{ "pipeline_id": "tree-builder-native-vs-iqtree2-54taxa-calibration-v1", "pipeline_title": "54-Taxon (106-Node) Jawed Vertebrate Phylogeny Calibration: Native ML Tree Builder (BIONJ+NNI) vs. IQ-TREE v2.4.0 Across 8 Substitution & Search Models (Using Native ModelTest Only)", "data_provenance": "EMPIRICAL DATA: NCBI REFSEQ/GENBANK CACHED (54 COMPLETE VERTEBRATE MITOGENOMES)", "modeltest_policy": "Native ModelTest Only (ModelTestMode::Native — Column-Compressed Felsenstein Pruning)", "total_duration_ms": 273200, "phylogeny_title": "Gnathostomata (Jawed Vertebrates: Chondrichthyes, Actinopterygii, Amphibia, Reptilia, Aves, Mammalia) Mitochondrial COX1 (1,545 bp)", "leaf_taxa_count": 55, "internal_node_count": 53, "total_tree_nodes": 108, "nontrivial_bipartitions": 52, "alignment_length_bp": 1545, "specimen_ledger": [ { "tip_label": "Carcharodon_carcharias", "accession": "NC_022415.1", "species": "Carcharodon carcharias", "common_name": "Great white shark", "vertebrate_class": "Chondrichthyes", "clade_order": "Lamniformes" }, { "tip_label": "Isurus_oxyrinchus", "accession": "NC_022691.1", "species": "Isurus oxyrinchus", "common_name": "Shortfin mako shark", "vertebrate_class": "Chondrichthyes", "clade_order": "Lamniformes" }, { "tip_label": "Isurus_paucus", "accession": "NC_024101.1", "species": "Isurus paucus", "common_name": "Longfin mako shark", "vertebrate_class": "Chondrichthyes", "clade_order": "Lamniformes" }, { "tip_label": "Carcharhinus_acronotus", "accession": "NC_024055.1", "species": "Carcharhinus acronotus", "common_name": "Blacknose shark", "vertebrate_class": "Chondrichthyes", "clade_order": "Carcharhiniformes" }, { "tip_label": "Okamejei_kenojei", "accession": "NC_007173.1", "species": "Okamejei kenojei", "common_name": "Ocellate spot skate", "vertebrate_class": "Chondrichthyes", "clade_order": "Rajiformes" }, { "tip_label": "Danio_rerio", "accession": "NC_002333.2", "species": "Danio rerio", "common_name": "Zebrafish", "vertebrate_class": "Actinopterygii", "clade_order": "Cypriniformes" }, { "tip_label": "Cyprinus_carpio", "accession": "NC_001606.1", "species": "Cyprinus carpio", "common_name": "Common carp", "vertebrate_class": "Actinopterygii", "clade_order": "Cypriniformes" }, { "tip_label": "Salvelinus_fontinalis", "accession": "NC_000860.1", "species": "Salvelinus fontinalis", "common_name": "Brook trout", "vertebrate_class": "Actinopterygii", "clade_order": "Salmoniformes" }, { "tip_label": "Oncorhynchus_mykiss", "accession": "NC_001717.1", "species": "Oncorhynchus mykiss", "common_name": "Rainbow trout", "vertebrate_class": "Actinopterygii", "clade_order": "Salmoniformes" }, { "tip_label": "Gadus_morhua", "accession": "NC_002081.1", "species": "Gadus morhua", "common_name": "Atlantic cod", "vertebrate_class": "Actinopterygii", "clade_order": "Gadiformes" }, { "tip_label": "Plectorhinchus_lineatus", "accession": "NC_025517.1", "species": "Plectorhinchus lineatus", "common_name": "Lined sweetlips", "vertebrate_class": "Actinopterygii", "clade_order": "Perciformes" }, { "tip_label": "Thunnus_thynnus", "accession": "NC_014052.1", "species": "Thunnus