{
  "study_id": "STUDY-2026-108-PRIMATE-TIMETREE-LSD2-TIER3",
  "slug": "primate-evolution-timetree-chronogram",
  "validation_set_id": "VAL-SET-041-PRIMATE-TIMETREE-56TAXA-1.42MB",
  "tier_trajectory": "Tier 1 (Exploratory 16-Taxon / 280 kb) -> Tier 2 (Dual-Pass Blinded 36-Taxon / 840 kb Validation + Chr5 NUMT Discordance Audit) -> Tier 3 (56-Taxon / 1.42 Mb Scientific Synthesis, B = 500 Replicates)",
  "beaker_prior": 5,
  "beaker_posterior": 5,
  "composite_z_score": 5.48,
  "runie_bootstrap_replicates": 500,
  "total_taxa": 56,
  "extant_taxa": 44,
  "fossil_and_ancient_dna_tips": 12,
  "total_aligned_sites": 1420569,
  "dual_pass_blinded_validation": {
    "pass1_blinded_tokens": "BLIND-PRIMATE-01..BLIND-PRIMATE-08 (SHA-256 De-Identified Sequence & Morphological Tensors)",
    "pass1_z_blind": 5.42,
    "pass2_z_ctx": 5.44,
    "authentic_cohorts_d_ctx": 0.02,
    "anomaly_cohort_id": "BLIND-PRIMATE-08 (Unblinds to Human Chr5p13.3 Nuclear Mitochondrial Pseudogene NUMT NT_006576.16)",
    "anomaly_d_ctx": 4.96,
    "anomaly_finding": "Pass 1 autonomously flagged BLIND-PRIMATE-08 as a neutral nuclear pseudogene (omega = 0.884, 4 internal stop codons) rather than a coding mitogenome (omega = 0.031). When left unfiltered under a strict clock, the slow nuclear mutation rate of the Chr5 NUMT coupled with saturated 3rd-codon mtDNA branches creates 5 negative branch violations and inflates the Pan-Homo divergence from 6.57 Ma to 14.82 Ma."
  },
  "key_divergence_nodes_ma": [
    {
      "node_label": "Euarchonta Root (Dermoptera vs. Primatomorpha)",
      "relaxed_lsd2_age_ma": 73.40,
      "ci95_low_ma": 71.80,
      "ci95_high_ma": 75.00,
      "strict_clock_unfiltered_ma": 81.20,
      "branch_rate_subs_per_site_myr": 0.00105
    },
    {
      "node_label": "Primatomorpha (†Purgatorius unio Stem Split)",
      "relaxed_lsd2_age_ma": 67.30,
      "ci95_low_ma": 66.20,
      "ci95_high_ma": 68.40,
      "strict_clock_unfiltered_ma": 74.60,
      "branch_rate_subs_per_site_myr": 0.00108
    },
    {
      "node_label": "Crown Primates (Strepsirrhini vs. Haplorhini — K-Pg Boundary)",
      "relaxed_lsd2_age_ma": 65.80,
      "ci95_low_ma": 64.20,
      "ci95_high_ma": 67.40,
      "strict_clock_unfiltered_ma": 72.90,
      "branch_rate_subs_per_site_myr": 0.00112
    },
    {
      "node_label": "Crown Haplorhini (Tarsiiformes †Archicebus vs. Simiiformes)",
      "relaxed_lsd2_age_ma": 59.25,
      "ci95_low_ma": 57.50,
      "ci95_high_ma": 61.00,
      "strict_clock_unfiltered_ma": 65.40,
      "branch_rate_subs_per_site_myr": 0.00114
    },
    {
      "node_label": "Crown Strepsirrhini (†Darwinius Adapiformes vs. Lemuriformes/Lorisiformes)",
      "relaxed_lsd2_age_ma": 56.00,
      "ci95_low_ma": 54.00,
      "ci95_high_ma": 58.00,
      "strict_clock_unfiltered_ma": 61.80,
      "branch_rate_subs_per_site_myr": 0.00102
    },
    {
      "node_label": "Crown Simiiformes (Platyrrhini vs. Catarrhini Trans-Atlantic Split)",
      "relaxed_lsd2_age_ma": 43.20,
      "ci95_low_ma": 41.50,
      "ci95_high_ma": 44.90,
      "strict_clock_unfiltered_ma": 49.80,
      "branch_rate_subs_per_site_myr": 0.00096
    },
    {
      "node_label": "Crown Catarrhini (Cercopithecoidea vs. Hominoidea)",
      "relaxed_lsd2_age_ma": 25.20,
      "ci95_low_ma": 24.10,
      "ci95_high_ma": 26.30,
      "strict_clock_unfiltered_ma": 31.40,
      "branch_rate_subs_per_site_myr": 0.00084
    },
    {
      "node_label": "Crown Hominoidea (Hylobatidae vs. Hominidae Great Apes)",
      "relaxed_lsd2_age_ma": 19.80,
      "ci95_low_ma": 18.70,
      "ci95_high_ma": 20.90,
      "strict_clock_unfiltered_ma": 25.60,
      "branch_rate_subs_per_site_myr": 0.00068
    },
    {
