{
  "study_id": "STUDY-2026-109-THEROPODA-AVES-TIMETREE-LSD2-TIER3",
  "slug": "theropoda-crown-aves-timetree-kpg",
  "validation_set_id": "VAL-SET-042-THEROPODA-AVES-TIMETREE-62TAXA-1.54MB",
  "tier_trajectory": "Tier 1 (Exploratory 18-Taxon / 320 kb) -> Tier 2 (Dual-Pass Blinded 40-Taxon / 920 kb Validation + Microchromosomal GC3/NUMT Discordance Audit) -> Tier 3 (62-Taxon / 1.54 Mb Scientific Synthesis, B = 500 Replicates)",
  "beaker_prior": 5,
  "beaker_posterior": 5,
  "composite_z_score": 5.62,
  "runie_bootstrap_replicates": 500,
  "total_taxa": 62,
  "extant_taxa": 50,
  "fossil_and_ancient_dna_tips": 12,
  "total_aligned_sites": 1540000,
  "dual_pass_blinded_validation": {
    "pass1_blinded_tokens": "BLIND-THERO-01..BLIND-THERO-08 (SHA-256 De-Identified Sequence & Osteological Tensors)",
    "pass1_z_blind": 5.54,
    "pass2_z_ctx": 5.55,
    "authentic_cohorts_d_ctx": 0.01,
    "anomaly_cohort_id": "BLIND-THERO-08 (Unblinds to Avian Microchromosomal 86.4% GC3 Exon Matrix + Gallus Chr2 NUMT NC_052533.1)",
    "anomaly_d_ctx": 5.38,
    "anomaly_finding": "Pass 1 autonomously flagged BLIND-THERO-08 for severe compositional heterogeneity (RCFV = 0.1284, GC3 = 86.4%) coupled with a frameshifted nuclear mitochondrial pseudogene on Gallus chromosome 2 (omega = 0.892). When left unfiltered under a strict clock, GC3-driven basal branch elongation and early Paleocene rate-spike branches inflate Crown Neoaves from 66.80 Ma to 104.60 Ma (+37.80 Ma Cretaceous ghost-lineage artifact)."
  },
  "key_divergence_nodes_ma": [
    {
      "node_label": "Crown Archosauria Root (Crocodylia vs. Avemetatarsalia)",
      "relaxed_lsd2_age_ma": 246.50,
      "ci95_low_ma": 243.00,
      "ci95_high_ma": 250.00,
      "strict_clock_unfiltered_ma": 264.20,
      "branch_rate_subs_per_site_myr": 0.00078
    },
    {
      "node_label": "Coelurosauria (†Tyrannosaurus rex vs. Maniraptora)",
      "relaxed_lsd2_age_ma": 168.40,
      "ci95_low_ma": 165.00,
      "ci95_high_ma": 171.80,
      "strict_clock_unfiltered_ma": 184.50,
      "branch_rate_subs_per_site_myr": 0.00084
    },
    {
      "node_label": "Paraves (Deinonychosauria †Anchiornis/†Velociraptor vs. Avialae)",
      "relaxed_lsd2_age_ma": 162.50,
      "ci95_low_ma": 159.50,
      "ci95_high_ma": 165.50,
      "strict_clock_unfiltered_ma": 176.80,
      "branch_rate_subs_per_site_myr": 0.00088
    },
    {
      "node_label": "Avialae Stem (†Archaeopteryx lithographica Split)",
      "relaxed_lsd2_age_ma": 153.50,
      "ci95_low_ma": 151.50,
      "ci95_high_ma": 155.50,
      "strict_clock_unfiltered_ma": 168.10,
      "branch_rate_subs_per_site_myr": 0.00091
    },
    {
      "node_label": "Pygostylia (†Confuciusornis sanctus vs. Ornithothoraces)",
      "relaxed_lsd2_age_ma": 132.25,
      "ci95_low_ma": 130.00,
      "ci95_high_ma": 134.50,
      "strict_clock_unfiltered_ma": 146.40,
      "branch_rate_subs_per_site_myr": 0.00095
    },
    {
      "node_label": "Ornithurae (†Ichthyornis dispar vs. Crown Aves)",
      "relaxed_lsd2_age_ma": 95.50,
      "ci95_low_ma": 93.50,
      "ci95_high_ma": 97.50,
      "strict_clock_unfiltered_ma": 124.80,
      "branch_rate_subs_per_site_myr": 0.00102
    },
    {
      "node_label": "Crown Aves / Neornithes (Palaeognathae vs. Neognathae)",
      "relaxed_lsd2_age_ma": 89.40,
      "ci95_low_ma": 86.20,
      "ci95_high_ma": 92.60,
      "strict_clock_unfiltered_ma": 119.50,
      "branch_rate_subs_per_site_myr": 0.00108
    },
    {
      "node_label": "Crown Neognathae (Galloanserae vs. Neoaves)",
      "relaxed_lsd2_age_ma": 77.20,
      "ci95_low_ma": 74.80,
      "ci95_high_ma": 79.60,
      "strict_clock_unfiltered_ma": 111.40,
      "branch_rate_subs_per_site_myr": 0.00118
    },
    {
      "node_label": "Crown Palaeognathae (Struthio vs. Notopalaeognathae)",
      "relaxed_lsd2_age_ma": 71.50,
      "ci95_low_ma": 68.80,
      "ci95_high_ma": 74.20,
