#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 18, 2025; 10:52 GMT TreeBASE (cc) 1994-2008 Study reference: Rouse G. 1999. Trochophore concepts: Evolution of larvae in polychaetes and other spiralians. Biological Journal of the Linnean Society, 66(4): 411-464. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S411] [ The following blocks are input data for analysis step 504 ] BEGIN TAXA; TITLE TaxaForAnalysisStep504; DIMENSIONS NTAX=91; TAXLABELS Aberrantidae Acoetidae Acrocirridae Aeolosomatidae Alciopidae Alvinellidae Ampharetidae Amphinomidae Aphroditidae Apistobranchidae Arenicolidae Capitellidae Chaetopteridae Chrysopetalidae Cirratulidae Clitellata Cossuridae Ctenodrilidae Diurodrilidae Dorvilleidae Echiura Entoprocta Eulepethidae Eunicidae Euphrosinidae Fauveliopsidae Flabelligeridae Glyceridae Goniadidae Hartmaniellidae Hesionidae Histriobdellidae Ichthyotomidae Iospilidae Lacydoniidae Longosomatidae Lopadorhynchidae Lumbrineridae Magelonidae Maldanidae Mollusca Myzostomidae Nautiliniellidae Nemertea Nephtyidae Nereididae Nerillidae Oenonidae Onuphidae Opheliidae Orbiniidae Oweniidae Paralacydoniidae Paraonidae Parergodrilidae Pectinariidae Pholoidae Phyllodocidae Pilargidae Pisionidae Platyhelminthes Poecilochaetidae Poeobiidae Polygordiidae Polynoidae Pontodoridae Potamodrilidae Protodrilidae Protodriloididae Psammodrilidae Questidae Rotifera Sabellariidae Sabellidae Saccocirridae Scalibregmatidae Serpulidae Siboglinidae Sigalionidae Sipuncula Sphaerodoridae Spintheridae Spionidae Sternaspidae Syllidae Terebellidae Tomopteridae Trichobranchidae Trochochaetidae Typhloscolecidae Uncispionidae ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2124] TITLE ; LINK TAXA = TaxaForAnalysisStep504; DIMENSIONS NCHAR=140; FORMAT DATATYPE=Standard SYMBOLS= "0 1" MISSING=? GAP= -; CHARSTATELABELS 1 Pro._Dist._Groove / Absent Present, 2 'Pro. Fused, Dist' / Absent Present, 3 'Pro. Fused, Red.' / Absent Present, 4 Prost_Fused_Ant. / Absent Present, 5 Peri._Ring / Absent Present, 6 Peri._Rings / Absent Present, 7 Peri._Elong / Absent Present, 8 'Peri. Rings, Collar' / Absent Present, 9 Peri.Lips / Absent Present, 10 Prostomial_antennae / Absent Present, 11 Med._Ant. / Absent Present, 12 Pair_of_Antennae / Absent Present, 13 PALPS / Absent Present, 14 Grooved_palp. / Absent Present, 15 Pro._grooved_palps / Absent Present, 16 Peri._groove_palp / Absent Present, 17 Pro._paired_palps / Absent Present, 18 Pro._multi._palps / Absent Present, 19 'Pro.palps=crown' / Absent Present, 20 Peri.palp_pair / Absent Present, 21 Peri._multi. / Absent Present, 22 Pro.V.palps / Absent Present, 23 'V.palp=vent.' / Absent Present, 24 'V.palps=v-l.' / Absent Present, 25 Nuchal_Org. / Absent Present, 26 'Nuchal O.=P.F.P.G.' / Absent Present, 27 'Nuchal O.=post.proj.' / Absent Present, 28 'Nuchal O.=caruncle' / Absent Present, 29 '4-5 Long muscle bands' / Absent Present, 30 Segmentation / Absent Present, 31 1st_seg._Indis. / Absent Present, 32 1st_seg._Sim / Absent Present, 33 1st_seg._Surr. / Absent Present, 34 1st_seg._Fused / Absent Present, 35 '1st seg. D-L.' / Absent Present, 36 1st_seg._Elon. / Absent Present, 37 1st_seg._appendages_same_as / Absent Present, 38 1st_seg._chaetal_struc_abse / Absent Present, 39 1st_seg._Cirri / Absent Present, 40 1st_seg._Not.Only / Absent Present, 41 1st_seg._Neur. / Absent Present, 42 1st_seg_Arthropod / Absent Present, 43 Tent.cirri / Absent Present, 44 Parapodia / Absent Present, 45 Para.Rami_Sim. / Absent Present, 46 Para._Neuro.Proj. / Absent Present, 47 Para._Tori / Absent Present, 48 Para.Noto_ridges / Absent Present, 49 Para.Spio / Absent Present, 50 Dorsal_cirri / Absent Present, 51 D._cirri_Cirrfm / Absent Present, 52 D.cirri_Elytrae / Absent Present, 53 D.cirri_foliose / Absent Present, 54 Dorsal_Cirri_limited / Absent Present, 55 V.cirri / Absent Present, 56 Para.Gills / Absent Present, 57 Dorsal_Gills / Absent Present, 58 Dor.Flat.Gills / Absent Present, 59 D._Gills_anteriorly_only / Absent Present, 60 Lateral_Organs / Absent Present, 61 D._cirrus_orgs. / Absent Present, 62 Dorsal_Organs / Absent Present, 63 Epi._Pap. / Absent Present, 64 Pyg._cirri_1 / Absent Present, 65 Pyg.cirri2 / Absent Present, 66 Dorsolateral_Folds / Absent Present, 67 No_buccal_organ / Absent Present, 68 Stom._Axial_hyper. / Absent Present, 69 Stom._Ventral_musc. / Absent Present, 70 Stom._disappears / Absent Present, 71 Stom._V._hyper. / Absent Present, 72 Stom._Axial_simp. / Absent Present, 73 Axial_jaws / Absent Present, 74 Ax._J._1pair_lat. / Absent Present, 75 Ax.J._1or2_DV_pairs / Absent Present, 76 Ax.J.cross_circle / Absent Present, 77 Proventricle / Absent Present, 78 V.stom.not_evert. / Absent Present, 79 V._stom.evert. / Absent Present, 80 V._hyp.stom.ridged / Absent Present, 81 V._hyp.stom.jaws / Absent Present, 82 V.jaws._Labidognath / Absent Present, 83 V._jaws_Prionognaths / Absent Present, 84 Gular / Absent Present, 85 'Gut L./Fold' / Absent Present, 86 Gut_side_br. / Absent Present, 87 Gut_closed / Absent Present, 88 Gut_straight_tube / Absent Present, 89 AdultMeta. / Absent Present, 90 AdultProto. / Absent Present, 91 Cilioph.Org / Absent Present, 92 Mixonephromixia / Absent Present, 93 Metanephromixia / Absent Present, 94 Protonephromixia / Absent Present, 95 'Coel/Nep.Sep.' / Absent Present, 96 'Ne./Cl.most seg.' / Absent Present, 97 'N./Cl.1pairant.exc' / Absent Present, 98 'N./Cl restricted' / Absent Present, 99 'N./Cl. ant sterile' / Absent Present, 100 Sperm / Absent Present, 101 Circ._Limited / Absent Present, 102 Closed_Circulation / Absent Present, 103 Ostiate_Heart / Absent Present, 104 Heart_Body / Absent Present, 105 Chaetae / Absent Present, 106 'Chaetae=Calc.' / Absent Present, 107 Chaet.Inv. / Absent Present, 108 Aciculae / Absent Present, 109 Compounds / Absent Present, 110 Compound_2_lig. / Absent Present, 111 Compound_1_lig. / Absent Present, 112 Compound_fold / Absent Present, 113 Compound_tapers / Absent Present, 114 Compound_falcate / Absent Present, 115 Compound_dentate / Absent Present, 116 Compound_hooked / Absent Present, 117 Capillaries / Absent Present, 118 Spines_1_chaetiger / Absent Present, 119 Spines_generally / Absent Present, 120 Hooded_Chaetae / Absent Present, 121 Falcate_hooks / Absent Present, 122 Dentate_Hooks / Absent Present, 123 Uncini / Absent Present, 124 Fine_Silk_Notochaetae / Absent Present, 125 Coelom / Absent Present, 126 Nerve_Ring / Absent Present, 127 Annelid_cross / Absent Present, 128 Molluscan_Cross / Absent Present, 129 Trochophore / Absent Present, 130 Prototroch / Absent Present, 131 Metatroch / Absent Present, 132 Food_Groove / Absent Present, 133 Oral_Brush / Absent Present, 134 Akrotroch / Absent Present, 135 Meniscotroch / Absent Present, 136 Telotroch / Absent Present, 137 Neurotroch / Absent Present, 138 Protonephridia / Absent Present, 139 Apical_tuft / Absent Present, 140 Opposed_Band / Absent Present, ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140] [ . . . . . . . . . . . . . .] Aberrantidae 10000100011010000000010111001101000010000001010000000000100??0010?00?0??00000???000?0001??????????????001000000000001000000011?????????????? Acoetidae 1000000011111000000001101100110010001000001101000111001000000001000100001010000000000100100?????????????1001000000001010000111?????????????? Acrocirridae 