#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on November 14, 2025; 8:45 GMT TreeBASE (cc) 1994-2008 Study reference: Messenger S., & Mcguire J. 1998. Morphology, molecules, and the phylogenetics of cetaceans. Systematic Biology, 47: 90-124. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S322] [ The following blocks are input data for analysis step 308 ] BEGIN TAXA; TITLE TaxaForAnalysisStep308; DIMENSIONS NTAX=72; TAXLABELS Antilocapra_americanus Archaeoceti Balaena_mysticetus Balaenoptera_acutorostrata Balaenoptera_physalus Berardius_bairdii Bos_taurus Camelus_dromedarius Cephalorhynchus_commersoni Cephalorhynchus_eutropia Cephalorhynchus_heavisidii Cephalorhynchus_hectori Delphinapterus_leucas Delphinus_delphis Eschrichtius_robustus Eubalaena_glacialis Feresa_attenuata Globicephala_macrorhynchus Globicephala_melaena Grampus_griseus Hyperoodon_planifrons Inia_geoffrensis Kogia_breviceps Kogia_simus Lagenodelphis_hosei Lagenorhynchus_acutus Lagenorhynchus_albirostris Lagenorhynchus_australis Lagenorhynchus_cruciger Lagenorhynchus_obliquidens Lagenorhynchus_obscurus Lipotes_vexillifer Lissodelphis_borealis Lissodelphis_peronii Megaptera_novaeangliae Mesoplodon_bidens Mesoplodon_carlhubbsi Mesoplodon_densirostris Mesoplodon_europaeus Mesoplodon_ginkgodens Mesoplodon_grayi Mesoplodon_hectori Mesoplodon_layardii Mesoplodon_peruvianus Mesoplodon_stejnegeri Monodon_monoceros Neophocaena_phocaenoides Orcaella_brevirostris Orcinus_orca Peponocephala_electra Phocoena_phocoena Phocoena_sinus Phocoena_spinipinnis Phocoenoides_dalli Physeter_catadon Platanista_gangetica Pontoporia_blainvillei Pseudorca_crassidens Sotalia_fluviatilis Sousa_chinensis Sousa_teuszii Stenella_attenuata Stenella_clymene Stenella_coeruleoalba Stenella_frontalis Stenella_longirostris Steno_bredanensis Tasmacetus_shepherdi Tayassua_tajacu Tragulus_napu Tursiops_truncatus Ziphius_cavirostris ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3475] TITLE Appendix_3; LINK TAXA = TaxaForAnalysisStep308; DIMENSIONS NCHAR=207; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4 5 6 7" MISSING=? GAP= -; CHARSTATELABELS 1 Facial_plane / concave 'flat to convex (Heyning 1989)', 2 Cranial_vertex / symmetric 'asymmetric (Muizon 1988 Heyning', 3 Supracranial_basin / absent 'present (Abel 1905 Heyning 1989', 4 Prenarial_basin / absent 'present (True 1910 Mead 1975 He', 5 Premaxillae / symmetric asymmetric, 6 Premaxillae / left_premaxilla_lies_lateral_to _left_premaxilla_enters_left_na, 7 Premaxillae / do_not_contribute_to_vertex_of 'contribute to vertex (Moore 196', 8 Premaxillae / dorsomedial_surfaces_of_premaxi dorsomedial_surfaces_of_premaxi, 9 Premaxillae / thin_and_plate_to_like_over_ent thin_and_plate_to_like_anterior, 10 Fremaxillae / not_displaced_laterally_from_na displaced_laterally_from_narial, 11 Premaxillae / no_reduction_of_posterior_edge reduction_of_posterior_edge_of only_ieft_posterior_edge_of_pro, 12 Premaxillae_at_vertex_of_skull / do_not_project_more_anteriorly right_premaxilla_projects_more both_premaxillae_project_more_a, 13 Ascending_processes_of_premaxil / bosses_absent 'bosses present (Flower 1867 Mui', 14 Premaxillary_sac_fossae / present 'absent (Heyning 1989)', 15 Premaxillary_artery_grooves / posterolateral_groove_does_not posterolateral_groove_does_exte, 16 Premaxillary_foremen / absent present, 17 Premaxillary_foremen / round 'laterally compressed (Muizon 19', 18 Premaxillary_foremen_size / right_and_left_equal left_much_larger_than_right, 19 Premaxillary_crest / absent 'present (Moore 1968)', 20 Posterior_extremity_of_premaxil / 'not angled inward (faces anteri' 'angled inward (faces medially)', 21 Maxillary_to_premaxillary_sutur / separate fused, 22 Maxillae / abut_supraorbital_processes_of overlay_supraorbital_process_of, 23 Maxillae / no_crest low_crest_forms_on_supraorbital, 24 Maxillae / no_crest pneumatic_maxillary_crest_prese, 25 Medial_maxillary_processes / absent 'present (Muizon 1984 1988)', 26 Facial_depression_for_maxillona / absent 'present (Mead 1975)', 27 Rostral_portion_of_maxillae / not_constricted_at_proximal_bas 'constricted at proximal base (M', 28 'Antorbital tubercle (= maxillar' / absent 'present (Moore 1963 Heyning 198', 29 Antorbital_notch_at_base_of_ros / absent 'present (Moore 1963 Heyning 198', 30 Antorbital_process_at_base_of_r / lies_along_lateral_edge_of_cran lies_within_supracranial_basin, 31 Vomer / exposed_between_maxillae_on_pal not_exposed_between_maxillae_on, 32 Mesorostral_canal / not_ossified 'ossified (Moore 1963 Heyning 19', 33 Lacrimal_and_jugal_bones / not_fused 'fused (Flower 1869 Schulte 1917', 34 Number_of_nasal_bones / two one 'zero (Kuzmin 1977 Heyning 1989', 35 Shape_of_nasals_in_dorsal_view / anteroposteriorly_compressed 'anteroposteriorly elongate (Mui', 36 Nasal_protuberances / absent 'present (Muizon 1988)', 37 Nasals / do_not_extend_as_high_as_fronta are_same_height_as_frontals 'raised higher than frontals (Mu', 38 Nasals / right_nasal_lies_between_premax right_nasal_does_not_lie_betwee, 39 Anterior_surface_of_nasals / 'incline vertically (flat)' incline_posteriorly_to_vertical incline_convex incline_anteriorly_to_vertical, 40 Narial_fossae / do_not_face_ventrolaterally face_ventrolaterally, 41 Narial_fossae / symmetric left_much_larger_than_right, 42 Palatines / not_fused_with_maxillae 'fused with maxillae (Muizon 198', 43 Palatines / not_covered_by_pterygoids 'covered by pterygoids (Muizon 1', 44 Palatines / positioned_medially 'positioned laterally (Muizon 19', 45 Palatine_grooves / absent 'present (Muizon 1984)', 46 Lateral_plates_of_palatines / absent 'present (Muizon 1984 1988 1991)', 47 Lateral_plates_of_palatines / do_not_form_bony_bridge_over_or 'form bony bridge over orbit (Mu', 48 Pterygoids / meet_at_midline 'widely separated (Flower 1883 M', 49 Lateral_plate_of_pterygoids / present 'absent (Kellogg 1936 Fraser and', 50 Pterygoid_hamuli / small 'large (Heyning 1989 Muizon 1991', 51 Lateral_plates_of_pterygoid_ham / absent 'present (Muizon 1984)', 52 Pterygoid_hamuli / have_smooth_ventral_surface 'have ventral keels (Muizon 1988', 53 Pterygoid_hamuli / meet_at_midline separated, 54 Pterygoid_sinus / does_not_expand_into_temporal_f 'expands into temporal fossa (Mu', 55 Pre_and_postorbital_lobes_of_pt / absent 'present (Muizon 1988 Heyning 19', 56 Temporal_fossa / not_roofed_over_by_lateral_expa roofed_over_by_lateral_expansio, 57 Mesethmoid / not_expanded_posterodorsally 'expanded posterodorsally (Muizo', 58 Mesethmoid / roofed_over_by_nasals 'exposed dorsally (Miller 1923)', 59 Ethmoturbinal_bones / present 'absent (Yablokov 1964)', 60 Exposed_surface_of_frontals / greater_than_area_of_nasals less_than_or_equal_to_area_of_n, 61 Supraorbital_processes_of_front / not_raised_dorsally raised_dorsally angled_ventrally_and_greatly_el, 62 Supraorbital_processes_of_front / no_temporal_muscle_attachment 'temporal muscle attachment (Mea', 63 Frontals / not_excavated_by_air_sinus 'excavated by air sinus (Muizon', 64 Frontal_protuberance_on_vertex / absent 'present (Muizon 1984 1988)', 65 Spiny_process_of_the_squamosal / absent 'present (Muizon 1987)', 66 Cranial_hiatus / absent 'present (Heyning 1989)', 67 Posterior_sinus / absent 'present (Muizon 1984 1991)', 68 Mandibular_symphysis / extends_less_than_half_of_the_l extends_greater_than_half_of_th, 69 Mandibular_symphysis / mandibles_fused mandibles_connected_by_ligament, 70 Tooth_number_of_upper_jaw / 7_to_11_in_each_side_of_each_ja 'polydont (greater than 11 teeth' 'reduction of teeth (less than 7', 71 Tooth_number_of_lower_jaw / 7_to_11_in_each_side_of_each_ja 'polydont (greater than 11 teeth' 'reduction of teeth (less than 7', 72 Tooth_enamel / smooth reticulate 'nodular (Zhou 1982)', 73 Teeth / conical spatulate 'laterally compressed (Moore 196', 74 Teeth / deeply_rooted 'not deeply rooted (Moore 1968)', 75 Base_of_teeth / conical 'exhibit annular swelling (Muizo', 76 Accessory_shelf_on_posterior_te / absent 'present (Flower 1867)', 77 Upper_tooth_rows / separated_and_diverged tightly_spaced_and_run_parallel, 78 Teeth_in_females / erupt_in_adulthood 'do not erupt in adulthood (Moor', 79 Teeth_in_males / oriented_vertically incline_posteriorly 'incline anteriorly (Moore 1968)', 80 Enlarged_apical_mandibular_teet / absent 'present (Heyning 1989 Mead 1989', 81 Location_of_enlarged_apical_man / apical on_mandibular_symphysis posterior_to_mandibular_symphys, 82 Denticles_on_teeth / absent 'present (McCann 1962 Moore 1968', 83 Location_of_denticles_on_teeth / posterior_edge medial_edge between_medial_and_anterior_edg anterior_edge lateral_edge, 84 Tympano_to_squamosal_suture / present 'absent (Kasuya 1973 Muizon 1984', 85 Posterior_process_of_the_tympan / equal_to_or_greater_in_size_tha much_smaller_in_size_than_tympa, 86 Density_of_bone_of_posterior_pr / smooth_bone spiny_or_irregular_edges cauliflower_to_like_bony_growth 'rounded and pachyostotic (Kasuy', 87 Anterior_spine_of_the_tympanic / absent 'present (Kasuya 1973 Muizon 198', 88 Lateral_furrow_of_the_tympanic / absent shallow_groove 'deep well to defined groove (Ka', 89 Sigmoid_process_of_the_tympanic / anteriorly_to_anteroiaterally 'laterally to posterolaterally (', 90 Involucrum_of_tympanic / not_excavated 'excavated (Muizon 1988)', 91 Involucrum_of_tympanic / anterior_portion_not_expanded 'anterior portion expanded (Muiz', 92 Size_of_bone_of_anterior_proces / equal_to_or_greater_than_size_o much_smaller_than_pars_cochlea, 93 Anterior_process_of_periotic_an / present 'absent (ligamentous) (Heyning 1', 94 Posterior_process_of_periotic_a / present 'absent (ligamentous) (Fraser an', 95 Shape_of_bone_of_posterior_proc / robust 'thin plate (Kasuya 1973)', 96 Size_of_bone_of_posterior_proce / much_larger_than_pars_cochlea 'smaller than pars cochlea (Yama', 97 Articular_process_of_the_periot / absent 'present (Muizon 19#7 Messenger', 98 Styloid_process_on_the_anterior / absent 'present (Muizon 1988)', 99 Epitubarienne_fossa / absent 'present (Kellogg 1936 Muizon 19', 100 Internal_aperture_of_the_fallop / lies_within_internal_auditory_m does_not_lie_within_internal_au, 101 Internal_auditory_meatus / pyriform 'circular (Muizon 1984)', 102 Tuberculum_of_malleus / large_such_that_malleus_is_elon nearly_absent_such_that_the_mal, 103 Muscular_process_of_the_malleus / smaller_than_the_manubrium 'larger than the manubrium (Muiz', 104 Cervical_vertebrae / unfused C2_to_C7_fused C1_to_C7_fused 'Cl C2 fused (De Smet 1977 Romme', 105 Transverse_processes_of_the_lum / anterior_and_posterior_border_r 'triangular (Muizon 1984 1985 19', 106 Ventrolateral_processes_of_the / absent present_in_the_form_of_small_ra present_as_well_to_developed_el, 107 Coracoid_process_of_the_scapula / present 'absent (True 1904 Muizon 1984 1', 108 Acromion_process_of_the_scapula / lies_along_lateral_edge_of_scap lies_along_anterior_edge_of_sca, 109 Deltopectoral_tuberosity_of_hum / lies_at_proximal_end_of_humerus lies_midway_down_the_humeral_sh, 110 Olecranon_process_of_the_ulna / present_as_a_distinct_process present_as_a_slightly_raised_pr 'absent (Muizon 1984)', 111 Panbone_in_mandible / 'absent (mandible solid)' present, 112 False_gills / absent 'present (Leatherwood and Reeves', 113 Prenarial_basin / not_fat_filled fat_filled, 114 Spermaceti_organ / absent 'present (Norris and Harvey 1972', 115 Museau_de_singe / absent 'present (Norris 1964 Cranford e', 116 Throat_grooves / absent present, 117 Throat_groove_shape / multiple_parallel single_V_to_shaped irregular_in_number_and_shape, 118 Nasal_passages / separate separate_until_just_proximal_to confluent, 119 Nasal_passages / oriented_vertically angled_anteriorly, 120 Left_nasal_passage / straight U_to_shaped, 121 Melon / absent present, 122 Melon / small_compared_to_that_of_odont 'large (Heyning and Mead 1990)', 123 Melon / not_divided_by_connective_tissu divided_by_connective_tissue, 124 Melon / does_not_extend_into_right_nasa extends_into_right_nasal_plug, 125 Nasal_plug / symmetric asymmetric, 126 Nasal_plug / does_not_have_lateral_lips has_lateral_lips, 127 Cartilage_in_nasal_septum / absent present, 128 Blowhole_shape / comma_to_shaped_openings transverse_crescentic_apices_fa transverse_crescentic_apices_fa longitudinal_rectangle sigmoidally_shaped_longitudinal transverse_crescentic_apices_ac longitudinal_slit diagonal_V_to_shaped, 129 Blowhole_location / midpoint_of_rostrum apex_of_rostrum, 130 Blowhole_ligament / absent present, 131 Blowhole_ligament / not_appressed_against_skull appressed_against_skull, 132 Cartilage_in_blowhole_ligament / absent present, 133 Blowhole_ligament / not_attached_to_lateral_premaxi attached_to_lateral_premaxilla, 134 'Proximal sacs (nasal sac)' / absent present, 135 'Proximal sacs (nasal sac)' / modified_into_frontal_sac modified_into_inferior_vestibul, 136 'Distal sac (nasal sac)' / absent present, 137 Posterior_nasal_sacs / absent present, 138 Posterior_nasal_sacs / single divided, 139 'Nasofrontal sac (anterior secti' / absent present, 140 Nasofrontal_sac / anterior_sac_smooth anterior_sac_trabeculate, 141 'Premaxillary sacs (nasal sac)' / absent present, 142 'Premaxillary sacs (nasal sac)' / no_diverticula lateral_diverticula_in_right_pr, 143 Premaxillary_cleft / not_filled_with_connective_tiss filled_with_connective_tissue_a, 144 'Vestibular sac (nasal sac)' / absent present, 145 'Vestibular sac (nasal sac)' / not_pigmented lined_with_black_pigment, 146 'Vestibular sac (nasal sac)' / floor_not_rigid floor_rigid, 147 'Vestibular sac (nasal sac)' / undivided bilaterally_divided, 148 'Vestibular sac (nasal sac)' / right_and_left_side_same_size right_side_larger, 149 'Vestibular sac (nasal sac)' / no_intrinsic_muscle_in_sac intrinsic_muscle_in_sac, 150 'Vestibular sac (nasal sac) floo' / smooth wrinkled, 151 