      "node_label": "Crown Hominidae (Ponginae Pongo vs. Homininae — Slowdown Inflection)",
      "relaxed_lsd2_age_ma": 15.40,
      "ci95_low_ma": 14.50,
      "ci95_high_ma": 16.30,
      "strict_clock_unfiltered_ma": 21.80,
      "branch_rate_subs_per_site_myr": 0.00055
    },
    {
      "node_label": "Crown Homininae (Gorillini Gorilla vs. Hominini)",
      "relaxed_lsd2_age_ma": 9.10,
      "ci95_low_ma": 8.60,
      "ci95_high_ma": 9.60,
      "strict_clock_unfiltered_ma": 13.90,
      "branch_rate_subs_per_site_myr": 0.00051
    },
    {
      "node_label": "Crown Hominini (Pan vs. Homo Divergence)",
      "relaxed_lsd2_age_ma": 6.57,
      "ci95_low_ma": 6.36,
      "ci95_high_ma": 6.79,
      "strict_clock_unfiltered_ma": 14.82,
      "branch_rate_subs_per_site_myr": 0.00048
    },
    {
      "node_label": "Crown Pan (Pan paniscus Bonobo vs. Pan troglodytes Chimpanzee)",
      "relaxed_lsd2_age_ma": 1.86,
      "ci95_low_ma": 1.75,
      "ci95_high_ma": 1.98,
      "strict_clock_unfiltered_ma": 3.42,
      "branch_rate_subs_per_site_myr": 0.00050
    },
    {
      "node_label": "Archaic–Modern Hominina Split (Sima/Denisova vs. Neanderthal/Modern Human)",
      "relaxed_lsd2_age_ma": 0.77,
      "ci95_low_ma": 0.74,
      "ci95_high_ma": 0.80,
      "strict_clock_unfiltered_ma": 1.48,
      "branch_rate_subs_per_site_myr": 0.00047
    },
    {
      "node_label": "Neanderthal–Modern Homo sapiens Split (Vindija 33.19 vs. Modern Human)",
      "relaxed_lsd2_age_ma": 0.46,
      "ci95_low_ma": 0.43,
      "ci95_high_ma": 0.49,
      "strict_clock_unfiltered_ma": 0.89,
      "branch_rate_subs_per_site_myr": 0.00046
    }
  ],
  "runie_pipeline_comparison_table": [
    {
      "rank": "1st (Best)",
      "tool_chain": "Super-BLAST -> Gotoh MSA -> Goldman-Yang Codon Filter (omega < 0.10) -> CAT-GTR+G4 Mixture -> Mk+FBD Tip-Dating -> LSD2 Relaxed-Clock Time-Tree",
      "model_summary": "NUMT reading-frame filter + autocorrelated log-normal relaxed clock LSD2 + 12 fossil/aDNA tip bounds (0 neg. branches, MAE = 0.0000 Ma)",
      "marginal_ln_l_nats": -128410.20,
      "delta_ln_l_vs_best": 0.00,
      "rcfv": 0.0094,
      "runie_bootstrap_b500": "99.6% +/- 0.2%",
      "posterior_z": "+5.48 SD"
    },
    {
      "rank": "2nd (Nearest)",
      "tool_chain": "*MAFFT -> *IQ-TREE 2 GTR+G4 -> *LSD2 Strict Clock (NUMT-Filtered)",
      "model_summary": "Uniform global rate r across all primate clades after NUMT removal (0 neg. branches, overestimates Hominidae ages by +4.8 to +6.4 Ma)",
      "marginal_ln_l_nats": -128942.60,
      "delta_ln_l_vs_best": -532.40,
      "rcfv": 0.0182,
      "runie_bootstrap_b500": "93.8% +/- 1.9%",
      "posterior_z": "+4.16 SD"
    },
    {
      "rank": "3rd (Medium)",
      "tool_chain": "Gotoh MSA -> BIONJ-NNI ML Tree -> Root-Midpoint Clock (No Fossil Tips)",
      "model_summary": "Extant-only root calibration without Paleogene/Miocene fossil tips or Pleistocene aDNA anchors (3 neg. branches, MAE = 6.84 Ma)",
      "marginal_ln_l_nats": -131280.45,
      "delta_ln_l_vs_best": -2870.25,
      "rcfv": 0.0468,
      "runie_bootstrap_b500": "68.4% +/- 7.4%",
      "posterior_z": "+1.85 SD"
    },
    {
      "rank": "4th (Rejected)",
      "tool_chain": "Gotoh MSA -> Unpartitioned GTR+G4 Tree -> Naive Linear Root-to-Tip Scaling (Unfiltered NUMT)",
      "model_summary": "Unfiltered Chr5 NUMT (NT_006576.16) + 3rd-codon saturation + unsmoothed linear clock (5 neg. branches, Pan-Homo inflated to 14.82 Ma)",
      "marginal_ln_l_nats": -134690.80,
      "delta_ln_l_vs_best": -6280.60,
      "rcfv": 0.0984,
      "runie_bootstrap_b500": "100.0% +/- 0.0% (NUMT/Clock Lock)",
      "posterior_z": "-4.96 SD"
    }
  ]
}