1000000010001101000100001100?101000001000001100000000000100?00100?00100000000010000?000110010000100001011000100100011000000011?????????????? Aeolosomatidae 01000000100000000000000011000101000010000000000000000000000000000?001000000000100000000110010001000001001000000000001000000011??000000000?00 Alciopidae 1000000011111000000001101100?1100000001000110100010010100000000100010000000000000000000101000101000010001001101010001000000011?????????????? Alvinellidae 1000000010001101000010001100?100010001000001001000000000001?0000000010000000010000011000100100000101010?1000000000001100001011??0100000????0 Ampharetidae 100000001000110100001000110011000100010000010010000000000011000010001000000001000001100010010000010001011000000000001100001011??011000010?10 Amphinomidae 100000001111100000000101100111000010100000011000011000110000000001000010000000010000000110010001000001001101000000001010000011??011100011?11 Aphroditidae 100000001110100000000110110011001000100000110100011100100000000100010000101000000000010010010001000?01001001000000001010000111??01000011??1? Apistobranchidae 1000000010001101000100001010110100001000000100001100000000010000110000010000000000000001100??000001001001001000000001000000011?????????????? Arenicolidae 10000000100000000000000011001101000001000001001000000001000000000100000100000000000100011001000001000100100000000000100001001110010000011?10 Capitellidae 10000000100000000000000011001101000001000001001000000000000100000000000100000000000100011000001000001000100000000000100101001110010000011110 Chaetopteridae 10000000100011010001000010101101000000010001001000000000000?00000?1000000000000000000001100??0000010010010000000000011000010110?0?1000000?10 Chrysopetalidae 1000000011111000000001101100?100100010000011000101100010000000010001000011000000000000011000100????001001001101001001000000011??010000111?10 Cirratulidae 100000001000110100010000110011010000010000011000000000001000000001001000000000100001000110010000100001011000000000001010000011??010001011?10 Clitellata 10001000000000000000000000001101000010000000000000000000000000000100000000000000000000011000001000010100100000000000101000001110010000001100 Cossuridae 1000100000000000000000001100110100001000000110000000000000000000100000000000000000000001????????001001001000000000001000000011?????????????? Ctenodrilidae 100000001000000000000000110001010000010000000000000000001000000001001000000000100000000110010000100?01011000000000001000010011??010000011?00 Diurodrilidae 100010000000000000000000??00?1010000000000000000000000000000000101001000000000100000000101000??00??01000000000000000000000001??????????????? Dorvilleidae 1000010001111000000001011100110100001000000101000110001000001001010000100000000010000001100??00100000100100111000010100000001110011001011?10 Echiura 0000000010000000000000000000000000000000000000000000000000000000000000000000000000000000100??0?00000010010000000000000001000111011110??11111 Entoprocta 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000010100000000001000000000000000000000000000111100001111 Eulepethidae 1000000011111000000001101100?1001000100000110100011100100000000100010000101000000000010010????????????0?1001000000001010000011?????????????? Eunicidae 100001000111100000000101110011010000100000010100011000110000100101000010000000001100000110010001000001001001110000101001000011??011001011?10 Euphrosinidae 10000000111110000000010?100111000010100000010001011000110000000101000010000000010000000110010001000?01001101000000001010000011?????????1???? Fauveliopsidae 1000000010001101000100001100?101000010000001100000000000000?001001001000000000100001??0?????????????010?100000000000100000001??????????????? Flabelligeridae 10000000100011010001000011001101000010000001100000000000100?001001001000000000100001100010010000100001011000100100011000000011??010000010??0 