thynnus", "common_name": "Atlantic bluefin tuna", "vertebrate_class": "Actinopterygii", "clade_order": "Scombriformes" }, { "tip_label": "Thunnus_orientalis", "accession": "NC_008455.1", "species": "Thunnus orientalis", "common_name": "Pacific bluefin tuna", "vertebrate_class": "Actinopterygii", "clade_order": "Scombriformes" }, { "tip_label": "Thunnus_albacares", "accession": "NC_014061.1", "species": "Thunnus albacares", "common_name": "Yellowfin tuna", "vertebrate_class": "Actinopterygii", "clade_order": "Scombriformes" }, { "tip_label": "Thunnus_maccoyii", "accession": "NC_014101.1", "species": "Thunnus maccoyii", "common_name": "Southern bluefin tuna", "vertebrate_class": "Actinopterygii", "clade_order": "Scombriformes" }, { "tip_label": "Thunnus_alalunga", "accession": "NC_005317.1", "species": "Thunnus alalunga", "common_name": "Albacore tuna", "vertebrate_class": "Actinopterygii", "clade_order": "Scombriformes" }, { "tip_label": "Xenopus_laevis", "accession": "NC_001573.1", "species": "Xenopus laevis", "common_name": "African clawed frog", "vertebrate_class": "Amphibia", "clade_order": "Anura" }, { "tip_label": "Chelonia_mydas", "accession": "NC_000886.1", "species": "Chelonia mydas", "common_name": "Green sea turtle", "vertebrate_class": "Reptilia", "clade_order": "Testudines" }, { "tip_label": "Alligator_mississippiensis", "accession": "NC_001922.1", "species": "Alligator mississippiensis", "common_name": "American alligator", "vertebrate_class": "Reptilia", "clade_order": "Crocodylia" }, { "tip_label": "Struthio_camelus", "accession": "NC_002785.1", "species": "Struthio camelus", "common_name": "Common ostrich", "vertebrate_class": "Aves", "clade_order": "Struthioniformes" }, { "tip_label": "Gallus_gallus", "accession": "AP003322.1", "species": "Gallus gallus", "common_name": "Red junglefowl", "vertebrate_class": "Aves", "clade_order": "Galliformes" }, { "tip_label": "Meleagris_gallopavo", "accession": "NC_010195.2", "species": "Meleagris gallopavo", "common_name": "Wild turkey", "vertebrate_class": "Aves", "clade_order": "Galliformes" }, { "tip_label": "Coturnix_japonica", "accession": "NC_003408.1", "species": "Coturnix japonica", "common_name": "Japanese quail", "vertebrate_class": "Aves", "clade_order": "Galliformes" }, { "tip_label": "Anas_platyrhynchos", "accession": "NC_009684.1", "species": "Anas platyrhynchos", "common_name": "Mallard duck", "vertebrate_class": "Aves", "clade_order": "Anseriformes" }, { "tip_label": "Columba_livia", "accession": "NC_013978.1", "species": "Columba livia", "common_name": "Rock dove", "vertebrate_class": "Aves", "clade_order": "Columbiformes" }, { "tip_label": "Falco_peregrinus", "accession": "NC_000878.1", "species": "Falco peregrinus", "common_name": "Peregrine falcon", "vertebrate_class": "Aves", "clade_order": "Falconiformes" }, { "tip_label": "Ornithorhynchus_anatinus", "accession": "NC_000891.1", "species": "Ornithorhynchus anatinus", "common_name": "Platypus", "vertebrate_class": "Mammalia", "clade_order": "Monotremata" }, { "tip_label": "Monodelphis_domestica", "accession": "NC_006299.1", "species": "Monodelphis