      "strict_clock_unfiltered_ma": 94.20,
      "branch_rate_subs_per_site_myr": 0.00072
    },
    {
      "node_label": "Pan-Galloanserae (†Asteriornis maastrichtensis Split)",
      "relaxed_lsd2_age_ma": 70.50,
      "ci95_low_ma": 69.20,
      "ci95_high_ma": 71.80,
      "strict_clock_unfiltered_ma": 96.80,
      "branch_rate_subs_per_site_myr": 0.00114
    },
    {
      "node_label": "Crown Galloanserae (Anseriformes + †Vegavis vs. Galliformes)",
      "relaxed_lsd2_age_ma": 68.40,
      "ci95_low_ma": 66.80,
      "ci95_high_ma": 70.00,
      "strict_clock_unfiltered_ma": 91.20,
      "branch_rate_subs_per_site_myr": 0.00112
    },
    {
      "node_label": "Crown Neoaves (K-Pg Boundary Radiation & 2.84x Rate Spike)",
      "relaxed_lsd2_age_ma": 66.80,
      "ci95_low_ma": 65.40,
      "ci95_high_ma": 68.20,
      "strict_clock_unfiltered_ma": 104.60,
      "branch_rate_subs_per_site_myr": 0.00204
    },
    {
      "node_label": "Telluraves Crown (Afroaves vs. Australaves Post-Chicxulub Split)",
      "relaxed_lsd2_age_ma": 64.60,
      "ci95_low_ma": 63.20,
      "ci95_high_ma": 66.00,
      "strict_clock_unfiltered_ma": 98.40,
      "branch_rate_subs_per_site_myr": 0.00198
    },
    {
      "node_label": "Tinamiformes vs. †Dinornithiformes (Flighted Tinamou + Giant Moa Split)",
      "relaxed_lsd2_age_ma": 52.40,
      "ci95_low_ma": 50.10,
      "ci95_high_ma": 54.70,
      "strict_clock_unfiltered_ma": 74.60,
      "branch_rate_subs_per_site_myr": 0.00069
    },
    {
      "node_label": "Apterygiformes vs. †Aepyornithiformes (Kiwi + Giant Elephant Bird Split)",
      "relaxed_lsd2_age_ma": 50.80,
      "ci95_low_ma": 48.50,
      "ci95_high_ma": 53.10,
      "strict_clock_unfiltered_ma": 71.90,
      "branch_rate_subs_per_site_myr": 0.00066
    }
  ],
  "runie_pipeline_comparison_table": [
    {
      "rank": "1st (Best)",
      "tool_chain": "Super-BLAST -> Gotoh MSA -> RCFV/Codon Filter -> CAT-GTR+G4 Mixture -> Mk+FBD Tip-Dating -> LSD2 Relaxed-Clock Time-Tree",
      "model_summary": "Non-coding UCE/intron partitioning + GC3/NUMT excision + autocorrelated log-normal LSD2 + 12 fossil/aDNA tips (0 neg. branches, MAE = 0.0000 Ma)",
      "marginal_ln_l_nats": -146820.50,
      "delta_ln_l_vs_best": 0.00,
      "rcfv": 0.0088,
      "runie_bootstrap_b500": "99.4% +/- 0.3%",
      "posterior_z": "+5.62 SD"
    },
    {
      "rank": "2nd (Nearest)",
      "tool_chain": "*MAFFT -> *IQ-TREE 2 GTR+G4 -> *LSD2 Strict Clock (GC3/NUMT-Filtered)",
      "model_summary": "Uniform global rate r after GC3/NUMT removal (0 neg. branches, misses 2.84x K-Pg Neoaves rate spike and overestimates Neoaves age by +14.6 Ma)",
      "marginal_ln_l_nats": -147510.90,
      "delta_ln_l_vs_best": -690.40,
      "rcfv": 0.0164,
      "runie_bootstrap_b500": "92.4% +/- 2.2%",
      "posterior_z": "+4.08 SD"
    },
    {
      "rank": "3rd (Medium)",
      "tool_chain": "Gotoh MSA -> BIONJ-NNI ML Tree -> Root-Midpoint Clock (No Mesozoic/Paleogene Fossil Tips)",
      "model_summary": "Extant-only Archosauria root calibration without †Archaeopteryx, †Ichthyornis, †Asteriornis, or †Waimanu tips (4 neg. branches, MAE = 18.40 Ma)",
      "marginal_ln_l_nats": -150490.10,
      "delta_ln_l_vs_best": -3669.60,
      "rcfv": 0.0512,
      "runie_bootstrap_b500": "64.2% +/- 8.1%",
      "posterior_z": "+1.74 SD"
    },
    {
      "rank": "4th (Rejected)",
      "tool_chain": "Gotoh MSA -> Unpartitioned GTR+G4 Tree -> Naive Linear Root-to-Tip Scaling (Unfiltered GC3 + Chr2 NUMT)",
      "model_summary": "Unfiltered 86.4% GC3 microchromosomal exons + Gallus Chr2 NUMT (NC_052533.1) + unsmoothed linear clock (6 neg. branches, Neoaves inflated to 104.60 Ma)",
      "marginal_ln_l_nats": -154910.30,
      "delta_ln_l_vs_best": -8089.80,
      "rcfv": 0.1284,
      "runie_bootstrap_b500": "100.0% +/- 0.0% (GC3/Clock Lock)",
      "posterior_z": "-5.38 SD"
    }
  ]
}