#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 September 06, 2025; 8:26 GMT TreeBASE (cc) 1994-2008 Study reference: Wolfe J.M., & Hegna T.A. 2013. Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages. Cladistics, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13368] [ The following blocks are input data for analysis step 11980 ] BEGIN TAXA; TITLE TaxaForAnalysisStep11980; DIMENSIONS NTAX=121; TAXLABELS Argulus_japonicus_1 Argulus_japonicus_2 Argulus_japonicus_3 Argulus_japonicus_4 Argulus_japonicus_5 Argulus_japonicus_6 Argulus_japonicus_7 Baccalaureus_falsiramus_Adult Baccalaureus_falsiramus_Ascothoracid_larva Baccalaureus_falsiramus_Nauplius_1 Baccalaureus_falsiramus_Nauplius_2 Baccalaureus_falsiramus_Nauplius_3 Baccalaureus_falsiramus_Nauplius_4 Baccalaureus_falsiramus_Nauplius_5 Baccalaureus_falsiramus_Nauplius_6 Bredocaris_admirabilis_1 Bredocaris_admirabilis_2 Bredocaris_admirabilis_3 Bredocaris_admirabilis_4 Bredocaris_admirabilis_5 Bredocaris_admirabilis_6 Darwinula_stevensoni_1 Darwinula_stevensoni_2 Darwinula_stevensoni_3 Darwinula_stevensoni_4 Darwinula_stevensoni_5 Darwinula_stevensoni_6 Darwinula_stevensoni_7 Darwinula_stevensoni_8 Darwinula_stevensoni_9 Derocheilocaris_remanei_1 Derocheilocaris_remanei_2 Derocheilocaris_remanei_3 Derocheilocaris_remanei_4 Derocheilocaris_remanei_5 Derocheilocaris_remanei_6 Derocheilocaris_remanei_7 Derocheilocaris_remanei_8 Derocheilocaris_remanei_9 Eubranchipus_grubii_1 Eubranchipus_grubii_2 Eubranchipus_grubii_3 Eubranchipus_grubii_Adult Glomeris_marginata_Adult Hesslandona_angustata_1 Hesslandona_angustata_2 Hesslandona_unisulcata_6 Hutchinsoniella_macracantha_1 Hutchinsoniella_macracantha_10 Hutchinsoniella_macracantha_11 Hutchinsoniella_macracantha_12 Hutchinsoniella_macracantha_13 Hutchinsoniella_macracantha_14 Hutchinsoniella_macracantha_15 Hutchinsoniella_macracantha_16 Hutchinsoniella_macracantha_17 Hutchinsoniella_macracantha_18 Hutchinsoniella_macracantha_2 Hutchinsoniella_macracantha_3 Hutchinsoniella_macracantha_4 Hutchinsoniella_macracantha_5 Hutchinsoniella_macracantha_6 Hutchinsoniella_macracantha_7 Hutchinsoniella_macracantha_8 Hutchinsoniella_macracantha_9 Hutchinsoniella_macracantha_Adult Klausmuelleria_salopensis Labidocera_aestiva_Adult Labidocera_aestiva_Copepodid_1 Labidocera_aestiva_Copepodid_2 Labidocera_aestiva_Copepodid_3 Labidocera_aestiva_Copepodid_4 Labidocera_aestiva_Copepodid_5 Labidocera_aestiva_Nauplius_1 Labidocera_aestiva_Nauplius_2 Labidocera_aestiva_Nauplius_3 Labidocera_aestiva_Nauplius_4 Labidocera_aestiva_Nauplius_5 Labidocera_aestiva_Nauplius_6 Lepas_anatifera_Cyprid Lepas_anatifera_Nauplius_1 Lepas_anatifera_Nauplius_2 Lepas_anatifera_Nauplius_6 Manawa_staceyi_4 Manawa_staceyi_6 Nebalia_brucei_Adult Nebalia_sp._g Nebalia_sp._i Orchestia_cavimana_3 Orchestia_cavimana_4 Orchestia_cavimana_5 Orchestia_cavimana_6 Orchestia_cavimana_Hatchling Pleomothra_apletocheles_1 Pleomothra_apletocheles_Adult Porcellio_scaber_14 Porcellio_scaber_15 Porcellio_scaber_16 Porcellio_scaber_17 Porcellio_scaber_18 Porcellio_scaber_Manca_1 Porcellio_scaber_Manca_2 Rehbachiella_kinnekullensis_A_14_ts10a Rehbachiella_kinnekullensis_A_2_l2a Rehbachiella_kinnekullensis_B_17_ts13b Rehbachiella_kinnekullensis_B_4_l4b Rehbachiella_kinnekullensis_B_8_ts4b Triops_cancriformis_1 Triops_cancriformis_2 Triops_cancriformis_3 Triops_cancriformis_4 Triops_cancriformis_5 Triops_cancriformis_Adult Vargula_hilgendorfii_1 Vargula_hilgendorfii_2 Vargula_hilgendorfii_3 Vargula_hilgendorfii_4 Vargula_hilgendorfii_5 Yicaris_dianensis_1 Yicaris_dianensis_2 Yicaris_dianensis_3 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M18996] TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; DIMENSIONS NCHAR=146; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4 5 6 7 8 9 E F I J L O P Q X" MISSING=? GAP= -; CHARSTATELABELS 1 Antennule / absent rudimentary_limb_bud present, 2 'Antennule, with a secondary annulated branch (flagellum)' / flagellum_absent present, 3 'Antennule, with a tertiary branch (flagellum)' / tertiary_flagellum_absent present, 4 'Antennule, with a scale' / absent present, 5 'Antennule, number of annulations' / not_annulated two three four_ five six seven eight_ nine ten_or_more, 6 'Antennule, extent of setation' / 'setation setae/sensilla not confined to tip' 'setae/sensillae confined to tip' No_setae, 7 'Antennule, insertion of anterior setae' / seta_absent setae_insert_medially_ setae_insert_anteriorly, 8 Distinctive_large_seta_on_antennule / large_seta_absent present, 9 Aesthetascs_on_antennule / hundreds_ one_on_every_or_almost_every_antennular_segment only_a_few_aesthetascs_situated_distally_on_the_antennule No_aesthetascs, 10 'Antennule, shape ' / 'shape elongate, tubular' as_small_buds 'as horn-like structure' with_proximal_hook as_chelicerae Sacculina_Cyprid, 11 'Antennule, positioning' / remain_separate 'basally close to each other in "''V"''-shaped pattern', 12 Antennule_with_an_attachment_disc_covered_with_cuticular_villi / absent present, 13 'Antennule with (motile) distal claw for mechanical attachment' / absent present, 14 Antenna / absent rudimentary_limb_bud present, 15 'Antennae, length of protopod' / length_of_protopod_less_than_half_total_length_of_limb more_than_half_total_length_of_limb protopod_undifferentiated, 16 'Antenna with masticatory/arthritic/gnathobasic process' / absent present, 17 'Antenna, morphology of masticatory process' / 'cluster of about 2-5 spines' divided_in_two_branches single_spine 'brush-like fringe of stiff bristles', 18 'Antenna, anterior branch of masticatory process' / 'with brush-like setae' 'with single comb-row' no_visible_setae, 19 Antennal_endopod / absent present, 20 'Antenna, endopod setation' / endopod_setation_not_distal_setation_alone only_distal_setation no_setation, 21 'Second antennae: exopod' / absent present, 22 'Antenna, number of setae on exopod' / many seven six five two None, 23 'Second antennae: basipodite' / with_small_segment_absent present, 24 Antennal_endopod_segments / endopod_not_clearly_divided_into_segments two_clear_segments three_clear_segments four_clear_segments five_segments six_segments Flagellum, 25 'Antennal exopod multi-annulated' / 'not multiannulated or paddle-shaped' multiannulated, 26 'Second antennal exopod paddle-shaped' / 'not paddle-shaped' 'exopod forms a leaf-shaped paddle ', 27 Antennal_exopod_setation_type / no_setae single_row_of_setae_on_inner_surface 'plumose/feathered', 28 'Antenna, segmentation of exopod' / segments_of_same_size_or_gradually_getting_smaller_distally 'one or two small segments proximally, followed by larger segment, again followed by three setae-bearing segments' Original_segmentation_obscurred_by_the_fusion_of_segments, 29 Antenna_with_proximal_endite / absent present, 30 Proximal_endite_on_antenna_is_enlarged_to_form_a_coxa / median_structure coxa, 31 Mandible / absent rudimentary_limb_bud present, 32 'Mandibular endopod (palp)' / absent present, 33 'Mandible, segmentation of endopod' / three_segments_ two_segments segmentation_indistinct one_segment 'none"-coxa only' four, 34 'Mandibular palp: setation of endopod segment 1' / more_than_two_setae two_setae one_seta no_setae, 35 'Mandibular palp as filter screen of >3 setae' / absent present, 36 Mandibular_exopod / absent present, 37 'Mandibular exopod multi-annulated' / 'paddle-shaped or a lamellae-bearing shaft' made_up_of_a_number_of_tubular_articles_, 38 'Mandibular exopod paddle-shaped' / 