Inferior_vestibule / symmetric asymmetric, 152 'Accessory sacs (nasal sac)' / absent present, 153 Diagonal_membrane / absent present, 154 Spiracular_plate / smooth rugose, 155 Spiracular_cavity / slitlike round, 156 Pars_posteroexternus_muscle / absent present, 157 Pars_intermedius_muscle / absent present, 158 Pars_anteroexternus_muscle / does_not_extend_over_premaxilla extends_over_premaxilla, 159 Pars_posterointernus_muscle / absent present, 160 Pars_anterointernus_muscle / 1_insertion 2_insertion, 161 Vertex_muscle / absent present, 162 Rostral_muscle / absent present, 163 Rostral_muscle / does_not_originate_from_mandibl originates_from_mandible, 164 Sexual_dimorphism / males_larger_than_females females_larger_than_males 'males and females same size (Le', 165 Dorsal_fin / absent present 'dorsal hump (Leatherwood and Re', 166 Maxillae / abut_supraorbital_process extend_posteriorly_beneath_supr, 167 Temporal_crest / lies_at_ventral_surface_of_supr lies_at_dorsal_surface_of_supra, 168 Baleen / absent present, 169 Palate / narrow_with_flat_ventral_surfac wide_with_prominent_ventral_kee, 170 Rostrum / straight transversely_compressed_and_arc transversely_compressed_and_ext, 171 Mandible / mandibular_condyle_slightly_cur mandibular_condyle_rounded_and, 172 Dentary / narrow_and_straight expanded_and_arched_dorsoventra, 173 Squamosal / glenoid_fossa_and_zygomatic_por glenoid_fossa_and_zygomatic_por, 174 Pterygoids / do_not_reach_the_basicranium_po extend_posteriorly_beneath_basi, 175 Baleen_plates / 'short (less than 6% of body len' 'long (greater than 15% of body', 176 Nucleus_of_lateral_olfactory_ne / present 'absent (Pilleri and Gihr 1970)', 177 Ribs / first_rib_not_attached_to_cervi first_rib_attached_to_several_c, 178 Manus / pentadactyl 'tetradactyl (Yablokov 1964 Van', 179 Sternum / comprised_of_several_bones 'comprised of one bone (Yablokov', 180 Sternum / several_ribs_attach_to_sternum 'one rib attaches to sternum (Ya', 181 Tympanic_membrane / present_in_the_form_of_a_thin_c 'present in the form of "glove f', 182 Tympanic_bulla / not_attached_to_mandibular_ramu attached_to_posterior_margin_of, 183 Middle_ear_ossicles / ligamentous_attachment_to_bulla fused_to_bulla_and_joints_stiff, 184 Horizontal_caudal_fluke_for_pro / absent present, 185 Flippers_as_forelimbs / absent present, 186 External_hind_limbs / present absent, 187 Sacral_segment_of_the_vertebrae / present absen, 188 Cervical_vertebrae / not_compressed anteroposteriorly_compressed, 189 Haemal_arches_with_caudal_verte / absent present, 190 Rotational_movement_in_the_elbo / present absent, 191 Middle_ear_sinus / does_not_surround_region_of_tym extends_into_the_region_around, 192 Mandibular_foremen / small large, 193 External_hair / present absent_or_extremely_reduced, 194 Blubber / absent present, 195 Gall_bladder / present absent, 196 True_vocal_cords / present absent, 197 Palatine_foramina / present absent, 198 Falcate_processes_of_the_basioc / small large, 199 Maxillary_foramina / single multiple, 200 Vomer / does_not_extend_posteriorly_to extends_onto_basicranium_coveri, 201 Number_of_phalanges / three greater_than_3, 202 Eustachian_tube / does_not_enter_pterygoid_sinus expanded_into_pterygoid_sinus, 203 Primary_blood_supply_to_brain / by_way_of_internal_carotid_arte by_way_of_intravertebral_rete_m, 204 External_auditory_meatus / large_with_clear_opening_to_aud small_and_obstructed_by_dense_c, 205 Body / not_fusiform torpedo_shaped_or_fusiform, 206 Crus_longum_of_incus / elongate_and_thin shortened_and_greatly_inflated, 207 Mallear_joint_of_incus / opposite_crus_longum rotated_4¡ 'rotated 90¡ (Thewissen and Huss', ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 ] [ . . . . . . . . . . . . . . . . . . . . . ] Antilocapra_americanus 1000000000??0100??0?000000000?1000100??0000000?1000?1??000000?0000000000000?0000?0??????????00?????????0??0?0000?000?0?00?????10?0???0?00?0?0??0???????00??00?0?00?00000000000?00100000000000000000000000000000 Archaeoceti 1000000000??01?0??0?00000?000?1000100??0000000?1000?1??0?0?00??00?000000{02}00?0?00???0100100000000000010000000000??????????????????????????????????????????????????????000000000???000?????00010?0????11000????11 Balaena_mysticetus 10000010000?0100??0?000000000?1000101??0000000?100001??000002??00?00122????????0???00100???00000000??0?20000?000?000?00010??000700???0?00?0?0??0???????0???00?0?00?1011112001?10?011000111111111111111111111112 Balaenoptera_acutorostrata 10000000000?0100??0?000000000?0000101??0000000?100001000000000000000122????????0???00100?0000000000??0100000?000?001000010??000700???0?00?0?0??0???????????00?0?00?11111100000001111000111111111111111111111112 Balaenoptera_physalus 10000000000?0100??0?000000000?0000{01}01??0000000?100001000000000000000122????????0???00100?0000000000??01000000000?001000010??000700???0?00?0?0??0???????????00?0?00?11111100000001111000111111111111111111111112 Berardius_bairdii 01001010000000010010010001001?