#NEXUS [written Mon Oct 14 23:22:56 SGT 2013 by Mesquite version 2.75 (build 566) at Simba.local/192.168.1.6] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=23; TAXLABELS Argulus_japonicus_Instar_1 Baccalaureus_falsiramus_Nauplius_1 Bredocaris_admirabilis_Instar_1 Darwinula_stevensoni_Instar_1 Derocheilocaris_remanei_Instar_1 Eubranchipus_grubii_Stage_1 Glomeris_marginata_Adult Hesslandona_angustata_Instar_1 Hutchinsoniella_macracantha_Instar_1 Klausmuelleria_salopensis Labidocera_aestiva_Nauplius_1 Lepas_anatifera_Nauplius_1 Manawa_staceyi_Instar_2 Nebalia_sp._Stage_g Orchestia_cavimana_Stage_1 Pleomothra_apletocheles_Nauplius_1 Porcellio_scaber_Stage_14 Rehbachiella_kinnekullensis_A_Instar_2_l2a Rehbachiella_kinnekullensis_B_Instar_4_l4b Sacculina_carcini_Nauplius_1 Triops_cancriformis_Stage_1 Vargula_hilgendorfii_Instar_1 Yicaris_dianensis_Instar_1 ; END; BEGIN CHARACTERS; TITLE Early_semaphoronts; DIMENSIONS NCHAR=146; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 E F I J L O P Q X"; 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 Argulus_japonicus_Instar_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?????? 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?????? Bredocaris_admirabilis_Instar_1 200090?1?0000200--1010??10101121000110101100??11-----0-000-----------100??0000--0-00--------10-00001010000010000?10010?0----000010-?00-010???????? Darwinula_stevensoni_Instar_1 2000400030000200--111512000211210000----1100300----------0-----------1????0000--0-00------?-00-0000120?000000000??010-0-21-010001?000??00-2000???? Derocheilocaris_remanei_Instar_1 20007000?0000201101010?2101011210?0110101100??20----1?-000-----------100??0?00--0-00---------0-00002?100100011002?0010-0-----00000-00??00-???????? Eubranchipus_grubii_Stage_1 20000100300002112011100010100-210100--0-1100??0---------00---------0-100?00000--0-00-0-00---?0-00?010000000010008100120------000-0-00100??2??????? 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_Instar_1 2000?100?10002?1??101?1110101121110110101100??21100010-000-----------100110?00--0-00------?-?0-0?000--0000000000?001??0021101000??0?02?00-???????? Hutchinsoniella_macracantha_Instar_1 20005010200002010-10100110001121220110001100201101?010-001---??0-000-100??0010--0-00------?-00-000010120010010102?0010-0----0000?0-000-00-2?0????? 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_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? 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????? Manawa_staceyi_Instar_2 200030?0?00002?0--1?1??400????210?01???0???0??1----------1-----------101??0?-0--0-00---------0-00000--?00?00?000??010-0-12-00000??0000-00-2??????? Nebalia_sp._Stage_g 2000020031000220--?2?50???0?0-202--?----0-?05-10---000?0010---000000?101?000010-1015004?0-1001200001000000001000I?000--------00110-000-00-2??????? Orchestia_cavimana_Stage_1 1--------1---1----------------1---------------0----------0-----------0--000--0--0-00---------0-00000---00-100000?1000--------000??-000-0???0?????0 Pleomothra_apletocheles_Nauplius_1 2000??00?00002????1?1?????????2???????????????0----------0-----------0--??0--0--0-00------0-10-00000--?0000000000?00??-?-----00000-000-00-21?????0 Porcellio_scaber_Stage_14 20002200310002?0--120-?5----??1---------------2??????00002?????000000100110?011010150040100001600000--0000001000F00012-0-----000??-000-00-?0?????0 Rehbachiella_kinnekullensis_A_Instar_2_l2a 20009??0?00002012?10100310100-215001101?11014-0----------0-----------100100--0--0-00---------0-0000200001000000011001?-0-----000?0-00??0102??????? Rehbachiella_kinnekullensis_B_Instar_4_l4b 200090?0?00002010-10110310100-215001101?11002-21010001-0011??0000000-100??01?0--0-00---------0-00001010000001000?1001?