{
  "schema_version": "2.0.0",
  "study_slug": "synapsida-mammaliaformes-timetree",
  "discovery_id": 121,
  "validation_set_id": "VAL-SET-049-SYNAPSIDA-MAMMALIAFORMES-CROWN-MAMMALIA-TIMETREE-66TAXA-1.82MB",
  "title": "Carboniferous–Cenozoic Synapsid-to-Mammaliaformes Stem Transition, Detached Three-Bone Middle Ear Evolution, and the 318–0 Ma Crown Mammalia Total-Evidence Time-Tree",
  "created_at_utc": "2026-11-05T20:45:00Z",
  "updated_at_utc": "2026-11-06T05:25:00Z",
  "tier": 3,
  "beaker_prior": 5,
  "beaker_posterior": 5,
  "z_posterior_positive": 5.49,
  "z_posterior_all": 4.82,
  "p_value": 1.9e-8,
  "bootstrap_replicates": 500,
  "empirical_sequence_telemetry": {
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    "cox1CoreCount": 66,
    "nucCount": 39,
    "totalRecords": 105,
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    "hPos1": 0.2353,
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    "hPos3": 1.3269,
    "at1All": 48.04,
    "at2All": 57.55,
    "at3All": 65.43,
    "at3Sauropsida": 63.33,
    "at3Monotremata": 66.85,
    "at3Marsupialia": 73,
    "at3Placentalia": 62.9,
    "rcfvPos3": 0.1866,
    "rcfvFullMt": 0.058,
    "rcfvPos12": 0.0195,
    "rcfvAa20": 0.0351,
    "rcfvDayhoff6": 0.0113,
    "lnLMtNt": -15168.3715,
    "treeLenMtNt": 40.8322,
    "lnLMtAa": -1831.4507,
    "treeLenMtAa": 3.5302,
    "pairwiseDistances": [
      {
        "pair": "Homo_sapiens (NC_012920.1) vs. Pan_troglodytes (NC_001643.1)",
        "label": "Hominini (~6.5 Ma)",
        "dK2P": 0.1109,
        "tiTv": 17,
        "pRaw": 0.1,
        "aaDist": 0.0056
      },
      {
        "pair": "Ornithorhynchus_anatinus (NC_000891.1) vs. Tachyglossus_aculeatus (NC_003321.1)",
        "label": "Crown Monotremata (Node N9: 54.8 Ma)",
        "dK2P": 0.2076,
        "tiTv": 3.32,
        "pRaw": 0.1759,
        "aaDist": 0.0056
      },
      {
        "pair": "Homo_sapiens (NC_012920.1) vs. Loxodonta_africana (NC_000934.1)",
        "label": "Crown Placentalia: Boreoeutheria vs. Afrotheria (Node N11: 78.2 Ma)",
        "dK2P": 0.2892,
        "tiTv": 1.65,
        "pRaw": 0.2352,
        "aaDist": 0.0667
      },
      {
        "pair": "Monodelphis_domestica (NC_006299.1) vs. Phascolarctos_cinereus (NC_008133.1)",
        "label": "Crown Marsupialia: Ameridelphia vs. Australidelphia (Node N10: 81.4 Ma)",
        "dK2P": 0.225,
        "tiTv": 1.26,
        "pRaw": 0.1926,
        "aaDist": 0.0333
      },
      {
        "pair": "Homo_sapiens (NC_012920.1) vs. Monodelphis_domestica (NC_006299.1)",
        "label": "Crown Theria: Placentalia vs. Marsupialia (Node N8: 158.4 Ma)",
        "dK2P": 0.266,
        "tiTv": 1.07,
        "pRaw": 0.2222,
        "aaDist": 0.0667
      },
      {
        "pair": "Ornithorhynchus_anatinus (NC_000891.1) vs. Homo_sapiens (NC_012920.1)",
        "label": "Crown Mammalia: Monotremata vs. Theria (Node N6: 184.6 Ma)",
        "dK2P": 0.2803,
        "tiTv": 2.08,
        "pRaw": 0.2278,
        "aaDist": 0.0556
      },
      {
        "pair": "Gallus_gallus (NC_001323.1) vs. Homo_sapiens (NC_012920.1)",
        "label": "Crown Amniota Root: Sauropsida vs. Synapsida (Node N0: 318.4 Ma)",
        "dK2P": 0.537,
        "tiTv": 0.56,
        "pRaw": 0.3833,
        "aaDist": 0.4333
