#NEXUS [written Mon Oct 14 23:18:52 SGT 2013 by Mesquite version 2.75 (build 566) at Simba.local/192.168.1.6] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=22; TAXLABELS Argulus_japonicus_Instar_7 Baccalaureus_falsiramus_Adult Bredocaris_admirabilis_Instar_6 Darwinula_stevensoni_Instar_9 Derocheilocaris_remanei_Instar_9 Eubranchipus_grubii_Adult Glomeris_marginata_Adult Hesslandona_unisulcata_Instar_6 Hutchinsoniella_macracantha_Adult Labidocera_aestiva_Adult Lepas_anatifera_Cyprid Manawa_staceyi_Instar_6 Nebalia_brucei_Adult Orchestia_cavimana_Hatchling Pleomothra_apletocheles_Adult Porcellio_scaber_manca_2 Rehbachiella_kinnekullensis_A_Instar_14_ts10a Rehbachiella_kinnekullensis_B_Instar_17_ts13b Sacculina_carcini_Cyprid Triops_cancriformis_Adult Vargula_hilgendorfii_Instar_5 Yicaris_dianensis_Instar_6 ; END; BEGIN CHARACTERS; TITLE late_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_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?????? Bredocaris_admirabilis_Instar_6 200090?1?0000200--10101?1010112100011010110030211000100002110010000011001100010-1017-0000-?010-00001010000010000?10010?0----000010-?00-010???????? Darwinula_stevensoni_Instar_9 2000401020000200--10141300021121001100001100302100?1?10002100??0000011????00010-1000---00-?-00-0100121?000000000??010-0-21-010001?0003?00-2000???? Derocheilocaris_remanei_Instar_9 2000700020000200--1010?2101011210201101011002-20----1?00020---1000000100110?01101012-0300-?000-0?001?100000112008?0010-0-----00000-004?00-2?1????? 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_unisulcata_Instar_6 200070?0?10002?10-101?111010112101011010111-2-211000101002110010000011001100010-1000---00-?0?0-0?001--0000000000?001??0021101000??0?02?00-2??????? Hutchinsoniella_macracantha_Adult 2000501020000200--10100110001120---0----1100202101?0100002101?1100001100??00110-1015101?0-?000-0?001012001001010Q00010-0----000010-000-00-2001???? 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???? 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???? Manawa_staceyi_Instar_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???? 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_Adult 2100900010000200--1010?201101120---1???011000120----1000120---1000?101?01100011-101900?????0?0-0?001??1000001000Q00010-0-----00000-000-00-20?1???- 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_Instar_14_ts10a 20009??0?00002????????????????2?????????11?02-2101001?100210101000001100?11?110-101700000-?000-00001012000001000E10010-0-----000?0-00??0102??????? Rehbachiella_kinnekullensis_B_Instar_17_ts13b 20009??0?00002????????????????2?????????11?02-2101001?1002?0101000001100?11?110-101900000-?000-00001012000001000I10010-0-----000?0-00??0102??????? Sacculina_carcini_Cyprid 2000?00025?100----------------0------------0--0----------0-----------????00--10-101300400-?0?0-00001?0?00?0??000??1011-0-----10011-001?00-???????? Triops_cancriformis_Adult 20000100?0000{0 2}20--????00??