-0-----000?0-00??0102??????? Sacculina_carcini_Nauplius_1 2000?100?0?002?0--1?1???10????21?--110?0???05-0----------0-----------1???00--0--0-00---------0-00001?00000000000???010-0-----110??-00??00-???????? Triops_cancriformis_Stage_1 20000100?000021122111300101011211100----11005-0---------00---------0-100100--0--0-00------?--0-00000--00000010002101110002-00000?0000110??2??????? Vargula_hilgendorfii_Instar_1 2000501020000210--11101210001121000100001100?02100?0??0002?00??110000100??00010-0-00--300-?-00-0000110?0000000003?010-0-21-110001?0001?01020?????? Yicaris_dianensis_Instar_1 20003?00?10002????1???1?1010??20---110101100??210100100001?0101100000???110010--0-00---?--?-00-0?000--0000?01000??0010?0----0000-?-?0??010???????? ; END; BEGIN TREES; Title early_semaphoronts; LINK Taxa = Taxa; TRANSLATE 1 Argulus_japonicus_Instar_1, 2 Baccalaureus_falsiramus_Nauplius_1, 3 Bredocaris_admirabilis_Instar_1, 4 Darwinula_stevensoni_Instar_1, 5 Derocheilocaris_remanei_Instar_1, 6 Eubranchipus_grubii_Stage_1, 7 Glomeris_marginata_Adult, 8 Hesslandona_angustata_Instar_1, 9 Hutchinsoniella_macracantha_Instar_1, 10 Klausmuelleria_salopensis, 11 Labidocera_aestiva_Nauplius_1, 12 Lepas_anatifera_Nauplius_1, 13 Manawa_staceyi_Instar_2, 14 Nebalia_sp._Stage_g, 15 Orchestia_cavimana_Stage_1, 16 Pleomothra_apletocheles_Nauplius_1, 17 Porcellio_scaber_Stage_14, 18 Rehbachiella_kinnekullensis_A_Instar_2_l2a, 19 Rehbachiella_kinnekullensis_B_Instar_4_l4b, 20 Sacculina_carcini_Nauplius_1, 21 Triops_cancriformis_Stage_1, 22 Vargula_hilgendorfii_Instar_1, 23 Yicaris_dianensis_Instar_1; TREE equal_traditional = (7,((3,18,19,23,1,9,11,15,5,13,16,2,12,20,((8,10)61,(22,4)44)26,(6,21)58)73,(14,17)60)100); TREE implied1_traditional = (7,((6,(21,(1,11,15,16,(3,2)10,((23,(13,((8,10)48,(22,4)33)24)3)7,(12,20)45)17,(18,5)46,(19,9)9)6)13)86,(14,17)75)100); TREE implied1_NT = (7,((6,(21,(1,11,15,16,(3,2)10,((23,(13,((8,10)48,(22,4)33)24)3)7,(12,20)45)17,(18,5)46,(19,9)9)6)13)86,(14,17)75)100); TREE implied3_traditional = (7,((1,((11,15,16,(3,2)16,((23,(13,((8,10)50,(22,4)52)34)10)4,(12,20)36)23,(18,5)25,(19,9)10)7,(6,21)45)9)88,(14,17)78)100); TREE implied3_NT = (7,((1,((11,15,16,(3,2)16,((23,(13,((8,10)50,(22,4)52)34)10)4,(12,20)36)23,(18,5)25,(19,9)10)7,(6,21)45)9)88,(14,17)78)100); TREE implied10_traditional = (7,((1,((11,((3,((15,13,16,2)27,(12,20)24)23)23,(18,(19,(9,(23,(5,((8,10)59,(22,4)58)39)23)23)23)24)25)7)0,(6,21)65)21)85,(14,17)75)100); TREE implied10_NT = (7,((1,((11,((3,((15,13,16,2)27,(12,20)24)23)23,(18,(19,(9,(23,(5,((8,10)59,(22,4)58)39)23)23)23)24)25)7)0,(6,21)65)21)85,(14,17)75)100); TREE implied100_traditional = (7,((1,((11,((3,((15,13,16,2)26,(12,20)23)21)21,(18,(19,(9,(23,(5,((8,10)60,(22,4)57)34)21)21)21)22)22)7)0,(6,21)71)26)81,(14,17)70)100); TREE implied100_NT = (7,((1,((11,((3,((15,13,16,2)26,(12,20)23)21)21,(18,(19,(9,(23,(5,((8,10)60,(22,4)57)34)21)21)21)22)22)7)0,(6,21)71)26)81,(14,17)70)100); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 146; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 146; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1381764176375; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3907343395067478262; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2987022121294236211; mqVersion 275; checksumv 0 3 498386257 null getNumChars 146 numChars 146 getNumTaxa 23 numTaxa 23 short false bits 7167 states 7167 sumSquaresStatesOnly 2.6323883E7 sumSquares 2.6323883E7 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 206; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;