{ "study_id": "DISC-114-BASAL-METAZOA-CTENO-PORIFERA-CNIDARIA-TIMETREE", "slug": "cteno-porifera-cnidaria-timetree", "preprint_slug": "basal-metazoa-timetree-preprint", "preprint_id": "PREPRINT-05", "validation_set_id": "VAL-SET-044-BASAL-METAZOA-CTENO-PORIFERA-CNIDARIA-TIMETREE-64TAXA-1.64MB", "generated_at": "2026-11-04T23:12:00.000Z", "engine": "RuNIE v1.27.0 (Rust Native Inference Engine)", "mode": "Dual-Pass Blinded Dry-Lab Mode (SHA-256 + D_ctx) -> Full Step-Up (Tier 1 -> Tier 2 -> Tier 3) -> Final-Report-Only Publication Mode", "bootstrap_replicates": 500, "prior_beakers": 5, "posterior_beakers": 5, "tier_trajectory": { "tier_1_exploratory": { "taxa": 18, "cohorts": 8, "aligned_bp": 312000, "rate_cv": 0.3842, "ctenophore_aa_rate_subs_per_site_myr": 0.00188, "porifera_aa_rate_subs_per_site_myr": 0.00055, "anthozoa_aa_rate_subs_per_site_myr": 0.00058, "cteno_to_sponge_rate_ratio": 3.42, "strict_clock_20state_root_ma": 1148.0, "relaxed_clock_dayhoff6_root_ma": 792.4, "strict_clock_inflation_ma": 355.6, "posterior_z": 3.62, "posterior_beakers": 3 }, "tier_2_blinded_validation": { "taxa": 42, "cohorts": 24, "dev_cohorts": 12, "reserve_cohorts": 12, "aligned_bp": 884000, "rcfv_20state": 0.142, "rcfv_dayhoff6": 0.023, "rcfv_reduction_pct": 83.8, "concordant_cohorts": 20, "mean_abs_delta_z_concordant": 0.0, "dev_mean_z": 4.45, "reserve_mean_z": 4.39, "overall_posterior_z": 4.42, "posterior_beakers": 4, "intercepted_anomalies": [ { "token": "BLIND-METAZOA-04", "split": "DEV", "accession": "NC_016117.1", "issue": "Hyper-compact 10,326 bp Mnemiopsis leidyi mitochondrial genome (84.2% AT, missing atp6/atp8, >12x rate acceleration) co-aligned under a single strict clock with slow 18-20 kb anthozoan/sponge mtDNA, inflating Crown Metazoa to 1,284.0 Ma", "d_ctx_sd": 5.46 }, { "token": "BLIND-METAZOA-09", "split": "DEV", "accession": "GCF_000002865.3", "issue": "High-RCFV choanoflagellate Monosiga brevicollis outgroup + unrecoded 20-state amino-acid ribosomal supermatrix inducing Porifera-sister LBA inversion and +294.0 Ma basal stem stretch", "d_ctx_sd": 5.12 }, { "token": "BLIND-METAZOA-16", "split": "RESERVE", "accession": "CRYOGENIAN-24IPC-STERANE", "issue": "Cryogenian 24-isopropylcholestane sterane biomarker applied as a hard 660.0 Ma Crown Demospongiae minimum bound despite rhizarian/algal sterol diagenesis, stretching the sponge stem by +138.0 Ma", "d_ctx_sd": 4.88 }, { "token": "BLIND-METAZOA-21", "split": "RESERVE", "accession": "GCF_013753865.1-SYMBIO", "issue": "Endosymbiotic dinoflagellate (Symbiodinium) transcriptomic contig chimera embedded in an Acropora reef-coral ortholog supermatrix", "d_ctx_sd": 4.76 } ] }, "tier_3_scientific_synthesis": { "taxa": 64, "extant_taxa": 54, "fossil_tips": 10, "cohorts": 32, "aligned_bp": 1642800, "nuclear_orthologs": 212, "ancestral_linkage_groups": 29, "irreversible_bcns_fusions_benthozoa": 7, "bcns_fisher_exact_p": 1.4e-21, "bootstrap_replicates": 500, "map_topology_support_pct": 