'multi-annulated or a lamellae-bearing shaft ' 'exopod forms a leaf-shaped paddle ', 39 Exopods_of_mandibular_segments_with_inwardly_directed_setae / absent row_of_setae 'plumose/feathered', 40 'Mandibular exopod with 3-2 setation pattern' / absent present, 41 Mandible_with_proximal_endite / absent present, 42 Proximal_endite_of_mandible_enlarged_to_form_a_coxa / median_structure coxa, 43 Mandibular_coxa_fused_with_basis / separate_coxa_and_basis '"normal" coxal podomere secondarily fused with basis' coxa_only, 44 Mandibular_basis_with_toothed_endite / absent present, 45 Mandibular_gnathal_edge / consisting_of_molar_and_incisor_process_ only_ellipsoid_molar_present number_of_teeth_arranged_in_a_row shovel_with_terminal_teeth 'series of 1-3 long spines' 'none (larval)' '''blade'' with one plumose seta', 46 'Mandible: row of teeth along edge of molar surface' / absent present, 47 Maxillule / absent__ rudimentary_limb_bud present, 48 Maxillular_exopod / absent present, 49 'Maxillular exopod multi-annulated' / 'paddle-shaped or a lamellae-bearing shaft' made_up_of_a_number_of_slightly_flattened_tubular_articles_, 50 'Maxillular exopod paddle-shaped' / 'multi-annulated or a lamellae-bearing shaft ' 'exopod forms a leaf-shaped paddle', 51 Maxillular_exopod_reaching_into_arthrodial_membrane / 'exopod arises from limb stem, does not reach into arthrodial membrane' basipod_not_completely_closed_sclerotised_ring, 52 Maxillular_exopod_modification_as_branchial_plate / absent present, 53 Maxillule_with_proximal_endite / absent present, 54 Maxillular_palp / absent present, 55 Maxillule_differentiated_from_thoracopods / differentiated not_differentiated, 56 'Maxillular modification (Branchiura)' / absent hooks suction_discs, 57 Maxillular_endopod_chelate_ / absent present, 58 Maxilla / absent rudimentary_limb_bud present, 59 Maxillary_exopod / absent present, 60 'Maxillary exopod multi-annulated' / 'paddle-shaped or lamellae-bearing shaft' made_up_of_a_number_of_slightly_flattened_tubular_articles_, 61 'Maxillary exopod paddle-shaped' / 'multi-annulated or a lamellae-bearing shaft ' 'exopod forms a leaf-shaped paddle', 62 Maxillary_exopod_reaching_into_limb_membrane / 'exopod arises from limb stem, does not reach into arthrodial membrane' basipod_not_completely_closed_sclerotized_ring, 63 Maxilla_with_proximal_endite / absent present, 64 Epipodite_on_maxilla / absent present, 65 Maxilla_with_tooth / absent present, 66 Maxilla_as_labium / absent present, 67 'Maxillary palp (labial palp)' / absent composed_of_3_or_4_segments 'short, unsegmented, or replaced by a row of short setae' transformed_into_a_setigerous_plate transformed_into_labella, 68 Maxillary_endopod_chelate / absent present, 69 Maxilla_differentiated_from_thoracopods / differentiated not_differentiated, 70 Labrum / absent present, 71 'Labrum, number of major posterior spines' / none one three four '>four', 72 Labrum_reduced / absent 'present (reduced)', 73 Sternum / unfused fused, 74 Paragnaths / absent present, 75 'Post-cephalic filter feeding apparatus with sternitic food groove' / absent present, 76 'Postmandibular limbs with limb base differentiated as basipod + coxa' / absent present, 77 'Protopodite of post-mandibular limbs elongate, fleshy, extended as numerous soft, setiferous endites ' / absent present, 78 'First thoracopod (sixth limb)' / absent present, 79 First_thoracopod_as_maxilliped / normal transformed_into_maxilliped, 80 Epipodite_on_maxilliped_respiratory / absent present, 81 'Second thoracopod (seventh limb)' / absent present, 82 Seventh_limb_as_cleaning_limb / absent 'present, articulated' 'present, vermiform', 83 'Third thoracopod (eighth limb)' / absent present, 84 Number_of_additional_thoracic_limbs / none one two three four five six seven eight nine_or_more, 85 'Eighth thoracopod modified into small, subspherical appendages' / absent present, 86 'Trunk limbs, dorsal lobe of exopods' / absent small long, 87 'Sixth limb, number of endites' / about_eight six five less_than_five_ 'none/undifferentiated/indistinct' one, 88 Trunk_limbs_with_lobate_endites_formed_by_folds_in_limb_bud / absent present, 89 Thoracopods_with_epipodites / absent present, 90 'Thoracopod epipodites paddle-shaped' / absent present, 91 'Trunk limb tips, developmental direction' / points_ventrally points_laterally, 92 'Intercoxal sclerites on thoracopods 2-6' / absent 'present (as couplers)', 93 Denticles_on_limbs / absent present, 94 Differentiated_pleopods / absent present, 95 Number_of_pleopods / one two 'three (pleopods 1, 2, & 3)' 'three (third to fifth pleopods missing)' four five six, 96 Uropods / absent present, 97 Gonopods / absent gonopods_formed_from_one_pair_of_limbs_in_males 'genitals in both sexes (gonopods) formed from two pairs of limbs', 98 Paired_thoracic_dorsal_setae / Absent present, 99 Annulated_caudal_filament / absent present, 100 'Furcal rami/cerci' / absent present 'present, not multi-annulated (reduced to buds with or without setae)', 101 Furcal_position / 'terminal, in line with anus' posterior_to_anus anterior_to_anus, 102 Furcal_setae / absent present, 103 Telson_shape / round laterally_depressed 'dorso-ventrally depressed', 104 Dorsal_pair_of_telsonal_setae / absent present, 105 Dorsocaudal_spine / absent present, 106 Telson_cleft / absent 'distinct, shallow to almost reaching the base', 107 Caudal_papilla / absent 'present, anteroventrally folded, derived from preanal growth zone', 108 Caudal_process / absent present, 109 Body_segmentation_externally_visible / absent present, 110 Toothed_furrows / absent type_1_with_5_lobes 'type 1 with 4 lobes (forming X-shape)', 111 Tergopleural_outgrowths / absent present, 112 Coxal_plates / absent present, 113 Number_of_somites / three five eight nine 10 11 12 13 14 15 16 18 19 20 21 22 24 25_or_more, 114 'Neck (dorsal) organ' / absent present, 115 Lattice_organs / absent present, 116 Carapace / absent present, 117 Presence_of_headshield / absent present, 118 Headshield_extension / 'develops as a simple posterior extension of the head shield to cover post-cephalic body' headshield_fuses_with_paired_carapace_anlagen_to_cover_postcephalic_limbs 'absent (does not extent to cover post-cephalic body)', 119 Cephalic_shield_continuous_with_free_trunk_dorsum / absent present, 120 Cephalic_shield_with_distinct_facetotectan_ridges / absent present, 121 Carapace_with_distinct_hinge_line / absent 'Dorsal fold or crease (carina) along the midline' 'discrete valves physically separated at the midline (hinge)', 122 Ventral_extent_of_the_carapace / Carapace_partially_covers_limbs Carapace_can_enclose_limbs_with_the_margins_of_the_carapace_meeting_ventrally 'Carapace small (larval)', 123 Dorsal_area_of_bivalved_carapace / with_dorsal_furrow with_interdorsum, 124 Incisur / absent present, 125 Doublure / absent present, 126 'Frontolateral horns/pores' / absent present, 127 Frontal_filaments / absent present, 128 Rostrum / absent present_and_fused_to_head present_and_hinged_to_head, 129 Carapace_adductor_muscles / absent present, 130 Postoral_adductor_muscle / absent present, 131 'Carapace molt retention (i.e. ''growthlines'')' / absent present, 132 Corpora_allata / absent present, 133 Wings / absent present, 134 Number_of_median_eyes / none one two three four, 135 'Naupliar eye, number of ocelli' / three four, 136 Number_of_lateral_eyes / none one two, 137 Number_of_compound_eyes / none two, 138 Internalized_compound_eyes / absent present, 139 'Head/mouth