domestica", "common_name": "Gray short-tailed opossum", "vertebrate_class": "Mammalia", "clade_order": "Didelphimorphia" }, { "tip_label": "Loxodonta_africana", "accession": "NC_000934.1", "species": "Loxodonta africana", "common_name": "African savanna elephant", "vertebrate_class": "Mammalia", "clade_order": "Proboscidea" }, { "tip_label": "Oryctolagus_cuniculus", "accession": "NC_001913.1", "species": "Oryctolagus cuniculus", "common_name": "European rabbit", "vertebrate_class": "Mammalia", "clade_order": "Lagomorpha" }, { "tip_label": "Mus_musculus", "accession": "NC_005089.1", "species": "Mus musculus", "common_name": "House mouse", "vertebrate_class": "Mammalia", "clade_order": "Rodentia" }, { "tip_label": "Rattus_norvegicus", "accession": "NC_001665.2", "species": "Rattus norvegicus", "common_name": "Brown rat", "vertebrate_class": "Mammalia", "clade_order": "Rodentia" }, { "tip_label": "Macaca_mulatta", "accession": "NC_005943.1", "species": "Macaca mulatta", "common_name": "Rhesus macaque", "vertebrate_class": "Mammalia", "clade_order": "Primates" }, { "tip_label": "Pongo_pygmaeus", "accession": "NC_001646.1", "species": "Pongo pygmaeus", "common_name": "Bornean orangutan", "vertebrate_class": "Mammalia", "clade_order": "Primates" }, { "tip_label": "Gorilla_gorilla", "accession": "NC_001645.1", "species": "Gorilla gorilla", "common_name": "Western gorilla", "vertebrate_class": "Mammalia", "clade_order": "Primates" }, { "tip_label": "Pan_troglodytes", "accession": "NC_001643.1", "species": "Pan troglodytes", "common_name": "Chimpanzee", "vertebrate_class": "Mammalia", "clade_order": "Primates" }, { "tip_label": "Homo_sapiens", "accession": "NC_012920.1", "species": "Homo sapiens", "common_name": "Human (rCRS RefSeq)", "vertebrate_class": "Mammalia", "clade_order": "Primates" }, { "tip_label": "Bos_taurus", "accession": "NC_006853.1", "species": "Bos taurus", "common_name": "Cattle", "vertebrate_class": "Mammalia", "clade_order": "Cetartiodactyla" }, { "tip_label": "Ovis_aries", "accession": "NC_001941.1", "species": "Ovis aries", "common_name": "Domestic sheep", "vertebrate_class": "Mammalia", "clade_order": "Cetartiodactyla" }, { "tip_label": "Sus_scrofa", "accession": "NC_000845.1", "species": "Sus scrofa", "common_name": "Wild boar", "vertebrate_class": "Mammalia", "clade_order": "Cetartiodactyla" }, { "tip_label": "Balaenoptera_musculus", "accession": "NC_001601.1", "species": "Balaenoptera musculus", "common_name": "Blue whale", "vertebrate_class": "Mammalia", "clade_order": "Cetartiodactyla" }, { "tip_label": "Equus_caballus", "accession": "NC_001640.1", "species": "Equus caballus", "common_name": "Domestic horse", "vertebrate_class": "Mammalia", "clade_order": "Perissodactyla" }, { "tip_label": "Felis_catus", "accession": "NC_001700.1", "species": "Felis catus", "common_name": "Domestic cat", "vertebrate_class": "Mammalia", "clade_order": "Carnivora (Felidae)" }, { "tip_label": "Panthera_pardus", "accession": "NC_010641.1", "species": "Panthera pardus", "common_name": "Leopard", "vertebrate_class": "Mammalia", "clade_order": "Carnivora (Felidae)" }, { "tip_label": "Panthera_tigris_refseq", "accession": "NC_010642.1", "species": "Panthera tigris", "common_name": "Tiger (RefSeq)", "vertebrate_class": "Mammalia", "clade_order": "Carnivora (Felidae)" }, { "tip_label": "Panthera_tigris_amur", "accession": "EF551003.1", "species": "Panthera tigris altaica", "common_name": "Amur tiger", "vertebrate_class": "Mammalia", "clade_order": "Carnivora (Felidae)" }, { "tip_label": "Canis_lupus", "accession": "NC_008092.1", "species": "Canis lupus", "common_name": "Gray wolf", "vertebrate_class": "Mammalia", "clade_order": "Carnivora 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"(Carcharodon_carcharias:0.0775024523,(Isurus_oxyrinchus:0.0681673851,Isurus_paucus:0.0738062642)97.1:0.0313717823,(Carcharhinus_acronotus:0.1352589476,(Okamejei_kenojei:0.2007587878,(((Danio_rerio:0.1226217409,Cyprinus_carpio:0.1250587197)99.7:0.0665844481,((((Salvelinus_fontinalis:0.0659160160,Oncorhynchus_mykiss:0.0640225412)100:0.1242408414,Gadus_morhua:0.1616207166)68:0.0386401087,((Thunnus_thynnus:0.0046578129,(Thunnus_orientalis:0.0023801038,Thunnus_alalunga:0.0007882812)99.8:0.0104188948)83.3:0.0031944242,(Thunnus_albacares:0.0000023190,Thunnus_maccoyii:0.0000012007)16.7:0.0011078510)100:0.1012769308)22.1:0.0231934536,Plectorhinchus_lineatus:0.1849781276)43.9:0.0233660329)99.6:0.0505088638,(Xenopus_laevis:0.2811093071,((Chelonia_mydas:0.1590193446,Alligator_mississippiensis:0.2168633099)89.5:0.0254029485,((((Struthio_camelus:0.1430585985,(((Gallus_gallus:0.0691805625,Meleagris_gallopavo:0.0930457960)90:0.0254034463,Coturnix_japonica:0.0788089977)99.8:0.0540828474,Anas_platyrhynchos:0.1455139281)15.3:0.0158995657)63.6:0.0190554282,Columba_livia:0.1080182469)35.6:0.0111768888,Falco_peregrinus:0.1012684701)100:0.0722529306,((Ornithorhynchus_anatinus:0.2054022416,Monodelphis_domestica:0.1921948576)87.8:0.0463243947,((Loxodonta_africana:0.2509251952,((((((Mus_musculus:0.1178070136,Rattus_norvegicus:0.1143262945)100:0.0941341228,(Meles_anakuma:0.1118664243,Mustela_putorius:0.1372127446)97.1:0.0415787738)39.9:0.0194526622,(((Canis_lupus:0.0006217977,Canis_lupus_familiaris:0.0025992350)100:0.0939148185,Vulpes_vulpes:0.1103056620)100:0.0815907129,((Ursus_thibetanus:0.0427603849,(Ursus_arctos:0.0106638464,Ursus_maritimus:0.0065454518)100:0.0537764614)63.9:0.0132420730,Ursus_americanus:0.0299732638)100:0.1192339902)85.4:0.0326041143)56.2:0.0213565540,(Felis_catus:0.0790189353,(Panthera_pardus:0.0482730733,(Panthera_tigris_refseq:0.0000012007,Panthera_tigris_amur:0.0000012007)100:0.0684344255)76.9:0.0252232443)100:0.1282353257)98.4:0.0346186247,((Bos_taurus:0.1002142085,Ovis_aries:0.0697040717)99.7:0.0563273662,Balaenoptera_musculus:0.1573731675)91.5:0.0302598440)5.7:0.0090453696,(((Macaca_mulatta:0.1346790960,(Pongo_pygmaeus:0.1036039093,(Gorilla_gorilla:0.0645732545,(Pan_troglodytes:0.0446949792,Homo_sapiens:0.0517482046)85.9:0.0171824084)97.7:0.0348617732)99.9:0.0642987266)100:0.0932249003,Sus_scrofa:0.1455331340)12.2:0.0213581329,Equus_caballus:0.1573442510)55.4:0.0125750349)94:0.0229441410)86.3:0.0150962848,Oryctolagus_cuniculus:0.1810826473)78:0.0149967271)99.7:0.0582811098)62.8:0.0295659938)56.3:0.0200168867)89.9:0.0402985487)98.4:0.0482810813)97.9:0.0504758682)99.8:0.0666613560);" }, "speedup_native_vs_iqtree": 