{01}{01}000020{12}0000000?01100010101100100000002202100000100?00202000011010011010?00000010?001121?1101111201110110110010?0???????11000001101011000000000?10000111111111111111111111111112 Bos_taurus 1000000001??0100??0?000000000?1000100??0000000?1000?1??000000?0000000000000?0000?0??????????00?????????0??0?0000?000?0?00?????10?0???0?00?0?0??0???????00??00?0?00?00000001000?00100000000000000000000000000000 Camelus_dromedarius 000000000???01????0??00000000?1000100??00?0?0??1000?1??000000?000?000000000?0000?0??????????00?????????0??0?0000?000?0?00?????10?0???0?00?0?0??0???????00??00?0?00?00000001000?00100000000000000000000000000000 Cephalorhynchus_commersoni 01000000002?0011000?010001001?1010001??00100011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11001111010001100?1010?11000011110011?10010?1000000000?10000111111111111111111111111112 Cephalorhynchus_eutropia 01000000002?0011000?010001001?1010001??00100011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11001111010001100?1010?11000011110011?10010?1000000000?10000111111111111111111111111112 Cephalorhynchus_heavisidii 01000000002?0011000?010001001?1010001??00100011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11001111010001100?1010?11000011110011?10010?1000000000?10000111111111111111111111111112 Cephalorhynchus_hectori 01000000002?0011000?010001001?1010001??00100011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11001111010001100?1010?11000011110011?10010?1000000000?10000111111111111111111111111112 Delphinapterus_leucas 11000000000?0{01}{01}1000?010011001?1010000??000000101{01}0001101111101000110000000000000?0?11100110111010000001011000110?000?21?1101111101010110111010?11010001111111?0001002000000000?10000111111111111111111111111112 Delphinus_delphis 01000000002?00010?0?010011001?1010001??00100011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Eschrichtius_robustus 10000000000?0100??0?000000001?0000101??0000000?100001000000000000000122????????0???00100?0000000000??0???0????00?001200010??000700???0?00?0?0??0???????????00?0?00?1211101??00001011000111111111111111111111112 Eubalaena_glacialis 10000000000?0100??0?000000000?1000{01}01??0000000?100001000000020000000122????????0???00100?0000000000??0120010?100?000?00010??000700???0?00?0?0??0???????????00?0?00?10111021{01}11101011000111111111111111111111112 Feresa_attenuata 01000000002?0001000?010011001?1010001??00000011010100111111101000110000000000000?0?11100110111010000000301001010?000?21?11011111010001100?1010?11000011110011?10010?1000000000?10000111111111111111111111111112 Globicephala_macrorhynchus 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10000000000000?0?111{01}0110111010000000301001010?000?21?11000111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Globicephala_melaena 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10000000000000?0?111{01}0110111010000000301001010?000?21?11000111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Grampus_griseus 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10000001000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001021000000000?10000111111111111111111111111112 Hyperoodon_planifrons 01001010100200010010110001001?{01}000002130000000?01100010101100100000002200100010100?002020000110100110?0200000010?001120?1101101101110110110010?0???????110000011010{01}1000000000?10000111111111111111111111111112 Inia_geoffrensis 01001001010?1101{01}00?010001001?0010000??10100111010000110011011010111011200010000?0?111{01}2110111010000{01}01012000210?000?21?1101101101000110110?10?110?10011100???000??02000000000?10000111111111111111111111111112 Kogia_breviceps 01101100000?0101010?01000100110012?????0100000?010000100011?01000000021000000000?0?00200001011110001010200000011?110?1?1110?101500???1010?0?0??0???????00?000?000??21000000000?10000111111111111111111111111112 Kogia_simus 01101100000?0101010?01000100110012?????0100000?010000100011?01000000020000000000?0?00200001011110001010200000011?11121?1110?101500???1010?0?0??0???????00?000?000??21000000000?10000111111111111111111111111112 Lagenodelphis_hosei 01000000002?0001000?010011001?1010001??00000011010110111111101000110011000000000?0?1110011?1110100?0001301001010?000?21?11011111010001100?1011?11000011110010?1001001000000000?10000111111111111111111111111112 