orientation' / 'prognathous, mouth directed anteroventrally' 'hypognathous, mouth directed ventrally' mouth_directed_posteriorly, 140 Gut / present absent_or_reduced, 141 Bellonci_organ / absent present, 142 Dorsal_heart_with_segmental_ostia_and_pericardial_sinus / absent present, 143 'Role of serosa (= cuticle secreting membrane) in definitive dorsal closure (formation of dorsal body wall)' / serosa_and_embryo_contribute_to_definitive_dorsal_closure 'provisional dorsal closure (serosa degenerates without contributing to definitive dorsal closure)', 144 Differentiation_of_amnion_as_provisional_dorsal_closure_of_embryo / absent present, 145 'Blastodermal cuticle (cuticular egg envelope)' / absent present, 146 'Ectoteloblasts (forming part of metanaupliar/egg-naupliar region of germ band)' / absent present_, ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 ] [ . . . . . . . . . . . . . . ] Argulus_japonicus_1 2000200033000200--1010?20022??21300-----??????20----??01?20---?0000?0?????0?010-0-00-04-0-0-00-00002?1200?001000??01110000-0000000000??010?0?????? Argulus_japonicus_2 2000200033000200--100-?3----??20--------????2-20----??01?20---?0000?0?????0?010-1011-04-0-?000-00002?1200?00?000??01110000-0000000000??010?0?????? Argulus_japonicus_3 2000200033000200--100-??----??20--------??????20----??02?20---?0000?0?????0?010-1011-04-0-?000-00002?1200100?000??01110000-0000000000??010?0?????? Argulus_japonicus_4 2000200033000200--100-?3----??20--------??????20----??02?20---?0000?0?????0?010-1011-04-0-?000-00002?1200100?000??01110000-0000000000??010?0?????? Argulus_japonicus_5 2000200033000200--100-?3----??20--------??????20----??02?20---?0000?0?????0?010-1011-04-0-?000-00000--200100?000??01110000-0000000000??010?0?????? Argulus_japonicus_6 200020003300020???1?0-??----??20--------??????20----??02?20---?0000?0?????0?010-1011-04-0-?000-00000--200100?000??01110000-0000000000??010?0?????? Argulus_japonicus_7 200020003300020???1?0-??----??20--------????2-20----??02?20---?0000?0101110?010-1011-04-0-?000-0?000--2001000000??01110000-00000000003?010?0?1???? Baccalaureus_falsiramus_Adult 200030?0200010----------------20---1001????0??2?00????0002?????000000100?00??10-101200400-?0?0-0?001?100000010009?110-0-21-0?000?10000-00-?0?????? Baccalaureus_falsiramus_Ascothoracid_larva 200050?0200012????1?1?????????2?????00?????0??2?00????0002?????000000100?00??10-101300400-?010-0?001?1000?0?10009?110-0-21-0?010??0001?00-???????? Baccalaureus_falsiramus_Nauplius_1 2000?0?0?0000200--1013100010??212-011010???05-0----------0-----------101?00--0--0-00---------0-00002?1200?010000???01000-----000??-001?00-?1?????? Baccalaureus_falsiramus_Nauplius_2 200040?0?0000200--1011121010??2101011010???05-1----------0-----------101?00--0--0-00---------0-00002?1200?010000???01000-----010??-001?00-?1?????? Baccalaureus_falsiramus_Nauplius_3 200030?0?0000200--1010121010??2101011010???05-1--------0-0-----------101?00--0--0-00---------0-00002?12001010000???01000-----010??-001?00-?1?????? Baccalaureus_falsiramus_Nauplius_4 2000?0?0?0000200--1010121010??2101011010???05-1--------0-0-----------101?00--0--0-00---------0-00002?12001010000???01000-----010??-001?00-?1?????? Baccalaureus_falsiramus_Nauplius_5 2000?0?0?0000200--1010121010??2101011010???05-1--------0-1-----------101?00--0--0-00---------0-00002?12001010000???01000-----010??-001?00-?1?????? Baccalaureus_falsiramus_Nauplius_6 200030?0?0001200--1010121010??2101011010???0??1--------0-1-----------101?00--0--0-00---------0-00002?12001010000???01000-----010??-001?00-?1?????? Bredocaris_admirabilis_1 200090?1?0000200--1010??10101121000110101100??11-----0-000-----------100??0000--0-00--------10-00001010000010000?10010?0----000010-?00-010???????? Bredocaris_admirabilis_2 200090?1?0000200--1010??101011210001101011003?21100010-000-----------100??0000--0-00-------010-00001010000010000?10010?0----000010-?00-010???????? Bredocaris_admirabilis_3 200090?1?0000200--1010??101011210001101011003?211000100002??????-??-?100??00010-1000-0?00-?010-00001010000010000?10010?0----000010-?00-010???????? Bredocaris_admirabilis_4 200090?1?0000200--1010??101011210001101011003?21100010000211001000001100??00010-1011-0?00-?010-00001010000010000?10010?0----000010-?00-010???????? Bredocaris_admirabilis_5 200090?1?0000200--1010??101011210001101011003?21100010000211001000001100??00010-101?-0?00-?010-00001010000010000?10010?0----000010-?00-010???????? Bredocaris_admirabilis_6 200090?1?0000200--10101?1010112100011010110030211000100002110010000011001100010-1017-0000-?010-00001010000010000?10010?0----000010-?00-010???????? Darwinula_stevensoni_1 2000400030000200--111512000211210000----1100300----------0-----------1????0000--0-00------?-00-0000120?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_2 2000401020000200--10141200021121000100001100301--------000-----------1????0000--0-00------?-00-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_3 2000401020000200--10141200021121000100001100302100?1?0-000-----------1????0000--0-00------?-00-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_4 2000401020000200--10141200021121001100001100302100?1?10001-----------1????0000--0-00------?--0-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_5 2000401020000200--10141200021121001100001100302100?1?10002100??00000-1????00010-0-00---00-?-00-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_6 2000401020000200--10141300021121001100001100302100?1?10002100??0000011????00010-1000---00-?-00-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_7 2000401020000200--10141300021121001100001100302100?1?10002100??0000011????00010-1000---00-?-00-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_8 2000401020000200--10141300021121001100001100302100?1?10002100??0000011????00010-1000---00-?-00-0000121?000000000??010-0-21-010001?000??00-2000???? Darwinula_stevensoni_9 2000401020000200--10141300021121001100001100302100?1?10002100??0000011????00010-1000---00-?-00-0100121?000000000??010-0-21-010001?0003?00-2000???? Derocheilocaris_remanei_1 20007000?0000201101010?2101011210?0110101100??20----1?-000-----------100??0?00--0-00---------0-00002?100100011002?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_2 20007000?0000201101010?2101011210?0110101100??20----1?-000-----------100??0?00--0-00---------0-00001?100000011004?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_3 20007000?0000201101010?2101011210?0110101100??20----1?-000-----------1?0??0?00--0-00---------0-00001?10000001100??0010-0-----00000-00??00-???????? Derocheilocaris_remanei_4 20007000?0000201101010?2101011210?0110101100??20----1??001------0000-1?00?0?00--0-01---------0-00001?100000011007?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_5 20007000?0000201101010?2101011210?0110101100??20----1?0001------0000-1?01?0?01101011---------0-00001?10000011?008?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_6 20007000?0000201101010?2101011210?0110101100??20----1?00020---10000001?01?0?01101012-0300-?000-00001?10000011?008?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_7 20007000?0000200--1010?2101011210?0110101100??20----1?00020---10000001?01?0?01101012-0300-?000-00001?100000112008?