2026-07-26T18:17:01.609Z"
  },
  "site": {
    "id": "denisova-cave",
    "name": "Denisova Cave",
    "country": "Russia",
    "region": "Altai Krai, Soloneshensky District",
    "latitude": "51.397500",
    "longitude": "84.676110",
    "coordinates_precision": "exact",
    "site_type": "karstic cave",
    "excavating_institution": "Institute of Archaeology and Ethnography SB RAS, Novosibirsk",
    "notes": null,
    "verification_state": "pending-verification",
    "created_at": "2026-07-26T18:01:51.160Z",
    "updated_at": "2026-07-26T18:01:51.160Z"
  },
  "analyses": [
    {
      "id": "cac595dc-2936-44fd-b894-13f882150ab4",
      "publication_id": "10.1016/j.ajhg.2011.09.005",
      "method": null,
      "dating_method": null,
      "lab": null,
      "analysis_date": null,
      "result_summary": "(see raw markdown)",
      "result_summary_source_quote": "Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a \\",
      "verification_state": "draft"
    },
    {
      "id": "8e074782-eb9e-4e43-8efd-86cacd956501",
      "publication_id": "10.1038/nature09710",
      "method": "aDNA-mitochondrial",
      "dating_method": null,
      "lab": "Max Planck Institute for Evolutionary Anthropology, Leipzig (verify)",
      "analysis_date": null,
      "result_summary": "Complete mtDNA genome at 58× average coverage; 15,094 identified sequences.",
      "result_summary_source_quote": "A total of 15,094 sequences were identified which allowed the complete mtDNA genome to be assembled at an average coverage of 58-fold.",
      "verification_state": "draft"
    },
    {
      "id": "c1795f5c-e1ac-4bc3-9d18-9e7980fbc56f",
      "publication_id": "10.1038/nature09710",
      "method": "aDNA-nuclear",
      "dating_method": null,
      "lab": "Max Planck Institute for Evolutionary Anthropology, Leipzig (implied — Pääbo group; verify from paper Methods)",
      "analysis_date": "2010-01-01T00:00:00.000Z",
      "result_summary": "1.9× nuclear genome coverage; approximately 5.2 gigabases of DNA sequence; assigned to a novel archaic hominin population (\"Denisovan\"); shares common origin with Neanderthals; contributed 4–6% to present-day Melanesian genomes.",
      "result_summary_source_quote": "A total of 82,227,320 sequences mapped uniquely (mapping quality ≥30) to the human genome, yielding about 5.2 gigabases of DNA sequences (1.9-fold genomic coverage)",
      "verification_state": "draft"
    },
    {
      "id": "c8507c6a-e1a6-4b6c-a66e-de412a1ea18c",
      "publication_id": "10.1126/science.1224344",
      "method": "aDNA-nuclear",
      "dating_method": null,
      "lab": "Max Planck Institute for Evolutionary Anthropology, Leipzig",
      "analysis_date": "2012-01-01T00:00:00.000Z",
      "result_summary": "Established the reference Denisovan genome at ~30× coverage using single-strand library method. Enabled all subsequent Denisovan population-genetic inference.",
      "result_summary_source_quote": "The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size.",
      "verification_state": "draft"
    }
  ],
  "comparisons": [
    {
      "id": 1,
      "specimen_a_id": "sima-femur-xiii",
      "specimen_b_id": "denisova-3",
      "comparison_type": "sister-lineage",
      "claim": "Sima de los Huesos mtDNA shares a common ancestor with Denisovan mtDNAs to the exclusion of Neanderthal, modern human, chimpanzee and bonobo mtDNAs.",
      "claim_source_quote": "All three trees support a topology in which the Sima de los Huesos mtDNA shares a common ancestor with Denisovan mtDNAs to the exclusion of the other mtDNAs analysed.",
      "method": "aDNA-mitochondrial",
      "publication_id": "10.1038/nature12788",
      "quantitative_result": null,
      "verification_state": "pending-verification",
      "verification_notes": "Autoseed 2026-07-26 from T2.4 Meyer 2014 ingest markdown. Note: interpretation later updated by Meyer 2016 (10.1038/nature17405) — nDNA shows Sima on Neanderthal lineage; mtDNA-Denisovan relationship is ancestral state replaced in Neanderthals.",
      "created_at": "2026-07-26T19:55:47.749Z",
      "updated_at": "2026-07-26T19:55:47.749Z",
      "other_id": "sima-femur-xiii",
      "other_name": "Sima de los Huesos femur (nuclear-DNA-yielding specimen #1)",
      "other_taxon": "early Neanderthal lineage (Middle Pleistocene)"
    }
  ]
}