      }
    ],
    "nkxMotifs": [
      {
        "label": "Gallus_NKX3-2",
        "acc": "NM_204137.1",
        "bp": 1842,
        "motif": ""
      },
      {
        "label": "Alligator_NKX3-2",
        "acc": "XM_019477992.2",
        "bp": 4051,
        "motif": ""
      },
      {
        "label": "Tachyglossus_NKX3-2",
        "acc": "XM_038745604.1",
        "bp": 2055,
        "motif": ""
      },
      {
        "label": "Monodelphis_NKX3-2",
        "acc": "XM_007496719.3",
        "bp": 2315,
        "motif": ""
      },
      {
        "label": "Phascolarctos_NKX3-2",
        "acc": "XM_020993171.2",
        "bp": 2374,
        "motif": ""
      },
      {
        "label": "Sarcophilus_NKX3-2",
        "acc": "XM_031942329.1",
        "bp": 2201,
        "motif": ""
      },
      {
        "label": "Loxodonta_NKX3-2",
        "acc": "XM_010591479.2",
        "bp": 999,
        "motif": ""
      },
      {
        "label": "Dasypus_NKX3-2",
        "acc": "XM_058299881.1",
        "bp": 2167,
        "motif": ""
      },
      {
        "label": "Homo_NKX3-2",
        "acc": "XM_054350659.1",
        "bp": 4310,
        "motif": ""
      },
      {
        "label": "Mus_NKX3-2",
        "acc": "NM_007524.3",
        "bp": 1437,
        "motif": ""
      },
      {
        "label": "Chelonia_NKX3-2",
        "acc": "XM_037896438.2",
        "bp": 2312,
        "motif": ""
      }
    ]
  },
  "dataset_scale": {
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    "extant_mitogenomes": 66,
    "cox1_coding_cores": 66,
    "nuclear_coding_mrnas": 39,
    "total_ncbi_refseq_records": 105,
    "raw_sequence_bp": 1194667,
    "aligned_supermatrix_bp": 1241520,
    "fossil_taxa": 18,
    "morphological_characters_mkv": 340
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  "step_up_trajectory": {
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      "sites_bp": 458400,
      "rate_asymmetry_ratio": 3.94,
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      "cox1_h_pos1_bits": 0.2353,
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      "cox1_h_pos3_bits": 1.3269,
      "at3_monotremata_pct": 66.85,
      "at3_marsupialia_pct": 73,
      "at3_placentalia_pct": 62.9,
      "rcfv_pos3": 0.1866,
      "rcfv_full_mtdna": 0.058,
      "iqtree2_cox1_nt_lnL": -15168.3715,
      "iqtree2_cox1_nt_tree_len": 40.8322,
      "iqtree2_cox1_aa_lnL": -1831.4507,
      "iqtree2_cox1_aa_tree_len": 3.5302,
      "strict_clock_crown_mammalia_ma": 234.2,
      "z_score": 3.65,
      "beakers": 3
    },
    "stage_2_blinded_validation": {
      "tier": 2,
      "ncbi_records": 52,
      "cohorts": 24,
      "dev_cohorts": 12,
      "reserve_cohorts": 12,
      "sites_bp": 824600,
      "authentic_cohorts_count": 20,
      "authentic_biotype_concordance_pct": 100,
      "authentic_mean_delta_z_sd": 0.03,
      "dayhoff6_rcfv": 0.0113,
      "rcfv_reduction_vs_pos3_pct": 93.9,
      "rcfv_reduction_vs_mtdna_pct": 80.5,
      "z_score": 4.5,
      "beakers": 4
    },
    "stage_3_scientific_synthesis": {
      "tier": 3,
      "ncbi_records": 105,
      "raw_bp": 1194667,
      "aligned_bp": 1241520,
      "bootstrap_replicates": 500,
      "z_posterior_positive": 5.49,
      "z_posterior_all": 4.82,
      "beakers": 5
    }
  }
}