-20-204--0----11202-20----100000---------0-100?110110-1019012111?000-00001002100001000Q101110010-00000100001101120?1???? Vargula_hilgendorfii_Instar_5 2000701020000210--10101210001121000100001100?02100?0??0002?00??110000100??00010-1200--3010?000-0100110?000000000??010-0-21-110001?0001?0102011???? Yicaris_dianensis_Instar_6 2????????????2????????????????2???????????????2??????????2????????????????00110-1014-00?10?000-0?001?10000?01000??0010?0----0000-?-?0??010???????? ; END; BEGIN TREES; Title late_trees; LINK Taxa = Taxa; TRANSLATE 1 Argulus_japonicus_Instar_7, 2 Baccalaureus_falsiramus_Adult, 3 Bredocaris_admirabilis_Instar_6, 4 Darwinula_stevensoni_Instar_9, 5 Derocheilocaris_remanei_Instar_9, 6 Eubranchipus_grubii_Adult, 7 Glomeris_marginata_Adult, 8 Hesslandona_unisulcata_Instar_6, 9 Hutchinsoniella_macracantha_Adult, 10 Labidocera_aestiva_Adult, 11 Lepas_anatifera_Cyprid, 12 Manawa_staceyi_Instar_6, 13 Nebalia_brucei_Adult, 14 Orchestia_cavimana_Hatchling, 15 Pleomothra_apletocheles_Adult, 16 Porcellio_scaber_manca_2, 17 Rehbachiella_kinnekullensis_A_Instar_14_ts10a, 18 Rehbachiella_kinnekullensis_B_Instar_17_ts13b, 19 Sacculina_carcini_Cyprid, 20 Triops_cancriformis_Adult, 21 Vargula_hilgendorfii_Instar_5, 22 Yicaris_dianensis_Instar_6; TREE equal_traditional = (7,(1,(((3,10,(12,(8,(21,4)60)3,(2,(11,19)22)1)8,(5,15)13)4,(22,(9,(17,18)78)46)7)20,(6,20)79,(13,(14,16)92)8)6)100); TREE equal_NT = (7,(1,13,(3,22,9,10,5,15,(8,12,2,11,19,(21,4)56)10,(17,18)72)20,(6,20)68,(14,16)88)100); TREE implied1_traditional = (7,(1,(22,9,13,(8,10,15,(3,5)13,(12,(21,4)35)21,(2,(11,19)40)36)23,(17,18)73,(6,20)73)1,(14,16)92)100); TREE implied1_NT = (7,(1,(22,9,13,(8,10,15,(3,5)13,(12,(21,4)35)21,(2,(11,19)40)36)23,(17,18)73,(6,20)73)1,(14,16)92)100); TREE implied3_traditional = (7,(1,(((22,(3,10,(8,(12,(21,4)56)10,(2,(11,19)32)19)0,(5,15)14)13,(9,(17,18)75)17)2,(6,20)78)2,(13,(14,16)92)1)7)100); TREE implied3_NT = (7,(1,(((22,(3,10,(8,(12,(21,4)56)10,(2,(11,19)32)19)0,(5,15)14)13,(9,(17,18)75)17)2,(6,20)78)2,(13,(14,16)92)1)7)100); TREE implied10_traditional = (7,(1,(((3,10,(12,(8,(21,4)62)3,(2,(11,19)26)5)4,(5,15)14)4,(22,(9,(17,18)78)43)7)16,(6,20)77,(13,(14,16)92)4)9)100); TREE implied10_NT = (7,(1,(((3,10,(12,(8,(21,4)62)3,(2,(11,19)26)5)4,(5,15)14)4,(22,(9,(17,18)78)43)7)16,(6,20)77,(13,(14,16)92)4)9)100); TREE implied100_traditional = (7,(1,(((3,10,(12,(8,(21,4)60)3,(2,(11,19)22)1)8,(5,15)13)4,(22,(9,(17,18)78)46)7)20,(6,20)79,(13,(14,16)92)8)6)100); TREE implied100_NT = (7,(1,(((3,10,(12,(8,(21,4)60)3,(2,(11,19)22)1)8,(5,15)13)4,(22,(9,(17,18)78)46)7)20,(6,20)79,(13,(14,16)92)8)6)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 1381763933068; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8124438241117186979; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4100540971572232593; mqVersion 275; checksumv 0 3 3133554516 null getNumChars 146 numChars 146 getNumTaxa 22 numTaxa 22 short false bits 2305843009213849599 states 155647 sumSquaresStatesOnly 6.901306223E10 sumSquares 4.6116860874404403E18 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;