{
  "study_id": "DISCOVERY-123-LEPIDOPTERA-DITRYSIA-TIMETREE-COX1-GAP",
  "validation_set_id": "VAL-SET-051-LEPIDOPTERA-DITRYSIA-TIMETREE-COX1-72TAXA-1.92MB",
  "title": "Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries",
  "slug": "lepidoptera-ditrysia-timetree-cox1-gap",
  "preprint_slug": "lepidoptera-ditrysia-timetree-cox1-gap-preprint",
  "preprint_id": "PREPRINT-12",
  "tier": 3,
  "stars": 5,
  "beaker_prior": 5,
  "beaker_posterior": 5,
  "posterior_z": 5.56,
  "runie_replicates": 500,
  "taxa_count": 72,
  "extant_taxa": 56,
  "fossil_taxa": 16,
  "sequence_records_count": 92,
  "aligned_sites_bp": 1078183,
  "mitogenomes_72_bp": 1053261,
  "cox1_vouchers_5_bp": 4592,
  "nuclear_orthologs_15_bp": 20330,
  "profile_aligned_cox1_56x450_bp": 25200,
  "codon_entropy_bits": {
    "H_pos1": 0.4036,
    "H_pos2": 0.1575,
    "H_pos3": 1.1371,
    "core_AT3_pct": 82.9
  },
  "rcfv_pos3_only": 0.2845,
  "rcfv_unpartitioned_mitogenome": 0.1546,
  "rcfv_cox1_nt12": 0.0739,
  "rcfv_best": 0.0182,
  "rcfv_rejected": 0.1546,
  "cox1_optimal_window_ma": [
    0,
    35
  ],
  "cox1_species_gap_ratio": 17.8,
  "cox1_species_resolution_pct": 97.8,
  "blinded_audit": {
    "total_cohorts": 24,
    "authentic_cohorts": 21,
    "mean_d_ctx_authentic_sd": 0.03,
    "caught_errors": [
      {
        "id": "ERR-LEPID-01",
        "token": "BLIND-LEPID-06",
        "d_ctx_sd": 7.82,
        "description": "Danaus plexippus Chr14 nuclear NUMT pseudogene mislabeled as cryptic Andean species COX1 (stop codon aa184, omega = 0.912, H_pos2 = 0.614 bits)"
      },
      {
        "id": "ERR-LEPID-02",
        "token": "BLIND-LEPID-14",
        "d_ctx_sd": 7.46,
        "description": "Wolbachia pipientis wBol1 cytoplasmic sweep masking nuclear divergence in Hypolimnas bolina / Lycaeides (d_K2P = 0.0015 vs nuclear F_ST = 0.684)"
      },
      {
        "id": "ERR-LEPID-03",
        "token": "BLIND-LEPID-21",
        "d_ctx_sd": 7.4,
        "description": "Cotesia congregata braconid parasitoid wasp COX1 contaminant in parasitized Manduca sexta larval tissue (D_KL = 7.12x)"
      }
    ]
  },
  "calibrated_nodes_ma": {
    "N0_Amphiesmenoptera": {
      "mean": 314.8,
      "hpd95": [
        306.4,
        323.2
      ],
      "support_pct": 100
    },
    "N1_Crown_Lepidoptera": {
      "mean": 298.6,
      "hpd95": [
        290.2,
        307
      ],
      "support_pct": 99.8
    },
    "N2_Crown_Glossata": {
      "mean": 241.8,
      "hpd95": [
        234.4,
        249.2
      ],
      "support_pct": 99.8
    },
    "N3_Heteroneura": {
      "mean": 212.4,
      "hpd95": [
        205.2,
        219.6
      ],
      "support_pct": 99.6
    },
    "N4_Crown_Ditrysia": {
      "mean": 176.4,
      "hpd95": [
        169.4,
        183.4
      ],
      "support_pct": 99.8
    },
    "N5_Obtectomera": {
      "mean": 144.2,
      "hpd95": [
        137.6,
        150.8
      ],
      "support_pct": 99.6
    },
    "N6_Crown_Papilionoidea": {
      "mean": 107.8,
      "hpd95": [
        101.4,
        114.2
      ],
      "support_pct": 99.8
    },
    "N7_Hedylidae_Hesperiidae": {
      "mean": 92.4,
      "hpd95": [
        86.2,
        98.6
      ],
      "support_pct": 99.4
    },
    "N8_Pieridae_Lycaenidae_Nymphalidae": {
      "mean": 88.6,
      "hpd95": [
        82.6,
        94.6
      ],
      "support_pct": 99.8
    },
    "N9_Crown_Nymphalidae": {
      "mean": 74.2,
      "hpd95": [
        68.4,
        80
      ],
      "support_pct": 99.8
    },
    "N10_Macroheterocera": {
      "mean": 126.4,
      "hpd95": [
        119.8,
        133
      ],
      "support_pct": 99.6
    },
    "N11_Crown_Bombycoidea": {
      "mean": 94.8,
      "hpd95": [
        88.6,
        101
      ],
      "support_pct": 99.8
    },
    "N12_Crown_Noctuoidea": {
      "mean": 82.4,
      "hpd95": [
        76.2,
        88.6
      ],
      "support_pct": 99.8
    }
  }
}