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_8 20007000?0000200--1010?2101011210?0110101100??20----1?00020---10000001?01?0?01101012-0300-?000-00001?100000112008?0010-0-----00000-00??00-???????? Derocheilocaris_remanei_9 2000700020000200--1010?2101011210201101011002-20----1?00020---1000000100110?01101012-0300-?000-0?001?100000112008?0010-0-----00000-004?00-2?1????? Eubranchipus_grubii_1 20000100300002112011100010100-210100--0-1100??0---------00---------0-100?00000--0-00-0-00---?0-00?010000000010008100120------000-0-00100??2??????? Eubranchipus_grubii_2 20000100300002112011100010100-210100--0-1100??10----1000010---1000000100?110110010140031110000-00101010000001000I100120------000-0-00100102??????? Eubranchipus_grubii_3 20000100300002111011100010100-210100--0-11001120----1000010---1000000100?110110010160011110000-02101010000001000J100120------000-0-001001020?????? Eubranchipus_grubii_Adult 20000100?0000210--0-150-00020-204--0--0-112-1120---01000010---1000000100?11011011018001111?000-02101010000001000Q100120------000-0-001001020?1???? Glomeris_marginata_Adult 2000??00300000----------------204--0----???00-20----?100020---?00??00100??0?010-10190-400-?000-0?000--000?001000F00012-------0000?-000-21000010010 Hesslandona_angustata_1 2000?100?10002?1??101?1110101121110110101100??21100010-000-----------100110?00--0-00------?-?0-0?000--0000000000?001??0021101000??0?02?00-???????? Hesslandona_angustata_2 2000???0?10002?1??101?111010112111011010111-??21100010-000-----------100110000--0-00------?-?0-0?000--0000000000?001??0021101000??0?02?00-???????? Hesslandona_unisulcata_6 200070?0?10002?10-101?111010112101011010111-2-211000101002110010000011001100010-1000---00-?0?0-0?001--0000000000?001??0021101000??0?02?00-2??????? Hutchinsoniella_macracantha_1 20005010200002010-10100110001121220110001100201101?010-001---??0-000-100??0010--0-00------?-00-000010120010010102?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_10 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1011-01?0-?000-00001012001001010P?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_11 2000501020000200--101001100011212200----1100202101?0100002101?1100001100??00110-1011-01?0-?000-00001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_12 2000501020000200--101001100011212200----1100202101?0100002101?1100001100??00110-1011-01?0-?000-00001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_13 2000501020000200--101001100011212200----1100202101?0100002101?1100001100??00110-1012-01?0-?000-00001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_14 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1013-01?0-?000-00001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_15 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1013-01?0-?000-00001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_16 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1014-01?0-?000-00001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_17 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1014-01?0-?000-0?001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_18 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1015101?0-?000-0?001012001001010Q?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_2 20005010200002010-10100110001121220110001100202101?010-001101??00000-100??0010--0-00------?-00-000010120010010104?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_3 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-0-00-01?0-?-00-000010120010010106?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_4 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1000-01?0-?000-000010120010010108?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_5 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1000-01?0-?000-00001012001001010E?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_6 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1000-01?0-?000-00001012001001010I?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_7 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1010-01?0-?000-00001012001001010J?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_8 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1010-01?0-?000-00001012001001010L?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_9 20005010200002010-10100110001121220110001100202101?0100002101?1100001100??00110-1010-01?0-?000-00001012001001010O?0010-0----0000?0-000-00-2?0????? Hutchinsoniella_macracantha_Adult 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1015101?0-?000-0?001012001001010Q00010-0----000010-000-00-2001???? Klausmuelleria_salopensis 2000???0?10002?10?1?1?12101011210?01101?1100??21100010-000-----------100110000--0-00---????-?0-0?00????00?000000?001??0011-01000??000??00-???????? Labidocera_aestiva_Adult 20009000?0?002?0--10101110111121300100?0???03-2100?0?10002?????000000?????0?011-1013-0400-?100-0?001010000001000?10010-0-----00000-003?00-20?1???? Labidocera_aestiva_Copepodid_1 20008000?0?002?0--1010111011112130010000???03-2100?0?100020---?000000?????0?011-1010-0400-??00-000010100000010003?0010-0-----00000-00??0??20?????? Labidocera_aestiva_Copepodid_2 20008000?0?002?0--1010111011112130010000???03-2100?0?100020---?000000?????0?011-1011-0400-??00-000010100000010004?0010-0-----00000-00??0??20?????? Labidocera_aestiva_Copepodid_3 20009000?0?002?0--1010111011112130010000???03-2100?0?100020---?000000?????0?011-1012-0400-??00-000010100000010004?0010-0-----00000-00??0??20?????? Labidocera_aestiva_Copepodid_4 20009100?0?002?0--1010111011112130010000???03-2100?0?100020---?000000?????0?011-1013-0400-??00-000010100000010004?0010-0-----00000-00??0??20?????? Labidocera_aestiva_Copepodid_5 20009000?0?002?0--1010111011112130010000???03-2100?0?100020---?000000?????0?011-1013-0400-??00-000010100000010004?0010-0-----00000-00??0??20?????? Labidocera_aestiva_Nauplius_1 2000200030?002?12-1012?010100-2120011010???05-0----------0-----------140??0--0--0-00------?--0-0000101000?000000??00??-0-----00000-00??0??20??000? Labidocera_aestiva_Nauplius_2 2000200030?002?12-1012?010100-2120011010???05-0----------0-----------140??0--0--0-00------?--0-0000101000?010000??00??-0-----00000-00??0??20?????? Labidocera_aestiva_Nauplius_3 2000200030?002?10-1011?01010102120011010???05-0----------0-----------140??0--0--0-00------?--0-0000101000?010000??00??-0-----00000-00??0??20?????? Labidocera_aestiva_Nauplius_4 2000200030?002?10-1010?01010102110011010???06-1----------0-----------140??0--0--0-00------?--0-0000101000?010000??00??-0-----00000-00??0??20?????? Labidocera_aestiva_Nauplius_5 2000200030?002?10-1010?01010102110011010???06-1----------0-----------140??0--0--0-00------?--0-0000101000?010000??00??-0-----00000-00??0??20?????? Labidocera_aestiva_Nauplius_6 2000200030?002?10-1010?01010112110011010???06-1----------1-----------140??0--0--0-00------?--0-00001010001010000??00??-0-----00000-00??0??20?????? Lepas_anatifera_Cyprid 20002???200102?0--1?1???1020??2????1102????0??2110????100211???000?011???00??10-0-00-???0-?-?0-000010100010?1000301011?0-----00011-00??0102000???? Lepas_anatifera_Nauplius_1 2000000030?00200--1013100010??212001101????04?0---------?0---------?-100?00--0--0-00------?--0-00001?0?000010000?0?01000-----110??-003?00-2?0????? Lepas_anatifera_Nauplius_2 20003000?0?002010-1011101020??211001102?11004?0----------0-----------130?00--0--0-00------?--0-00001?0?000010000?0?01000-----110??-003?00-2?0????? Lepas_anatifera_Nauplius_6 20004000?0?102013-1010131020??210001102?11004?10----?0-0-0-----------140?00?-0--0-00------?--0-00001?0?000010000?0?01000-----110??-003?00-2?0????? Manawa_staceyi_4 200030?0?00002?0--1?1??400????210001???0???0??2????0??0002?????00000110???0?010-0-00-0400-?