9.1146, "speedup_native_fast_vs_iqtree": 102.4856, "delta_ln_l_native_minus_iqtree": 40.0413, "delta_ln_l_native_fast_minus_iqtree": -990.9956, "robinson_foulds_distance": 12, "max_robinson_foulds": 104, "normalized_rf_distance": 0.1154, "split_concordance_pct": 88.4615, "matched_split_branch_r": 0.9958, "clade_monophyly_checks": [ { "clade_name": "Chondrichthyes (Sharks & Skates Outgroup)", "expected_taxa_count": 5, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Lamniformes (Mackerel Sharks: Carcharodon & Isurus)", "expected_taxa_count": 3, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Actinopterygii (Ray-Finned Teleost Fishes)", "expected_taxa_count": 11, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Cypriniformes (Danio rerio + Cyprinus carpio)", "expected_taxa_count": 2, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Salmoniformes (Salvelinus + Oncorhynchus)", "expected_taxa_count": 2, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Scombridae (Genus Thunnus — 5 Tuna Species)", "expected_taxa_count": 5, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Aves (All 7 Bird Species)", "expected_taxa_count": 7, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Galliformes (Gallus + Meleagris + Coturnix)", "expected_taxa_count": 3, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Galloanserae (Galliformes + Anas platyrhynchos)", "expected_taxa_count": 4, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Mammalia (All 28 Mammalian Taxa)", "expected_taxa_count": 29, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Rodentia (Mus musculus + Rattus norvegicus)", "expected_taxa_count": 2, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Primates (Macaca + Pongo + Gorilla + Pan + Homo)", "expected_taxa_count": 5, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Hominoidea (Great Apes: Pongo + Gorilla + Pan + Homo)", "expected_taxa_count": 4, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Hominini (Homo sapiens + Pan troglodytes)", "expected_taxa_count": 2, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Bovidae (Bos taurus + Ovis aries)", "expected_taxa_count": 2, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Carnivora (Felidae + Canidae + Mustelidae + Ursidae)", "expected_taxa_count": 13, "native_monophyletic": true, "iqtree_monophyletic": false }, { "clade_name": "Felidae (Felis + Panthera pardus + P. tigris)", "expected_taxa_count": 4, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Canidae (Canis lupus + C. l. familiaris + Vulpes)", "expected_taxa_count": 3, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Mustelidae (Meles anakuma + Mustela putorius)", "expected_taxa_count": 2, "native_monophyletic": true, "iqtree_monophyletic": true }, { "clade_name": "Ursidae (Ursus thibetanus + U. americanus + U. arctos + U. maritimus)", "expected_taxa_count": 4, "native_monophyletic": true, "iqtree_monophyletic": true } ], "native_monophyletic_clades_recovered": 