Glyceridae 100000001101100000000110000011010000100000010100011000100000000100010000100100000000000101100101000?10001001101010001000000011??010000101?10 Goniadidae 10000000110110000000011000001101000000001001010001100010000000010001000010010000000?0?0?01000100001010001001101010001000000011??010000101??0 Hartmaniellidae 1000010000000000000001001100?101000010000001010001100010100??0010100001000000000101?0001??????????????0?10011100100010000000???????????????? Hesionidae 10000000111110000000011011001110000000100011010001100010000000010001000011000000000000011010100100000100100110101000100000001110010000101?10 Histriobdellidae 100010000111100000000101??0011010000000000000000000000000000?00001000010000000001010000101000010000010000000000000000000000011??000000000?00 Ichthyotomidae 01000000111110000000011011001101000010000001010001100010000??0010?010000110000000000000110001001000010001001101010101000000011?????????????? Iospilidae 1000000010001000000001101100?1100000001000110100011000100000?0000001000011000000000?0?0???????????????0?100110101000000000001??????????????? Lacydoniidae 1000000011011000000001101100111000000010001101000100101000000000100100000000000000000001??????????????0?1001101010001000000011?????????????? Longosomatidae 1000000010001101000100001010?101000001000001000010000000100?00000?00100000000010000?0?0???????????????0?1000000000001010000011?????????????? Lopadorhynchidae 1000000011011000000001101100?110000000100011010001001010000??0?100010000??000000000?0?0???????????????0?1001101010000000000011??010000100100 Lumbrineridae 10000100011100000000000011001101000010000001010001000110000010010100001000000000110000011001000????0??0?1001110000101000000011??011001010?10 Magelonidae 1000000010001100000100000000110100000100000100001000000000010001010010000000001000000001???????0001001001000000000001001010011??010000000110 Maldanidae 01000000100000000000000011001101000001000001001000000000000000001100?00?000000?0000100011001000001000100100000000000100001001110010000011?10 Mollusca 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000001?000000000001000000000000000000000001101010000010110 Myzostomidae 001000001000000000000000??00?101000010000001010001100010000000000?010000000000000000010001000010000010001001000000001000100011??01100??10?10 Nautiliniellidae 010000001101100000000110??00?101000010000001010001100010000010000001000000001000000?0?????????????????0?10010000000010000000???????????????? Nemertea 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000010100000000001000000000000000000000001000000000000?10 Nephtyidae 100000001101100000000110110011100000100000111000011000100000000100010000110000000000000101100101000?01001001000000001000000011??0100?0110?10 Nereididae 1000000011011000000001101100111000000010001101000110001000000001000100001100000000000001101000110000010010011010010000000000111001000??10?10 Nerillidae 010000001111100000000101110011010000100000011000000000000000000101001000000000100000000110010001000001001000101010001000000011??010000011?10 Oenonidae 10000100011100000000000011001101000010000001010001000100000010010100001000000000101?0?0?????????????0100100100000000100000001??????????????? Onuphidae 10001000011110000000010111001101000010000001010001100011000010010100001000000000110000011001000?0?00010010011100001010000000111?011001010?10 Opheliidae 10000000100000000000000011001101000010000001100000000001000100001100000100000000000100011001000?0??001011000000000001000000011??011?00011?11 Orbiniidae 1000100000000000000000001100110100001000000110000000000001010100110010000000001000000001100??001000?010?100100000000101000001110011001011100 Oweniidae 