Lagenorhynchus_acutus 01000000002?0001000?010001001?1010001??00000011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Lagenorhynchus_albirostris 01000000002?0001000?010001001?10{01}0001??000000110{01}0110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1011?11000011110010?10010?1000000000?10000111111111111111111111111112 Lagenorhynchus_australis 01000000002?0001000?010001001?1010001??00000011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Lagenorhynchus_cruciger 01000000002?0001000?010001001?1010001??00000011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Lagenorhynchus_obliquidens 01000000002?0001000?010001001?1010001??00000011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Lagenorhynchus_obscurus 01000000002?0001000?010001001?1010001??00000011010110111111101000110011000000000?0?1110011?1110100?0001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Lipotes_vexillifer 01000001010?0001000?010001101?{01}010000??10000011010110110011111000111011100000000?0?11112110111010110100010000210?000?21?1101111301000110111010?110?10010100???000??11000000000?10000111111111111111111111111112 Lissodelphis_borealis 01000000002?0001000?010011001?1010001??00000011010110111111101000110011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001000000000000?10000111111111111111111111111112 Lissodelphis_peronii 01000000002?0001000?010011001?10?0001??000000110?011?111111101000110011000000000?0?1110011?1110100?00?1301001010?000?21?11011111010001100?1010?11000011110011?1001010000000000?10000111111111111111111111111112 Megaptera_novaeangliae 10000000000?0100??0?000000000?0000101??0000000?100001000000000000000122????????0???00100?0000000000??0?0001??100?001000010??000700???0?00?0?0??0???????????00?0?00?11111100000001111000111111111111111111111112 Mesoplodon_bidens 01001010100200010010110001001?1100002130000000?011000101011001000000022021000111113002020000110100110?0?00000010?001120?1101101101111110101010?0???????110000111010?1000000000?10000111111111111111111111111112 Mesoplodon_carlhubbsi 01001010100200010010110001011?1100002130000000?0110001010110010000000220210001011120020200?0110100?1010?00000010?001120?1101101101111110101010?0???????110000101110?1000000000?10000111111111111111111111111112 Mesoplodon_densirostris 01001010100200010010110001001?1100002130000000?01100010101100100000002202100012120?002020000110100110?0?00000010?001120?1111101101111110100010?0???????11000011101121000000000?10000111111111111111111111111112 Mesoplodon_europaeus 01001010100200010010110001001?1100002130000000?01100010101100100000002202100010111100202000011010011010?00000010?001120?110110110111111010??10?0???????110000111010?1000000000?10000111111111111111111111111112 Mesoplodon_ginkgodens 01001010100200010010110001001?1100002130000000?011000101011001000000022021000101111002020000110100110?0?00000010?001120?110110110111111010??10?0???????110000111010?1000000000?10000111111111111111111111111112 Mesoplodon_grayi 01001010100200010010110001001?1100002130000000?0110001010110010000000220210001011110020200?0110100?1010?00000010?001120?110110110111111010??10?0???????110000111010?1000000000?10000111111111111111111111111112 Mesoplodon_hectori 01001010100200010010110001001?1100002130000000?0110001010110010000000220210001?10100020200?0110100?10?0?00000010?001120?110110110111111010??10?0???????110000111010?1000000000?10000111111111111111111111111112 Mesoplodon_layardii 01001010100200010010110001001?1100002130000000?0110001010110010000000220210001111140020200?0110100?10?0?00000010?001120?110110110111111010??10?0???????110000111010?1000000000?10000111111111111111111111111112 Mesoplodon_peruvianus 01001010100200010011110001001?11000010?0000000?011000101011001000?00022021000?0120?0??020000110100110?????????10?00112??11??????????????????????????????????????????1000000000?100?0???111111111111111111111112 Mesoplodon_stejnegeri 01001010100200010010110001001?1100002130000000?011000101011001000000022021000111213002020000110100110?0?00000010?001120?1101101101111110101010?0???????110000111011?1000000000?10000111111111111111111111111112 Monodon_monoceros 11000000000?0{01}{01}1000?010011001?1010000??00000010110001101111101000{01}10022000000100?0?1110011011101000000000100??10?000?21?1101111101000110111010?110?0001111111?0001000000000000?10000111111111111111111111111112 Neophocaena_phocaenoides 01000000001?1111000?010011001?1010010??10000011110101111011101110110011010000000?0?113011101110100000?1301001110?000?21?1101111101000110111110?11110111111001?1001000000000000?10010111111111111111111111111112 Orcaella_brevirostris 01000000002?0001000?010011001?1010001??00000011110101111111101000110011000000000?0?11100110111010000000301000110?000?21?11011111010001100?1010?11000011110011?1001021000000000?10000111111111111111111111111112 Orcinus_orca 01000000002?0001000?010011001?1010001??00000011010110111111101000110000000000000?0?111001101110100000?1301000110?