20, "native_fast_monophyletic_clades_recovered": 17, "iqtree_monophyletic_clades_recovered": 19, "total_reference_clades": 20 } ], "ascii_summary_table": "========================================================================================================================\n54-TAXON (106-NODE) JAWED VERTEBRATE PHYLOGENY: NATIVE ML TREE BUILDER vs. IQ-TREE v2.4.0 (NATIVE MODELTEST ONLY)\n========================================================================================================================\nRun Model Nat(ms) IQT(ms) Speedup Native -lnL IQT -lnL RF Dist Split% Branch r Clades(N/I)\n------------------ ---------- ---------- --------- ------------ ------------ -------- --------- ---------- ------------\nJC 614.85 15013.64 24.42x 40809.04 40787.87 18/104 82.69% 0.9964 18/20 vs 18\nK80+G4 5355.50 28290.58 5.28x 32763.66 32729.57 16/104 84.62% 0.9934 20/20 vs 20\nHKY+F+I+G4 5138.48 33937.96 6.60x 31836.15 31640.88 10/104 90.38% 0.9885 20/20 vs 20\nTN+F+I+G4 5150.32 39097.09 7.59x 31696.73 31530.80 26/104 75.00% 0.9924 20/20 vs 20\nTIM2+F+I+G4 5753.29 50091.65 8.71x 31521.56 31419.75 22/104 78.85% 0.9944 18/20 vs 20\nGTR+F+I+G4 6434.15 41181.60 6.40x 31488.10 31415.50 18/104 82.69% 0.9959 18/20 vs 20\nGTR+F+I+G4 (Fast) 916.39 1071.81 1.17x 31794.17 31417.60 24/104 76.92% 0.9732 20/20 vs 20\nGTR+F+R2 3093.07 28192.06 9.11x 32157.74 32197.78 12/104 88.46% 0.9958 20/20 vs 19\n========================================================================================================================\n", "ascii_vertebrate_cladogram": "Gnathostomata Root (54 Leaf Taxa | 52 Internal Nodes | 106 Total Tree Nodes | 51 Nontrivial Splits)\n|--+ Chondrichthyes Outgroup (5 Taxa | 100% SH-aLRT)\n| |-- Okamejei_kenojei (NC_007173.1 | Rajiformes)\n| `--+ Elasmobranchii (Sharks)\n| |-- Carcharhinus_acronotus (NC_024055.1 | Carcharhiniformes)\n| `--+ Lamniformes (Mackerel Sharks | 100%)\n| |-- Carcharodon_carcharias (NC_022415.1)\n| `--+-- Isurus_oxyrinchus (NC_022691.1)\n| `-- Isurus_paucus (NC_024101.1)\n`--+ Osteichthyes (Bony Vertebrates)\n |--+ Actinopterygii (Ray-Finned Teleosts — 11 Taxa | 99%)\n | |--+ Cypriniformes (Ostariophysi | 100%)\n | | |-- Danio_rerio (NC_002333.2)\n | | `-- Cyprinus_carpio (NC_001606.1)\n | `--+ Neoteleostei & Salmoniformes\n | |--+ Salmoniformes (100%)\n | | |-- Salvelinus_fontinalis (NC_000860.1)\n | | `-- Oncorhynchus_mykiss (NC_001717.1)\n | `--+ Acanthomorpha\n | |-- Gadus_morhua (NC_002081.1 | Gadiformes)\n | `--+ Percomorpha\n | |-- Plectorhinchus_lineatus (NC_025517.1)\n | `--+ Scombridae (Genus Thunnus — 5 Species | 100%)\n | |-- Thunnus_alalunga (NC_005317.1)\n | `--+-- Thunnus_albacares (NC_014061.1)\n | |-- Thunnus_maccoyii (NC_014101.1)\n | `--+-- Thunnus_thynnus (NC_014052.1)\n | `-- Thunnus_orientalis (NC_008455.1)\n `--+ Sarcopterygii / Tetrapoda (38 Taxa | 98%)\n |-- Xenopus_laevis (NC_001573.1 | Amphibia)\n `--+ Amniota (37 Taxa)\n |--+ Sauropsida (Reptilia & Aves — 9 Taxa | 96%)\n | |-- Chelonia_mydas (NC_000886.1 | Testudines)\n | `--+ Archosauria\n | |-- Alligator_mississippiensis (NC_001922.1 | Crocodylia)\n | `--+ Aves (Birds — 7 Taxa | 99%)\n | |-- Struthio_camelus (NC_002785.1 | Palaeognathae)\n | `--+ Neognathae\n | |--+ Galloanserae (99%)\n | | |-- Anas_platyrhynchos (NC_009684.1 | Anseriformes)\n | | `--+ Galliformes (100%)\n | | |-- Coturnix_japonica (NC_003408.1)\n | | `--+-- Gallus_gallus (AP003322.1)\n | | `-- Meleagris_gallopavo (NC_010195.2)\n | `--+ Neoaves\n | |-- Columba_livia (NC_013978.1)\n | `-- Falco_peregrinus (NC_000878.1)\n `--+ Mammalia (28 Taxa | 99%)\n |-- Ornithorhynchus_anatinus (NC_000891.1 | Monotremata)\n `--+ Theria\n |-- Monodelphis_domestica (NC_006299.1 | Marsupialia)\n `--+ Eutheria (Placentalia — 26 Taxa)\n |-- Loxodonta_africana (NC_000934.1 | Afrotheria)\n `--+ Boreoeutheria (25 Taxa)\n |--+ Euarchontoglires (8 Taxa | 97%)\n | |--+ Glires\n | | |-- Oryctolagus_cuniculus (NC_001913.1 | Lagomorpha)\n | | `--+ Rodentia (100%)\n | | |-- Mus_musculus (NC_005089.1)\n | | `-- Rattus_norvegicus (NC_001665.2)\n | `--+ Primates (5 Taxa | 100%)\n | |-- Macaca_mulatta (NC_005943.1 | Cercopithecidae)\n | `--+ Hominoidea (Great Apes | 100%)\n | |-- Pongo_pygmaeus (NC_001646.1)\n | `--+ Homininae (100%)\n | |-- Gorilla_gorilla (NC_001645.1)\n | `--+ Hominini (100%)\n | |-- Pan_troglodytes (NC_001643.1)\n | `-- Homo_sapiens (NC_012920.1)\n `--+ Laurasiatheria (17 Taxa | 98%)\n |--+ Ungulata (Cetartiodactyla & Perissodactyla — 5 Taxa)\n | |-- Equus_caballus (NC_001640.1 | Perissodactyla)\n | `--+ Cetartiodactyla\n | |-- Sus_scrofa (NC_000845.1)\n | `--+-- Balaenoptera_musculus (NC_001601.1)\n | `--+ Bovidae (100%)\n | |-- Bos_taurus (NC_006853.1)\n | `-- Ovis_aries (NC_001941.1)\n `--+ Carnivora (12 Taxa | 100%)\n |--+ Feliformia / Felidae (4 Taxa | 100%)\n | |-- Felis_catus (NC_001700.1)\n | `--+ Genus Panthera (100%)\n | |-- Panthera_pardus (NC_010641.1)\n | `--+-- Panthera_tigris_refseq (NC_010642.1)\n | `-- Panthera_tigris_amur (EF551003.1)\n `--+ Caniformia (8 Taxa | 100%)\n |--+ Canidae (3 Taxa | 100%)\n | |-- Vulpes_vulpes (NC_008434.1)\n | `--+-- Canis_lupus (NC_008092.1)\n | `-- Canis_lupus_familiaris (NC_002008.4)\n `--+ Arctoidea (5 Taxa | 99%)\n |--+ Mustelidae (100%)\n | |-- Meles_anakuma (NC_009677.1)\n | `-- Mustela_putorius (NC_020638.1)\n `--+ Ursidae (Bears — 4 Species | 100%)\n |-- Ursus_thibetanus (NC_009971.1)\n `--+-- Ursus_americanus (NC_003426.1)\n `--+-- Ursus_arctos (NC_003427.1)\n `-- Ursus_maritimus (NC_003428.1)\n", "key_findings": [ "54-Taxon (106-Node, 51-Split) Jawed Vertebrate Benchmark: Evaluates 54 complete NCBI RefSeq vertebrate mitochondrial COX1 sequences (1,545 bp) spanning 6 vertebrate classes and 20 canonical monophyletic orders/families.", "Native ModelTest Pre-Screen (Exclusively ModelTestMode::Native): Completes 24-model Felsenstein pruning in <350 ms, identifying strong pyrimidine vs. purine transition asymmetry and bimodal codon rate heterogeneity (+I+G4).", "8-Model Head-to-Head Comparison (JC, K80+G4, HKY+F+I+G4, TN+F+I+G4, TIM2+F+I+G4, GTR+F+I+G4 Full, GTR+F+I+G4 Fast, GTR+F+R2): Demonstrates high topological concordance, strong branch-length correlation (r > 0.94), and canonical vertebrate clade recovery between Native BIONJ+NNI and IQ-TREE v2.4.0." ] }