{
  "schema_version": "2.9.0",
  "study_id": "VAL-SET-046-TIER3-CAMBRIAN-EXPLOSION-TOTAL-EVIDENCE",
  "validation_set_id": "VAL-SET-046-METAZOA-CAMBRIAN-EXPLOSION-TOTAL-EVIDENCE-68TAXA-1.84MB",
  "title": "The Metazoan Cambrian Explosion Tree: Total-Evidence Phylogenomics, Hox/miRNA Macrosynteny, and Ediacaran–Cambrian Fossil Tip-Dating Across 68 Taxa (1.84 Mb)",
  "tier": 3,
  "tier_label": "Tier 3: Scientific",
  "prior_beakers": 5,
  "posterior_beakers": 5,
  "star_label": "5🧪 Significant Biological Signal",
  "empirical_posterior_z_positive": 5.58,
  "empirical_posterior_z_overall": 4.88,
  "bootstrap_replicates": 500,
  "map_topology_support_pct": "99.6% ± 0.2%",
  "total_taxa": 68,
  "extant_taxa": 54,
  "fossil_taxa": 14,
  "total_aligned_bp": 1842600,
  "nuclear_orthologs": 248,
  "mkv_morphological_characters": 312,
  "bilaterian_linkage_groups": 24,
  "conserved_mirna_families": 34,
  "hypotheses": {
    "H1_ediacaran_fuse_cambrian_burst_chronogram": {
      "status": "CONFIRMED",
      "posterior_beakers": 5,
      "z_score": 5.64,
      "crown_bilateria_ma": 568.2,
      "crown_bilateria_ci_ma": [
        549.4,
        587
      ],
      "strict_clock_ma": 802.8,
      "clock_inflation_removed_myr": 234.6,
      "crown_protostomia_ma": 558.4,
      "crown_deuterostomia_ma": 554.6,
      "crown_ecdysozoa_ma": 542.8,
      "crown_spiralia_ma": 546.2,
      "crown_lophotrochozoa_ma": 534.6,
      "crown_panarthropoda_ma": 528.4,
      "crown_chordata_ma": 531.2,
      "cambrian_stage3_burst_window_ma": [
        521,
        514
      ]
    },
    "H2_hox_mirna_blg_synteny_topology": {
      "status": "CONFIRMED",
      "posterior_beakers": 5,
      "z_score": 5.52,
      "protostomia_mirna_families": 12,
      "kksc_p_value": 3.2e-15,
      "ecdysozoa_q1": 0.582,
      "ecdysozoa_lpp": 0.998,
      "spiralia_q1": 0.564,
      "spiralia_lpp": 0.996,
      "olfactores_q1": 0.618,
      "olfactores_lpp": 0.999
    },
    "H3_biomineralization_opsin_arms_race": {
      "status": "CONFIRMED",
      "posterior_beakers": 5,
      "z_score": 5.46,
      "alpha_carbonic_anhydrase_pdb": "1CA2",
      "alpha_ca_tm_score": 0.908,
      "biomineralization_omega2": 3.62,
      "biomineralization_beb_p": 0.997,
      "opsin_pdb": "1F88 / 2Z73",
      "morphological_rate_spike_fold": 3.86,
      "molecular_clock_surge_fold": 2.44
    },
    "H4_articulata_and_basal_acoel_falsification": {
      "status": "FALSIFIED_AS_EXPECTED",
      "posterior_beakers": 1,
      "z_score": 1.08,
      "articulata_delta_lnL": -4186.4,
      "articulata_au_p": 0.000001,
      "xenambulacraria_pp": 0.98
    }
  },
  "runie_pipeline_comparison": [
    {
      "rank": "1st (Best)",
      "chain": "Super-BLAST -> Gotoh MSA -> Dayhoff-6/RCFV Filter -> Dual-Track Domain + BLG/miRNA Polarizer -> CAT-GTR+G4 + Mkv Total-Evidence Tree -> LSD2/FBD Relaxed-Clock Time-Tree",
      "marginal_lnL": -228410.6,
      "delta_lnL": 0,
      "rcfv": 0.023,
      "bootstrap_support": "99.6% ± 0.2%",
      "posterior_z": 5.58
    },
    {
      "rank": "2nd (Nearest)",
      "chain": "*MAFFT -> *IQ-TREE 2 LG+C60+F+G4 -> *MrBayes Mkv -> *MCMCTree Uncorrelated Clock",
      "marginal_lnL": -229492.4,
      "delta_lnL": -1081.8,
      "rcfv": 0.0642,
      "bootstrap_support": "88.8% ± 2.9%",
      "posterior_z": 4.18
    },
    {
      "rank": "3rd (Medium)",
      "chain": "Gotoh MSA -> Unrecoded 20-State WAG+G4 Tree -> Root-Midpoint Strict Clock",
      "marginal_lnL": -235840.2,
      "delta_lnL": -7429.6,
      "rcfv": 0.148,
      "bootstrap_support": "52.4% ± 10.2%",
      "posterior_z": 2.08
    },
    {
      "rank": "4th (Rejected)",
      "chain": "Gotoh MSA -> Unfiltered Acoel/Nematode AA + Saturated mtDNA + Unweighted Segmentation Matrix -> Linear Root-to-Tip Scaling",
      "marginal_lnL": -244918.7,
      "delta_lnL": -16508.1,
      "rcfv": 0.234,
      "bootstrap_support": "100.0% ± 0.0% (LBA / Articulata Lock)",
      "posterior_z": -5.42
    }
  ],
  "timestamp": "2026-11-05T10:40:00.000Z"
}