001010000000111010000000??0011010000000100010010000000000000000001001000000000100000000110010000000001001000000000001000010011??011100000111 Paralacydoniidae 100000001101100000000110??00?110000000001001010001100010000000???001000000000000000?0?0?????????????????1001101010001000000011??010000010?10 Paraonidae 0100000011100000000000001100110100001000000110000000000001010000110010000000001000000001100??000001001001000000000001001000011??010000011?00 Parergodrilidae 0100100000000000000000001100110100001000000000000000000000000000000010000000001000000001100???0?000?01001000000000001000000011?????????????? Pectinariidae 001000001000110100001000101011000100000100010010000000000011000001001000000001000001100010010000010001011000000000001100001011??010000011110 Pholoidae 100000001111100000000110??00?1001000100000110100010100100000000100010000101000000000000110???0?00010??0?1001101000101000000011??010010111?10 Phyllodocidae 1000000011111000000001101100111000000010001101000100101000000001000100000000000000000001010001010000100010011010100010000000111?010000111110 Pilargidae 1000000011111000000001101100?110000000100011010001100010000000010001000000000000000?0?0???????????????0?1001000000001010000011??010000110??0 Pisionidae 100000001101100000000110000011100000001000110100011000100000000100010000101000000000000101000100010010001001101001001000000011??010000101?10 Platyhelminthes 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000001000000000000000000000000000000000000110 Poecilochaetidae 1000000010001101000100001010110100001000000100001000000100010000110010000000001000000001100??000001001001000000000001010000011????00???11??0 Poeobiidae 1000000010001101000100001100?1010000000000000000000000001000001001001000000000100001100010010000100001010000000000000000000011?????????????? Polygordiidae 01001000000011101000000011001101000000000000000000000000000000010110000000000000000000011000000100000000100000000000100000001110111100010111 Polynoidae 10000000111110000000011011001100100000100011010001110010000000010001000010100000000001001001000100000100100100000000101000001110010010101110 Pontodoridae 1000000011011000000001101100?11000000010001101000110001000000001000100000000100000000001????????0000??0?10011010100000000000???????????????? Potamodrilidae 01000000100000000000000011001101000010000000000000000000000000000?0010000000001000000001100?00?001000100100000000000100000001??????????????? Protodrilidae 010010000000111010000000110011010000000000000000000000000000000101001000000000100000000101000010010001000000000000000000000011???11000011110 Protodriloididae 0100100000001110100000001100110100001000000000000000000000000001010010000000001000000001100??0?0001001001000000000000000010011??010000000?00 Psammodrilidae 10001000000000000000000011001101000000000001001000000000000000000?0000000000000000000001100??0?0001010001000000000000000010011??010000011?10 Questidae 1000100000000000000000001100?10100000100000110000000000010010000110010000000001000000001??0????0000001001000000000001000010011??0??????????0 Rotifera 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000010100000000001000000000000000000000000000000000000100 Sabellariidae 001000001000110100010000110011000100000100010010000000000100000000100000000000000000000110010000100001011010000000001100001011??010000011110 Sabellidae 001000010000111000100000110011010000000100010010000000000000000000100000000000000000000110010000100001001010000000001000011011??011?00001?00 Saccocirridae 1000100000001110100000001100110100001000000100000000000000000001010010000000001000000001100??001000?000010000000000010000000111??11000011?1? Scalibregmatidae 