-00-00000--?00000?000??010-0-20-00000??0000-00-2??????? Manawa_staceyi_6 200030?0?00002?0--1?1??4001???210001???011002-2????0?100021????000001100??00010-1010-0400-?000-0100121?0000010002?010-0-21-000001?0000-00-200????? Nebalia_brucei_Adult 210190?0?0000200--100-06----0-211100----111-0-20----11000210101000?001?0??1?110-1015014010?001600001010000001000L?010-0-?0-00002100000-010?0?1???? Nebalia_sp._g 2000020031000220--?2?50???0?0-202--?----0-?05-10---000?0010---000000?101?000010-1015004?0-1001200001000000001000I?000--------00110-000-00-2??????? Nebalia_sp._i 2000020030000220--?2?50???0?0-212-00----???0??20----?10001??????000001?0??0?010-1015004?0-?001400001000000001000I?010-0-?2?00002100000-0102??????? Orchestia_cavimana_3 20001200300002?0--120-?3----??202--0----???05-1-------0--1----------0100010--10-101500300-1001600000---00-000001?1000--------000??-000-0???0?????0 Orchestia_cavimana_4 20004200300002?0--120-?5----??202--0----???05-20----?100020---?000000100110?0110101500300-?001610000--0000001001?1000--------000??-000-0??20?????0 Orchestia_cavimana_5 20004200300002?0--120-?5----??201--0----???05-20----?100020---?000000100110?0110101500300-?001610000--0000001001?10012-0-----000??-000-0??20?????0 Orchestia_cavimana_6 20004200300002?0--120-?5----??201--0----???00-20----?100020---?000000100110?0110101500300-?001610000--0000001001?10012-0-----000??-000-0??20?????0 Orchestia_cavimana_Hatchling 20004000?00002?0--100-?5----??201--0----???00-20----?000020---?000000100110?0110101500300-?00161?000--0000001001?10012-0-----000??-000-01020?????0 Pleomothra_apletocheles_1 2100?000?00002?0--1010?200??1121??01???0??????20----??00120---?000?00?????00011-101800?????0?0-00001??10000010008?0010-0-----00000-000-00-20?????- Pleomothra_apletocheles_Adult 2100900010000200--1010?201101120---1???011000120----1000120---1000?101?01100011-101900?????0?0-0?001??1000001000Q00010-0-----00000-000-00-20?1???- Porcellio_scaber_14 20002200310002?0--120-?5----??1---------------2??????00002?????000000100110?011010150040100001600000--0000001000F00012-0-----000??-000-00-?0?????0 Porcellio_scaber_15 20002200310002?0--120-?5----??1---------------20----?000020---?000000100110?01101015005010?001600000--0000001001?10012-0-----000??-000-00-?0?????0 Porcellio_scaber_16 20002200310002?0--120-?5----??1---------------20----?000020---?000000100110?0110101500?010?001410000--0000001001?10012-0-----000??-000-00-?0?????0 Porcellio_scaber_17 20002200310002?0--120-?5----??1---------------20----?000020---?000000100110?0110101500?010?001410000--0000001001?10012-0-----000??-000-010?0?1???0 Porcellio_scaber_18 20002200310002?0--120-?5----??1---------------20----?000020---?000000100110?0110101500?010?001410000--0000001001?10012-0-----000??-000-010?0?1???0 Porcellio_scaber_Manca_1 2000?200310002?0--110-?5----??202--0----???00-20----?000020---?000000100110?01101015005010?001410000--0000001001?10012-0-----000??-000-010?0?1???0 Porcellio_scaber_Manca_2 2000?200310002?0--110-?5----??202--0----???00-20----?000020---?000000100110?0110101500?010?001410000--0000001001?10012-0-----000??-000-010?0?1???0 Rehbachiella_kinnekullensis_A_14_ts10a 20009??0?00002????????????????2?????????11?02-2101001?100210101000001100?11?110-101700000-?000-00001012000001000E10010-0-----000?0-00??0102??????? Rehbachiella_kinnekullensis_A_2_l2a 20009??0?00002012?10100310100-215001101?11014-0----------0-----------100100--0--0-00---------0-0000200001000000011001?-0-----000?0-00??0102??????? Rehbachiella_kinnekullensis_B_17_ts13b 20009??0?00002????????????????2?????????11?02-2101001?1002?0101000001100?11?110-101900000-?000-00001012000001000I10010-0-----000?0-00??0102??????? Rehbachiella_kinnekullensis_B_4_l4b 200090?0?00002010-10110310100-215001101?11002-21010001-0011??0000000-100??01?0--0-00---------0-00001010000001000?1001?-0-----000?0-00??0102??????? Rehbachiella_kinnekullensis_B_8_ts4b 200090?0?00002010-10100310100-215101101?11002-2101001110021??010000011001111110?101100?0???000-00001010000001000410010-0-----000?0-00??0102??????? Triops_cancriformis_1 20000100?000021122111300101011211100----11005-0---------00---------0-100100--0--0-00------?--0-00000--00000010002101110002-00000?0000110??2??????? Triops_cancriformis_2 20000100?000021120111300101011211100----1100??10----100000---------0-100?000010-10130?21??0000-000010021000010004101110000-00000?0000110112??????? Triops_cancriformis_3 20000100?000021110111300101011211100----1100??20----100000---------0-100?010110-10160?21??0000-000010021000010006101110000-00000?0000110112??????? Triops_cancriformis_4 20000100?000021110111300101011211100----11002-20----100000---------0-100?110110-10190?21??0000-00001002100001000J1011100?0-00000?0000110112??????? Triops_cancriformis_5 20000100?000021120111300101011213100----11002-20----100000---------0-100?110110-10190?21??0000-00001002100001000O1011100?0-00000?0000110112??????? Triops_cancriformis_Adult 20000100?0000{02}20--????00??-20-204--0----11202-20----100000---------0-100?110110-1019012111?000-00001002100001000Q101110010-00000100001101120?1???? Vargula_hilgendorfii_1 2000501020000210--11101210001121000100001100?02100?0??0002?00??110000100??00010-0-00--300-?-00-0000110?0000000003?010-0-21-110001?0001?01020?????? Vargula_hilgendorfii_2 2000501020000210--10101210001121000100001100?02100?0??0002?00??110000100??00010-1000--300-?000-0000110?000000000??010-0-21-110001?0001?01020?????? Vargula_hilgendorfii_3 2000501020000210--10101210001121000100001100?02100?0??0002?00??110000100??00010-1200--3010?000-0000110?000000000??010-0-21-110001?0001?01020?????? Vargula_hilgendorfii_4 2000?01020000210--10101210001121000100001100?02100?0??0002?00??110000100??00010-1200--3010?000-0000110?000000000??010-0-21-110001?0001?01020?????? Vargula_hilgendorfii_5 2000701020000210--10101210001121000100001100?02100?0??0002?00??110000100??00010-1200--3010?000-0100110?000000000??010-0-21-110001?0001?0102011???? Yicaris_dianensis_1 20003?00?10002????1???1?1010??20---110101100??210100100001?0101100000???110010--0-00---?--?-00-0?000--0000?01000??0010?0----0000-?-?0??010???????? Yicaris_dianensis_2 2000?????????2????1??01?10101120---110101100??210100100002?0101100000???1100110-1000-00?10?000-0?001?10000?01000??0010?0----0000-?-?0??010???????? Yicaris_dianensis_3 2000?????????2????1??01?10101120---110101100??210100100002?01011000001001100110-1014-00?10?000-0?001?10000?01000??0010?0----0000-?-?0??010???????? ; END; [ The following blocks are output data for analysis step 11980 ] BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied10_traditional = [&R] (Glomeris_marginata_Adult,((Eubranchipus_grubii_1,(Rehbachiella_kinnekullensis_A_2_l2a,((((((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2)62,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)49)33)83,(Lepas_anatifera_Cyprid,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,(Hesslandona_angustata_2,Hesslandona_unisulcata_6)15)1)89)5)8,((Darwinula_stevensoni_1,((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)75)24)99,((Darwinula_stevensoni_2,Darwinula_stevensoni_3)8,(Darwinula_stevensoni_4,(Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)69)4)45)1)43)30,(Manawa_staceyi_4,(Manawa_staceyi_6,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)85)1)12)9)11,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)53)62)25,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)80,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)63)78)40)32)12)33)98)5,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)8)80)10)0,(((Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)41)93,((Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9,(Derocheilocaris_remanei_5,Derocheilocaris_remanei_6)16)49,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)94)5)6,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,Derocheilocaris_remanei_4)59)10)3,((((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)50)50)82)89,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)58)79)48)12,(Labidocera_aestiva_Nauplius_6,(Labidocera_aestiva_Nauplius_3,Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5)18)19)41,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)79)66)40)38,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)64)3)32)60,(((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)65)89,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)28)59)57)52,(Nebalia_sp._g,((Nebalia_sp._i,Nebalia_brucei_Adult)3,(Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_17,Porcellio_scaber_18,(Porcellio_scaber_16,(Porcellio_scaber_14,Porcellio_scaber_15)29)3)18,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)62)45)11)9)8)44)0)35)47)62)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67364] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied10_NT = [&R] (Glomeris_marginata_Adult,((Eubranchipus_grubii_1,(Rehbachiella_kinnekullensis_A_2_l2a,((((((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2)62,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)49)33)83,(Lepas_anatifera_Cyprid,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,(Hesslandona_angustata_2,Hesslandona_unisulcata_6)15)1)89)5)8,((Darwinula_stevensoni_1,((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)75)24)99,((Darwinula_stevensoni_2,Darwinula_stevensoni_3)8,(Darwinula_stevensoni_4,(Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)69)4)45)1)43)30,(Manawa_staceyi_4,(Manawa_staceyi_6,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)85)1)12)9)11,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)53)62)25,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)80,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)63)78)40)32)12)33)98)5,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)8)80)10)0,(((Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)41)93,((Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9,(Derocheilocaris_remanei_5,Derocheilocaris_remanei_6)16)49,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)94)5)6,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,Derocheilocaris_remanei_4)59)10)3,((((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)50)50)82)89,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)58)79)48)12,(Labidocera_aestiva_Nauplius_6,(Labidocera_aestiva_Nauplius_3,Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5)18)19)41,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)79)66)40)38,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)64)3)32)60,(((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)65)89,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)28)59)57)52,(Nebalia_sp._g,((Nebalia_sp._i,Nebalia_brucei_Adult)3,(Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_17,Porcellio_scaber_18,(Porcellio_scaber_16,(Porcellio_scaber_14,Porcellio_scaber_15)29)3)18,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)62)45)11)9)8)44)0)35)47)62)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67365] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied1_NT = [&R] (Glomeris_marginata_Adult,((Rehbachiella_kinnekullensis_A_2_l2a,((((((Manawa_staceyi_4,((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)52)39)85,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,(Hesslandona_angustata_2,Hesslandona_unisulcata_6)33)32)82,(Lepas_anatifera_Cyprid,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)29)3)11,(Manawa_staceyi_6,(Darwinula_stevensoni_1,(Darwinula_stevensoni_2,Darwinula_stevensoni_3,(Darwinula_stevensoni_4,(Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)64)14)55)40)38)6)19,(Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)72)12)99)17)16,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)48)61)23,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)78,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)62)79)39)30)11)39)90)4,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)7)85)4)19,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)18)93)17,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)94)23,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,(Derocheilocaris_remanei_4,(Derocheilocaris_remanei_5,(Derocheilocaris_remanei_6,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9)15)21)53)57)7)22,((((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)47)53)83)70,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)16)28)20)1,(Labidocera_aestiva_Nauplius_6,(Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5,(Labidocera_aestiva_Nauplius_3,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)45)13)4)43)16,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)54)46)16)21)14,((Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)63)88,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)33)62)38)31)39,(Porcellio_scaber_14,((Nebalia_brucei_Adult,(Nebalia_sp._g,Nebalia_sp._i)5)0,(Orchestia_cavimana_3,(Porcellio_scaber_15,((Orchestia_cavimana_Hatchling,(Orchestia_cavimana_6,(Orchestia_cavimana_4,Orchestia_cavimana_5)26)37)34,((Porcellio_scaber_16,Porcellio_scaber_17,Porcellio_scaber_18)8,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)60)18)29)3)1)32)17)3)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67361] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied100_NT = [&R] (Glomeris_marginata_Adult,(((((((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2)60,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)42)25)73,(Lepas_anatifera_Cyprid,(Hesslandona_unisulcata_6,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,Hesslandona_angustata_2)34)14)84)6)8,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)53)64)12,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)79,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)62)78)34)24)4)20)98)5,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)10)68)0)16,(((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)75)25)99,((Darwinula_stevensoni_1,Darwinula_stevensoni_2,Darwinula_stevensoni_3)22,(Darwinula_stevensoni_4,Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)71)26)63)43,(Manawa_staceyi_4,(Manawa_staceyi_6,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)79)9)6)30)8,(((Rehbachiella_kinnekullensis_A_2_l2a,(Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)55)83,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)9)59)9)12)58)20,(((Labidocera_aestiva_Nauplius_3,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)63,(Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5,Labidocera_aestiva_Nauplius_6)25)40,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)59)84)55)7,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)83)65)30)18,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,Derocheilocaris_remanei_4)63)23)31,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9,(Derocheilocaris_remanei_5,Derocheilocaris_remanei_6)20)54)31,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)46)93,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)92)22,((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)43)36)66)85,(Nebalia_brucei_Adult,(Nebalia_sp._i,(Nebalia_sp._g,(Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_17,Porcellio_scaber_18,(Porcellio_scaber_16,(Porcellio_scaber_14,Porcellio_scaber_15)31)6)19,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)63)63)3)8)5)33)4)16)26)18)33)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67367] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE equal_NT = [&R] (Glomeris_marginata_Adult,(((((((Lepas_anatifera_Cyprid,((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2)48,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)29)11)51,(Hesslandona_unisulcata_6,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,Hesslandona_angustata_2)48)4)76)0,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)51)52)0,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)78,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)60)73)32)15)12)6)96)12,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)1)55)6)19,(((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)69)13)99,(Darwinula_stevensoni_1,Darwinula_stevensoni_2,Darwinula_stevensoni_3,Darwinula_stevensoni_4,Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)66)71)39,(Manawa_staceyi_4,(Manawa_staceyi_6,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)74)1)8)33)15,(((Rehbachiella_kinnekullensis_A_2_l2a,(Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)41)68,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)2)51)5)11)52)11,(((Labidocera_aestiva_Nauplius_3,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)66,(Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5,Labidocera_aestiva_Nauplius_6)38)37,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)59)78)53)7,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)79)53)32)11,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,Derocheilocaris_remanei_4)57)16)19,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9,(Derocheilocaris_remanei_5,Derocheilocaris_remanei_6)21)54)22,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)46)89,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)90)10,(Argulus_japonicus_1,Argulus_japonicus_2,Argulus_japonicus_3,Argulus_japonicus_4,Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)76,(Nebalia_brucei_Adult,(Nebalia_sp._g,Nebalia_sp._i,Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_17,Porcellio_scaber_18,(Porcellio_scaber_16,(Porcellio_scaber_14,Porcellio_scaber_15)35)11)15,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)62)71)10)15)12)32)26)12)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67359] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied100_traditional = [&R] (Glomeris_marginata_Adult,(((((((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2)60,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)42)25)73,(Lepas_anatifera_Cyprid,(Hesslandona_unisulcata_6,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,Hesslandona_angustata_2)34)14)84)6)8,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)53)64)12,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)79,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)62)78)34)24)4)20)98)5,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)10)68)0)16,(((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)75)25)99,((Darwinula_stevensoni_1,Darwinula_stevensoni_2,Darwinula_stevensoni_3)22,(Darwinula_stevensoni_4,Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)71)26)63)43,(Manawa_staceyi_4,(Manawa_staceyi_6,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)79)9)6)30)8,(((Rehbachiella_kinnekullensis_A_2_l2a,(Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)55)83,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)9)59)9)12)58)20,(((Labidocera_aestiva_Nauplius_3,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)63,(Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5,Labidocera_aestiva_Nauplius_6)25)40,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)59)84)55)7,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)83)65)30)18,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,Derocheilocaris_remanei_4)63)23)31,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9,(Derocheilocaris_remanei_5,Derocheilocaris_remanei_6)20)54)31,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)46)93,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)92)22,((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)43)36)66)85,(Nebalia_brucei_Adult,(Nebalia_sp._i,(Nebalia_sp._g,(Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_17,Porcellio_scaber_18,(Porcellio_scaber_16,(Porcellio_scaber_14,Porcellio_scaber_15)31)6)19,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)63)63)3)8)5)33)4)16)26)18)33)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67366] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied3_NT = [&R] (Glomeris_marginata_Adult,((Rehbachiella_kinnekullensis_A_2_l2a,(((((((Manawa_staceyi_4,((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)51)37)87,(Hesslandona_angustata_1,Klausmuelleria_salopensis,(Hesslandona_angustata_2,Hesslandona_unisulcata_6)33)88)18,(Lepas_anatifera_Cyprid,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)79)3)8,(Manawa_staceyi_6,(Darwinula_stevensoni_1,((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)73)20)99,((Darwinula_stevensoni_2,Darwinula_stevensoni_3)13,(Darwinula_stevensoni_4,Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)67)54)34)24)18)8)1)18,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)51)58)34,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)79,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)62)80)42)33)14)39)97)18,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)7)84)17)8,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)33)96)13,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)95)15,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,(Derocheilocaris_remanei_4,(Derocheilocaris_remanei_5,(Derocheilocaris_remanei_6,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9)17)14)49)54)5)11,((((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)52)55)88)81,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)50)66)38)26,(Labidocera_aestiva_Nauplius_6,(Labidocera_aestiva_Nauplius_3,Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5)18)19)37,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)67)52)36)35,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)60)12)25,((Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)66)90,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)32)61)59)51)58,(((Nebalia_brucei_Adult,(Nebalia_sp._g,Nebalia_sp._i)4)5,(Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_16,Porcellio_scaber_17,Porcellio_scaber_18)4,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)60)3)34)31)33)9)38)41,(Porcellio_scaber_14,Porcellio_scaber_15)9)46)11)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67363] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied3_traditional = [&R] (Glomeris_marginata_Adult,((Rehbachiella_kinnekullensis_A_2_l2a,(((((((Manawa_staceyi_4,((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)51)37)87,(Hesslandona_angustata_1,Klausmuelleria_salopensis,(Hesslandona_angustata_2,Hesslandona_unisulcata_6)33)88)18,(Lepas_anatifera_Cyprid,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)79)3)8,(Manawa_staceyi_6,(Darwinula_stevensoni_1,((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)73)20)99,((Darwinula_stevensoni_2,Darwinula_stevensoni_3)13,(Darwinula_stevensoni_4,Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)67)54)34)24)18)8)1)18,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)51)58)34,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)79,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)62)80)42)33)14)39)97)18,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)7)84)17)8,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)33)96)13,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)95)15,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,(Derocheilocaris_remanei_4,(Derocheilocaris_remanei_5,(Derocheilocaris_remanei_6,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9)17)14)49)54)5)11,((((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)52)55)88)81,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)50)66)38)26,(Labidocera_aestiva_Nauplius_6,(Labidocera_aestiva_Nauplius_3,Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5)18)19)37,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)67)52)36)35,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)60)12)25,((Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)66)90,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)32)61)59)51)58,(((Nebalia_brucei_Adult,(Nebalia_sp._g,Nebalia_sp._i)4)5,(Orchestia_cavimana_3,(Orchestia_cavimana_4,(Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_16,Porcellio_scaber_17,Porcellio_scaber_18)4,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)60)3)34)31)33)9)38)41,(Porcellio_scaber_14,Porcellio_scaber_15)9)46)11)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67362] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE equal_traditional = [&R] (Glomeris_marginata_Adult,(Rehbachiella_kinnekullensis_A_2_l2a,Eubranchipus_grubii_1,Triops_cancriformis_1,(Lepas_anatifera_Cyprid,((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2)48,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)29)11)51,(Hesslandona_unisulcata_6,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,Hesslandona_angustata_2)48)4)76,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)51)52)0,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)78,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)60)73)32)15)12)6)96)12,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)1)55)6,(((Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)69)13)99,(Darwinula_stevensoni_1,Darwinula_stevensoni_2,Darwinula_stevensoni_3,Darwinula_stevensoni_4,Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)66)71)39,(Manawa_staceyi_4,(Manawa_staceyi_6,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)74)1)8)33)15,(Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)41)68,(Triops_cancriformis_2,Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)51,(Argulus_japonicus_1,Argulus_japonicus_2,Argulus_japonicus_3,Argulus_japonicus_4,Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)76,(((Labidocera_aestiva_Nauplius_3,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)66,(Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5,Labidocera_aestiva_Nauplius_6)38)37,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)59)78)53)7,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)79)53)32,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2,Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult)89,(Nebalia_sp._g,Nebalia_sp._i,Nebalia_brucei_Adult,Orchestia_cavimana_3,(Orchestia_cavimana_4,Orchestia_cavimana_5,(Orchestia_cavimana_6,(Orchestia_cavimana_Hatchling,((Porcellio_scaber_17,Porcellio_scaber_18,(Porcellio_scaber_16,(Porcellio_scaber_14,Porcellio_scaber_15)35)11)15,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)62)71)10)15)32)12,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,Derocheilocaris_remanei_4)57,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9,(Derocheilocaris_remanei_5,Derocheilocaris_remanei_6)21)54,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)90)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67358] END; BEGIN TREES; TITLE Missing_Semaphoronts; LINK TAXA = TaxaForAnalysisStep11980; TREE implied1_traditional = [&R] (Glomeris_marginata_Adult,((Rehbachiella_kinnekullensis_A_2_l2a,((((((Manawa_staceyi_4,((((Bredocaris_admirabilis_1,Bredocaris_admirabilis_2,(Bredocaris_admirabilis_3,(Bredocaris_admirabilis_4,Bredocaris_admirabilis_5,Bredocaris_admirabilis_6)52)39)85,(Klausmuelleria_salopensis,(Hesslandona_angustata_1,(Hesslandona_angustata_2,Hesslandona_unisulcata_6)33)32)82,(Lepas_anatifera_Cyprid,(Baccalaureus_falsiramus_Ascothoracid_larva,Baccalaureus_falsiramus_Adult)29)3)11,(Manawa_staceyi_6,(Darwinula_stevensoni_1,(Darwinula_stevensoni_2,Darwinula_stevensoni_3,(Darwinula_stevensoni_4,(Darwinula_stevensoni_5,(Darwinula_stevensoni_6,Darwinula_stevensoni_7,Darwinula_stevensoni_8,Darwinula_stevensoni_9)64)14)55)40)38)6)19,(Vargula_hilgendorfii_1,(Vargula_hilgendorfii_2,(Vargula_hilgendorfii_3,Vargula_hilgendorfii_4,Vargula_hilgendorfii_5)72)12)99)17)16,(((Rehbachiella_kinnekullensis_B_4_l4b,(Rehbachiella_kinnekullensis_B_8_ts4b,(Rehbachiella_kinnekullensis_A_14_ts10a,Rehbachiella_kinnekullensis_B_17_ts13b)48)61)23,((Hutchinsoniella_macracantha_1,Hutchinsoniella_macracantha_2)78,(Hutchinsoniella_macracantha_3,(Hutchinsoniella_macracantha_4,Hutchinsoniella_macracantha_5,Hutchinsoniella_macracantha_6,(Hutchinsoniella_macracantha_7,Hutchinsoniella_macracantha_8,Hutchinsoniella_macracantha_9,(Hutchinsoniella_macracantha_10,(Hutchinsoniella_macracantha_11,Hutchinsoniella_macracantha_12,Hutchinsoniella_macracantha_13,(Hutchinsoniella_macracantha_14,Hutchinsoniella_macracantha_15,Hutchinsoniella_macracantha_16,Hutchinsoniella_macracantha_17,Hutchinsoniella_macracantha_18,Hutchinsoniella_macracantha_Adult)62)79)39)30)11)39)90)4,(Yicaris_dianensis_1,(Yicaris_dianensis_2,Yicaris_dianensis_3)7)85)4)19,(Labidocera_aestiva_Copepodid_3,Labidocera_aestiva_Copepodid_4,Labidocera_aestiva_Copepodid_5,Labidocera_aestiva_Adult,(Labidocera_aestiva_Copepodid_1,Labidocera_aestiva_Copepodid_2)18)93)17,(Pleomothra_apletocheles_1,Pleomothra_apletocheles_Adult)94)23,(Derocheilocaris_remanei_1,Derocheilocaris_remanei_2,Derocheilocaris_remanei_3,(Derocheilocaris_remanei_4,(Derocheilocaris_remanei_5,(Derocheilocaris_remanei_6,(Derocheilocaris_remanei_7,Derocheilocaris_remanei_8,Derocheilocaris_remanei_9)15)21)53)57)7)22,((((Argulus_japonicus_1,(Argulus_japonicus_2,(Argulus_japonicus_3,Argulus_japonicus_4,(Argulus_japonicus_5,Argulus_japonicus_6,Argulus_japonicus_7)47)53)83)70,(Baccalaureus_falsiramus_Nauplius_1,(Baccalaureus_falsiramus_Nauplius_2,Baccalaureus_falsiramus_Nauplius_3,Baccalaureus_falsiramus_Nauplius_4,(Baccalaureus_falsiramus_Nauplius_5,Baccalaureus_falsiramus_Nauplius_6)16)28)20)1,(Labidocera_aestiva_Nauplius_6,(Labidocera_aestiva_Nauplius_4,Labidocera_aestiva_Nauplius_5,(Labidocera_aestiva_Nauplius_3,(Labidocera_aestiva_Nauplius_1,Labidocera_aestiva_Nauplius_2)45)13)4)43)16,(Lepas_anatifera_Nauplius_1,(Lepas_anatifera_Nauplius_2,Lepas_anatifera_Nauplius_6)54)46)16)21)14,((Eubranchipus_grubii_1,((Eubranchipus_grubii_2,(Eubranchipus_grubii_3,Eubranchipus_grubii_Adult)63)88,(Triops_cancriformis_1,(Triops_cancriformis_2,(Triops_cancriformis_3,Triops_cancriformis_4,Triops_cancriformis_5,Triops_cancriformis_Adult)33)62)38)31)39,(Porcellio_scaber_14,((Nebalia_brucei_Adult,(Nebalia_sp._g,Nebalia_sp._i)5)0,(Orchestia_cavimana_3,(Porcellio_scaber_15,((Orchestia_cavimana_Hatchling,(Orchestia_cavimana_6,(Orchestia_cavimana_4,Orchestia_cavimana_5)26)37)34,((Porcellio_scaber_16,Porcellio_scaber_17,Porcellio_scaber_18)8,(Porcellio_scaber_Manca_1,Porcellio_scaber_Manca_2)60)18)29)3)1)32)17)3)100); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr67360] END;