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Peponocephala_electra 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Phocoena_phocoena 01000000001?1101100?010011001?1010010??100000111{01}0101111011101110110011010000000?0?11301110111010000001301001010?000?21?1100111101000110111110?11110111111001?10010?1000000000?10000111111111111111111111111112 Phocoena_sinus 01000000001?1101100?010011001?1010010??100000111{01}0101111011101110110011010000000?0?11301110111010000001301001010?000?21?1100111101000110111110?11110111111001?10010?1000000000?10000111111111111111111111111112 Phocoena_spinipinnis 01000000001?1111100?010011001?1010010??10000011110101111011101110110011010000000?0?11301110111010000001301001010?000?21?1101111101000110111110?1111?111111001?10010?1000000000?10000111111111111111111111111112 Phocoenoides_dalli 01000000001?1101100?010011001?1010010??1000001{01}1{01}0111111011101110{01}10011000000000?0?11301110111010000001301001010?000?21?1101111101000110111110?11110111111001?1001001000000000?10000111111111111111111111111112 Physeter_catadon 0110110000??0101010?010001001000{01}1000??0100000?010000100011001000001021000000000?0?002000010110100010??100000010?1112101110?100410???1010?0?0??0???????00?000?000??02000000000?10000111111111111111111111111112 Platanista_gangetica 01001001000?0001{01}00?010101001?1010000??0001100?000100010011001011111011000001000?0?0111210011001111010?00011?210?000?2??1101111601010110111010?0???????0100???000??12000000000?10000111111111111111111111111112 Pontoporia_blainvillei 00000001010?1111000?111001101?1010100??10100010000100110011101000111011000100000?0?1130211011111000000101100?210?000?21?1101101101000110110?10?110?10011100???000??11000000000?10000111111111111111111111111112 Pseudorca_crassidens 01000000002?0001000?010011001?1010001??0000001{01}010000111111101000110000000000000?0?1110011?1110100?0001301001010?000?21?11011111010001100?1010?11000011110010?1001001000000000?10000111111111111111111111111112 Sotalia_fluviatilis 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Sousa_chinensis 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Sousa_teuszii 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Stenella_attenuata 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Stenella_clymene 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Stenella_coeruleoalba 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Stenella_frontalis 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Stenella_longirostris 01000000002?0001000?010011001?1010001??00000011010110111111101000{01}10011000000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Steno_bredanensis 01000000002?0001000?010011001?1010001??00000011010110111111101000110011100000000?0?11100110111010000001301001010?000?21?11011111010001100?1010?11000011110010?10010?1000000000?10000111111111111111111111111112 Tasmacetus_shepherdi 01000010100100010010110001001?{01}000002000000000?01100010101100100000001100100000100?002020000110100110?0?00000010?001121?1101101101110110100010?0???????11000001101021000000000?10000111111111111111111111111112 Tayassua_tajacu 1000000000??01????0?100000000?1000100??0010000?1000?1??000000?0000000000000?0000?0??????????00?????????0??0?0000?000?0?00?????10?0???0?00?0?0??0???????00??00?0?00?00000001000?00100000000000000000000000000000 Tragulus_napu 0000000000??0100??0?000000000?1000100??00?000??1000?1??000000?000?000000000?0000?0??????????00?????????0??0?0000?000?0?00?????10?0???0?00?0?0??0???????00??00?0?00??0000001000?00100000000000000000000000000000 Tursiops_truncatus 01000000002?0001000?010011001?1010001??00000011010110111111101000110011000000000?0?111{01}0110111010000001301001010?000?21?11011111010001100?1010?11000011110011?1001001000000000?10000111111111111111111111111112 Ziphius_cavirostris 01011010100000010{01}11110001001?