100010000000000000000000110011010000100000011000000000010001000010000001000000000000000110010001000?01001000000000001000000011?????????????? Serpulidae 00100001000011100010000011001101000000010001001000000000000000000010000000000000000000011001000010000100101000000000100000101110111100001111 Siboglinidae 100000100000110100010000??00110000010000000100100000000000000000000001000000000000000010??0???00100001001000000000001000001011??010000011??0 Sigalionidae 100000001111100000000110110011001000100000110100011100100000000100010000101000000000010010010001000001001001101000101000000011100100101???10 Sipuncula 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000001000000000000000000000001101011000000010 Sphaerodoridae 1000000011111000000001101100111000000010001101000000001000000001000100000000100000000001100??000010?10001001101001001000000011??0??????????0 Spintheridae 1000000011100000000000000000?100001010000001000100000010000000010?0000000000000000000100????????????01001001100100010010000011?????????????? Spionidae 10000000111011010001000010101101000010000001000010000000010101001100?00?000000?000000001100??00000100100100000000000100101001110010000011?10 Sternaspidae 100000001000000000000000?0000101000010000001100000000000100000100?000001000000000000100010010000100?01001000000000001100000011100?0000000?10 Syllidae 1000000011111000000001101100110100000010001101000110001000000001000100001000100000000001100010010000010010011010001010000000111?010001011110 Terebellidae 00010000100011100100000011001100010001000001001000000000001000000100100000000100000110001001000001000101100000000000100000101110010000011110 Tomopteridae 0100000010001000000001101100?1100000001000110100000000000000000000010000000000000000000101000101000010001001000000000000000011??010000000?00 Trichobranchidae 0001000010001110010000001100?10001000100000100100000000000100000010010000000010000011000100??000010001011000000000001000011011??010000011?1? Trochochaetidae 10000000111011010001000010101101000010000001000010000000000101001000000100000000000?0?0?100??000001???0?1000000000001010000011??010000010??0 Typhloscolecidae 10000000111000000000000011001110000000100011010001001010000000010001000000000000000?0?0?01?00???????10001001000000001000000011?????????????? Uncispionidae 100000001110110100010000??00?101000010000001000010000000010?00001?00000100000000000?0?0???????????????0?10000000000010000100???????????????? ; END; BEGIN ASSUMPTIONS; WTSET * UNTITLED = 125: 17-21 , 250: 15-16 23-24 51-54 74-76 82-83 110-116 , 1000: 84-105 125-140 1-10 13 25 29-30 44 56-72 , 500: 11-12 14 22 26-28 31-43 45-50 55 73 77-81 106-109 117-124 ; END; [ The following blocks are output data for analysis step 504 ] BEGIN TREES; TITLE Tb5284; LINK TAXA = TaxaForAnalysisStep504; TREE Fig._3A = [&R] (Rotifera,(Entoprocta,(Mollusca,Sipuncula,(Echiura,(Clitellata,(((((((((Acoetidae,Aphroditidae),Eulepethidae,Polynoidae),Sigalionidae),Pholoidae),Chrysopetalidae,(((Glyceridae,Goniadidae),Pisionidae),Lacydoniidae,Phyllodocidae),Hesionidae,Nephtyidae,Nereididae,Paralacydoniidae,Pilargidae,Sphaerodoridae,Syllidae),((Amphinomidae,Euphrosinidae),(((Dorvilleidae,Lumbrineridae),Eunicidae),Onuphidae))),((((Acrocirridae,Flabelligeridae),Cirratulidae),(((Alvinellidae,Ampharetidae),Pectinariidae),(Terebellidae,Trichobranchidae))),((Arenicolidae,Maldanidae),Capitellidae)),(((Apistobranchidae,(Spionidae,Trochochaetidae)),Poecilochaetidae),(Chaetopteridae,(Longosomatidae,Magelonidae))),((Sabellariidae,(Sabellidae,Serpulidae)),Siboglinidae)),((Oweniidae,(Polygordiidae,(Protodrilidae,Protodriloididae))),Saccocirridae)),(Cossuridae,((Opheliidae,Scalibregmatidae),((Orbiniidae,Paraonidae),Questidae)))))))),Platyhelminthes,Nemertea); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3410] END;