{ "schema_version": "1.0.0", "study_slug": "tetrapod-fin-limb-timetree", "companion_preprint_slug": "tetrapod-fin-limb-timetree-preprint", "preprint_id": "PREPRINT-09", "validation_set_id": "VAL-SET-048-SARCOPTERYGII-TETRAPODA-FIN-TO-LIMB-TIMETREE-64TAXA-1.78MB", "title": "Devonian Sarcopterygian Fin-to-Limb Transition, Dipnoi Sisterhood, and the 440–0 Ma Crown Tetrapoda Total-Evidence Time-Tree Chronogram", "created_at_utc": "2026-11-05T16:40:00Z", "tier": 3, "beaker_prior": 5, "beaker_posterior": 5, "z_posterior_positive": 5.47, "z_posterior_all": 4.81, "p_value": 2.2e-8, "bootstrap_replicates": 50, "dataset_scale": { "total_taxa": 64, "extant_taxa": 48, "fossil_taxa": 16, "aligned_sites_bp": 1782000, "total_cohorts": 32, "development_cohorts": 12, "untouched_reserve_cohorts": 12, "nuclear_orthologs": 216, "cne_enhancer_elements": 640, "morphological_characters_mkv": 268 }, "step_up_trajectory": { "stage_1_exploratory": { "tier": 1, "taxa": 18, "cohorts": 8, "sites_bp": 336000, "rate_asymmetry_ratio": 4.12, "cv_rate": 0.408, "unrecoded_rcfv": 0.136, "strict_clock_crown_tetrapoda_ma": 414.6, "z_score": 3.64, "beakers": 3 }, "stage_2_blinded_validation": { "tier": 2, "taxa": 42, "cohorts": 24, "dev_cohorts": 12, "reserve_cohorts": 12, "sites_bp": 924000, "authentic_cohorts_count": 20, "authentic_biotype_concordance_pct": 100.0, "authentic_mean_delta_z_sd": 0.0, "dayhoff6_rcfv": 0.022, "rcfv_reduction_pct": 83.8, "anomalies_intercepted": [ { "token": "BLIND-TETRA-05", "biotype_extrapolated": "Retrotransposon-Chimeric Intron Read-Through Artifact", "repository_label": "Protopterus annectens HoxD13 Giant Coding Exon (NW_025338142.1)", "omega_dn_ds": 0.914, "d_ctx_sd": 5.58 }, { "token": "BLIND-TETRA-11", "biotype_extrapolated": "High-GC3 (86.4%) gBGC Recombination Hotspot Exons", "repository_label": "Unfiltered Amniote/Anuran Neutral Coding Concatenate", "d_ctx_sd": 5.26 }, { "token": "BLIND-TETRA-18", "biotype_extrapolated": "Convergent Paedomorphic Aquatic Gill & Lateral-Line Characters", "repository_label": "Unweighted Stem/Crown Amphibian Mkv Matrix", "d_ctx_sd": 5.08 }, { "token": "BLIND-TETRA-23", "biotype_extrapolated": "Outlier Hard-Minimum Calibration Prior Violation", "repository_label": "397.0 Ma Zachelmie Trackway Forced on Crown Tetrapoda", "d_ctx_sd": 4.86 } ], "z_score": 4.48, "beakers": 4 }, "stage_3_scientific_synthesis": { "tier": 3, "taxa": 64, "cohorts": 32, "sites_bp": 1782000, "bootstrap_replicates": 50, "hypotheses": [ { "id": "H1", "name": "Rhipidistia Sisterhood (Dipnoi Lungfishes + Tetrapoda vs. Actinistia Coelacanth)", "bootstrap_support_pct": "99.6% ± 0.2%", "delta_lnL_vs_coelacanth_sister": 2148.4, "z_score": 5.54, "beakers": 5 }, { "id": "H2", "name": "Devonian Fin-to-Limb Transition (392.6–360.0 Ma) & Early Carboniferous Crown Tetrapoda (346.2 Ma)", "z_score": 5.44, "beakers": 5 }, { "id": "H3", "name": "HoxD13–ZRS–Gli3 Autopod Regulatory Epistasis (|J_ij| = 1.648) & CPS1 Ureotelic Terrestrialization", "z_score": 5.42, "beakers": 5 }, { "id": "H4", "name": "Pre-Devonian (Silurian >415 Ma) Crown Tetrapoda Origin Null Hypothesis", "status": "Falsified", "z_score": 1.08, "beakers": 1 } ] } }, "calibrated_nodes": [ { "node": "N0", "clade": "Crown Gnathostomata (Chondrichthyes vs. Osteichthyes)", "mean_ma": 456.4, "hpd_95_ma": [444.2, 468.6], "support_pct": "100.0% ± 0.0%" }, { "node": "N1", "clade": "Crown Osteichthyes (Actinopterygii vs. Sarcopterygii)", "mean_ma": 434.2, "hpd_95_ma": [425.0, 443.4], "support_pct": "100.0% ± 0.0%" }, { "node": "N2", "clade": "Crown Sarcopterygii (Actinistia Latimeria vs. Rhipidistia)", "mean_ma": 424.8, "hpd_95_ma": [416.2, 433.4], "support_pct": "99.8% ± 0.2%" }, { "node": "N3", "clade": "Crown Rhipidistia (Dipnoi Lungfishes vs. Tetrapodomorpha)", "mean_ma": 418.4, "hpd_95_ma": [410.0, 426.8], "support_pct": "99.6% ± 0.2%" }, { "node": "N4", "clade": "Tristichopteridae Split (†Eusthenopteron vs. Elpistostegalia)", "mean_ma": 392.6, "hpd_95_ma": [385.4, 399.8], "support_pct": "99.4% ± 0.3%" }, { "node": "N5", "clade": "Elpistostegalia (†Panderichthys / †Tiktaalik / †Elpistostege)", "mean_ma": 383.8, "hpd_95_ma": [377.6, 390.0], "support_pct": "99.4% ± 0.3%" }, { "node": "N6", "clade": "Digited Stem-Tetrapoda (Stegocephalia: †Acanthostega / †Ichthyostega / †Tulerpeton)", "mean_ma": 373.4, "hpd_95_ma": [367.4, 379.4], "support_pct": "99.6% ± 0.2%" }, { "node": "N7", "clade": "Post-Romer's Gap Stem-Tetrapoda (†Whatcheeria / †Pederpes vs. Crown)", "mean_ma": 356.8, "hpd_95_ma": [350.2, 363.4], "support_pct": "99.2% ± 0.4%" }, { "node": "N8", "clade": "Crown Tetrapoda (Batrachomorpha / Lissamphibia vs. Reptiliomorpha / Amniota)", "mean_ma": 346.2, "hpd_95_ma": [338.6, 353.8], "support_pct": "99.8% ± 0.2%" }, { "node": "N9", "clade": "Crown Lissamphibia (Gymnophiona vs. Batrachia)", "mean_ma": 294.6, "hpd_95_ma": [281.4, 307.8], "support_pct": "99.4% ± 0.3%" }, { "node": "N10", "clade": "Crown Batrachia (Urodela / Caudata vs. Salientia / Anura)", "mean_ma": 272.4, "hpd_95_ma": [259.8, 285.0], "support_pct": "100.0% ± 0.0%" }, { "node": "N11", "clade": "Crown Amniota (Synapsida / Mammalia vs. Sauropsida / Reptilia & Aves)", "mean_ma": 318.4, "hpd_95_ma": [311.6, 325.2], "support_pct": "100.0% ± 0.0%" }, { "node": "N12", "clade": "Crown Sauropsida (Lepidosauria vs. Archelosauria)", "mean_ma": 281.2, "hpd_95_ma": [271.0, 291.4], "support_pct": "99.8% ± 0.2%" } ], "runie_pipeline_comparison": [ { "rank": "1st (Best)", "toolchain": "seq_ingestor -> *MAFFT-L-INS-i -> dayhoff6_recoder -> gc3_gbgc_masker -> *PhyloBayes-CAT-GTR -> *IQ-TREE2-PMSF-C60-Mkv -> *MCMCTree-FBD-Soft -> dca_potts_coupler", "model_summary": "Dayhoff-6 + CAT-GTR + GC3-Filtered + Partitioned Mkv + Soft-Bound FBD Clock (16 Fossils)", "marginal_lnL_nats": -394128.6, "delta_lnL": 0.0, "rcfv": 0.022, "bootstrap_support": "99.6% ± 0.2% (Dipnoi+Tetrapoda Sister; 346.2 Ma Crown)", "posterior_z": "+5.47 SD (5🧪)" }, { "rank": "2nd", "toolchain": "seq_ingestor -> *MAFFT-L-INS-i -> gc3_gbgc_masker -> *IQ-TREE2-LG-C60-F-G4 -> *MCMCTree-UCLN", "model_summary": "20-State LG+C60+F+G4 Profile Mixture + GC3-Filtered + UCLN Relaxed Clock", "marginal_lnL_nats": -395412.0, "delta_lnL": -1283.4, "rcfv": 0.054, "bootstrap_support": "92.4% ± 1.6% (Dipnoi+Tetrapoda Sister; 354.8 Ma Crown)", "posterior_z": "+4.46 SD (4🧪)" }, { "rank": "3rd", "toolchain": "seq_ingestor -> *MAFFT-FFT-NS-2 -> *RAxML-NG-LG-G4 -> *LSD2-Hard-Node", "model_summary": "20-State LG+G4 + Unfiltered Exons + Hard-Minimum Node Dating", "marginal_lnL_nats": -397380.2, "delta_lnL": -3251.6, "rcfv": 0.089, "bootstrap_support": "74.0% ± 4.4% (Split Rhipidistia vs. Coelacanth; 372.0 Ma Crown)", "posterior_z": "+3.32 SD (3🧪)" }, { "rank": "4th (Rejected)", "toolchain": "seq_ingestor -> *ClustalW -> *FastTree2-WAG-G4 -> strict_clock_lsq", "model_summary": "Unrecoded 20-State WAG+G4 + Unweighted Morphology + Strict Clock + 397 Ma Trackway Crown Prior", "marginal_lnL_nats": -399482.9, "delta_lnL": -5354.3, "rcfv": 0.136, "bootstrap_support": "22.0% ± 5.1% (74.0% False Lungfish+Coelacanth Lock; 414.6 Ma Inflation)", "posterior_z": "+1.82 SD (1🧪)" } ] }