{01}100102020000000?01100010101100100000002200100010100?00202000011010011010?000000101001120?110110110111011010001010???????11000001101021000000000?10000111111111111111111111111112 ; END; [ The following blocks are output data for analysis step 308 ] BEGIN TREES; TITLE Tb5088; LINK TAXA = TaxaForAnalysisStep308; TREE Fig._1 = [&R] (Antilocapra_americanus,(Bos_taurus,Tayassua_tajacu,(Tragulus_napu,Camelus_dromedarius)),(Archaeoceti,(((Balaena_mysticetus,Eubalaena_glacialis),(Eschrichtius_robustus,(Balaenoptera_physalus,Megaptera_novaeangliae,Balaenoptera_acutorostrata))),((Physeter_catadon,(Kogia_breviceps,Kogia_simus)),((Berardius_bairdii,(Tasmacetus_shepherdi,(Ziphius_cavirostris,(Hyperoodon_planifrons,((Mesoplodon_peruvianus,Mesoplodon_densirostris),(Mesoplodon_hectori,(Mesoplodon_grayi,Mesoplodon_ginkgodens,Mesoplodon_carlhubbsi,Mesoplodon_europaeus,(Mesoplodon_layardii,Mesoplodon_bidens,Mesoplodon_stejnegeri)))))))),(Platanista_gangetica,(Lipotes_vexillifer,((Inia_geoffrensis,Pontoporia_blainvillei),((Monodon_monoceros,Delphinapterus_leucas),(Phocoena_phocoena,Phocoena_spinipinnis,Phocoenoides_dalli,Neophocaena_phocaenoides),(Orcaella_brevirostris,(Peponocephala_electra,Feresa_attenuata,Pseudorca_crassidens,Orcinus_orca,Steno_bredanensis,Lagenorhynchus_obscurus,Delphinus_delphis,Tursiops_truncatus,Cephalorhynchus_eutropia,Grampus_griseus,(Lagenorhynchus_albirostris,Lagenodelphis_hosei),(Lissodelphis_peronii,Lissodelphis_borealis),(Globicephala_melaena,Globicephala_macrorhynchus)))))))))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1479] END; BEGIN TREES; TITLE Tb5088; LINK TAXA = TaxaForAnalysisStep308; TREE Fig._3 = [&R] (Antilocapra_americanus,(Bos_taurus,Tayassua_tajacu,(Tragulus_napu,Camelus_dromedarius)),(Archaeoceti,((Balaena_mysticetus,(Eschrichtius_robustus,(Balaenoptera_physalus,Megaptera_novaeangliae))),((Physeter_catadon,(Kogia_breviceps,Kogia_simus)),((Ziphius_cavirostris,(Mesoplodon_peruvianus,Mesoplodon_europaeus)),(Inia_geoffrensis,(Delphinapterus_leucas,((Phocoena_spinipinnis,Phocoena_phocoena),(Delphinus_delphis,Tursiops_truncatus,Lagenorhynchus_albirostris,Lagenorhynchus_obscurus,Lissodelphis_peronii,Globicephala_melaena,Cephalorhynchus_eutropia))))))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1481] END; BEGIN TREES; TITLE Tb5088; LINK TAXA = TaxaForAnalysisStep308; TREE Fig._2 = [&R] (Antilocapra_americanus,(Bos_taurus,Tayassua_tajacu,(Tragulus_napu,Camelus_dromedarius)),(Archaeoceti,(((Balaena_mysticetus,Eubalaena_glacialis),(Eschrichtius_robustus,(Balaenoptera_physalus,Megaptera_novaeangliae,Balaenoptera_acutorostrata))),((Physeter_catadon,(Kogia_breviceps,Kogia_simus)),((Berardius_bairdii,(Tasmacetus_shepherdi,(Ziphius_cavirostris,(Hyperoodon_planifrons,((Mesoplodon_peruvianus,Mesoplodon_densirostris),(Mesoplodon_hectori,Mesoplodon_europaeus)))))),(Platanista_gangetica,(Lipotes_vexillifer,(Inia_geoffrensis,Pontoporia_blainvillei),((Monodon_monoceros,Delphinapterus_leucas),(Neophocaena_phocaenoides,(Phocoenoides_dalli,Phocoena_phocoena)),(Orcaella_brevirostris,(Delphinus_delphis,Tursiops_truncatus,(Lagenorhynchus_albirostris,Lagenodelphis_hosei),(Lissodelphis_peronii,Lissodelphis_borealis),(Globicephala_melaena,Globicephala_macrorhynchus))))))))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1478] END; BEGIN TREES; TITLE Tb5088; LINK TAXA = TaxaForAnalysisStep308; TREE 'Fig. 1+' = [&R] (Antilocapra_americanus,(Bos_taurus,Tayassua_tajacu,(Tragulus_napu,Camelus_dromedarius)),(Archaeoceti,(((Balaena_mysticetus,Eubalaena_glacialis)Balaenidae,(Eschrichtius_robustus,(Balaenoptera_physalus,Megaptera_novaeangliae,Balaenoptera_acutorostrata)Balaenopteridae))Mysticetes,((Physeter_catadon,(Kogia_breviceps,Kogia_simus))Physeteridae,((Berardius_bairdii,(Tasmacetus_shepherdi,(Ziphius_cavirostris,(Hyperoodon_planifrons,((Mesoplodon_peruvianus,Mesoplodon_densirostris),(Mesoplodon_hectori,(Mesoplodon_grayi,Mesoplodon_ginkgodens,Mesoplodon_carlhubbsi,Mesoplodon_europaeus,(Mesoplodon_layardii,Mesoplodon_bidens,Mesoplodon_stejnegeri))))))))Ziphiidae,(Platanista_gangetica,(Lipotes_vexillifer,((Inia_geoffrensis,Pontoporia_blainvillei),((Monodon_monoceros,Delphinapterus_leucas)Monodontidae,((Phocoena_phocoena,Phocoena_sinus),Phocoena_spinipinnis,Phocoenoides_dalli,Neophocaena_phocaenoides)Phocoenidae,(Orcaella_brevirostris,((Peponocephala_electra,Stenella_clymene,Stenella_attenuata,Sousa_teuszii,Sousa_chinensis,Stenella_longirostris,Stenella_frontalis,Stenella_coeruleoalba,Sotalia_fluviatilis),Feresa_attenuata,Pseudorca_crassidens,Orcinus_orca,Steno_bredanensis,(Lagenorhynchus_obscurus,Lagenorhynchus_obliquidens,Lagenorhynchus_cruciger,Lagenorhynchus_australis,Lagenorhynchus_acutus),Delphinus_delphis,Tursiops_truncatus,(Cephalorhynchus_eutropia,Cephalorhynchus_hectori,Cephalorhynchus_heavisidii,Cephalorhynchus_commersoni),Grampus_griseus,(Lagenorhynchus_albirostris,Lagenodelphis_hosei),(Lissodelphis_peronii,Lissodelphis_borealis),(Globicephala_melaena,Globicephala_macrorhynchus)))Delphinidae))))))Odontocetes))Cetacea); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1480] END;