99.6, "map_topology_support_sd_pct": 0.2, "posterior_z_pos": 5.48, "posterior_z_all": 4.82, "posterior_beakers": 5, "dated_nodes": [ { "node": "Choanozoa (Choanoflagellata vs. Metazoa)", "age_ma": 892.0, "ci_95_ma": [858.0, 926.0], "geological_stage": "Early Tonian", "genomic_synapomorphy": "29 Ancestral Linkage Groups (ALGs); cadherin extracellular repeats; proto-tyrosine kinase signaling" }, { "node": "Crown Metazoa (Ctenophora vs. Benthozoa/Myriazoa)", "age_ma": 792.4, "ci_95_ma": [762.0, 822.8], "geological_stage": "Late Tonian (Pre-Sturtian)", "genomic_synapomorphy": "Collagen IV NC1 sulfilimine basement membrane (Met93-Hyl211, PDB:1LI1); ancestral DEEA-pore Cav/Nav1 channels (PDB:6A90); Wnt/beta-catenin polarity" }, { "node": "Benthozoa / Myriazoa (Porifera vs. ParaHoxozoa)", "age_ma": 738.6, "ci_95_ma": [710.4, 766.8], "geological_stage": "Terminal Tonian / Sturtian Onset", "genomic_synapomorphy": "7 irreversible BCnS chromosome fusion-with-mixing events (A1a+A1b, C1+C2, E1+E2, G+H, J1+J2, L+M, N+O; p = 1.4e-21); primary pelago-benthic life cycle" }, { "node": "ParaHoxozoa (Placozoa vs. Planulozoa)", "age_ma": 684.2, "ci_95_ma": [658.0, 710.4], "geological_stage": "Cryogenian Interglacial", "genomic_synapomorphy": "ParaHox/Hox (Gsx, Xlox, Cdx) ANTP homeobox cluster; Classical Cadherin EC1-EC2 3xCa2+ hinge (PDB:3Q2V); PSD-95/DLG scaffold (PDB:1BE9)" }, { "node": "Planulozoa (Cnidaria vs. Bilateria)", "age_ma": 642.5, "ci_95_ma": [618.0, 667.0], "geological_stage": "Terminal Cryogenian / Early Ediacaran", "genomic_synapomorphy": "Striated muscle myosin heavy chain (ST-MHC) + Troponin/Tropomyosin; canonical Neuroligin-Neurexin chemical synapses; DEKA-pore Nav selectivity filter" }, { "node": "Crown Porifera (Silicea vs. Calcarea + Homoscleromorpha)", "age_ma": 614.8, "ci_95_ma": [590.2, 639.4], "geological_stage": "Early Ediacaran", "genomic_synapomorphy": "Choanocyte aquiferous collar complex; silicatein/carbonic anhydrase biomineralization toolkit" }, { "node": "Crown Cnidaria (Anthozoa vs. Medusozoa)", "age_ma": 586.4, "ci_95_ma": [564.8, 608.0], "geological_stage": "Mid-Ediacaran (Pre-Gaskiers)", "genomic_synapomorphy": "Cnidocyte minicollagen/nematogalectin capsule; Chordin/BMP-2/4 directive axis; anchored by 560 Ma †Auroralumina attenboroughii" }, { "node": "Crown Bilateria (Protostomia vs. Deuterostomia)", "age_ma": 568.2, "ci_95_ma": [549.0, 587.4], "geological_stage": "Late Ediacaran", "genomic_synapomorphy": "Collinear 7-13 gene Hox cluster; nephrozoan excretory/triploblastic mesoderm; anchored by 555 Ma †Kimberella & 518 Ma †Haikouichthys" }, { "node": "Crown Ctenophora (Cydippida/Lobata/Beroida Radiation)", "age_ma": 384.6, "ci_95_ma": [352.0, 417.2], "geological_stage": "Middle Devonian (after 407.8 Myr stem survival)", "genomic_synapomorphy": "Syncytial Innexin nerve net (12-14 paralogs); colloblasts; 8-comb-row macrocilia; stem anchored by 551 Ma †Eoandromeda & 518 Ma †Daihua" } ] } } }