#NEXUS [written Thu Jul 11 22:20:23 CEST 2013 by Mesquite version 2.72 (build 527) at zo-laptopTS-2.local/192.168.2.101] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=38; TAXLABELS Clitellata Pectinariidae Alvinellidae Arenicolidae Opheliidae Spionidae Serpulidae Echiuridae Capitellidae Flabelligeridae Cirratulidae Siboglinidae Glyceridae Phyllodocidae Nereiididae Syllidae Lumbrineridae Onuphidae Sigalionidae Orbiniidae Amphinomidae Sipuncula Chaetopteridae Brachiopoda Gastropoda Bivalvia Myzostomidae Nemertea Bryozoa Acrocirridae Eunicidae Magelonidae Nephtyidae Oweniidae Polynoidae Sabellidae Sabellariidae Tomopteridae ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=99; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A"; CHARSTATELABELS 1 Segmentation / absent present, 2 Longitudinal_muscles_bands / absent present, 3 Circular_muscles / present absent, 4 Coelom / absent present, 5 Head_structure / 'prostomium and ring-like peristomium' 'prostomium and two-ringlike peristomium' prostomium_and_peristomium_limited_to_lips, 6 Retractable_head / absent present, 7 Annulated_prostomium_formed_by_fused_palp_bases / absent present, 8 First_body_segment / 'similar to following segments, or more or less reduced' surrounding_head fused_to_head 'elongated to form frenular/vestimental region', 9 Second_body_segment / short elongated_to_form_trunk, 10 Anterior_cirri / absent present, 11 Palps / absent present buccal_tentacles sensory_palpodes, 12 Buccal_tentacles_retractable_into_mouth / absent present, 13 Palp_origin / prostomial peristomial, 14 Number_of_palps / one_pair_of_palps 'multiple palps, or branchial crown', 15 Median_prostomial_antenna / absent present, 16 Lateral_prostomial_antennae / absent present, 17 Peristomial_cirri / absent present, 18 Palp_structure / solid grooved internal_canal, 19 Parapodia / absent present, 20 Shape_of_notopodium / absent tori_or_small_lobes_ prominent_lobes_present, 21 Shape_of_neuropodium / absent tori_or_small_lobes promiment_lobes_present, 22 Presence_of_tori / absent present, 23 Dorsal_cirri / absent present some_transformed_into_elytra, 24 Ventral_cirri / absent present, 25 Parapodial_branchiae / absent present, 26 Dorsal_branchiae / absent present limited_to_a_few_anterior_segments, 27 'Lateral organs/dorsal cirrus organs' / absent present, 28 Dorsal_organs / absent present, 29 Epidermal_papillae / absent present, 30 Pygidial_cirri / absent present, 31 Number_of_pygidial_cirri / one_pair two_or_more_pairs, 32 Ventral_glandular_area_on_anterior_segments / absent present present_with_posterior_ventral_stripe, 33 Ventral_ciliary_field / absent present ciliary_groove, 34 Duogland_system / absent present, 35 Circulatory_system / absent_or_limited closed, 36 Heart_body / absent present, 37 Nervous_system / subepidermal intraepidermal, 38 Corpora_pedunculata / absent present, 39 Nuchal_organs / absent present internalized, 40 Nuchal_organ_structure / pits_or_grooves posterior_projections caruncles positioned_underneath_ventral_roots_of_circuesophageal_connect, 41 Branchial_ocelli / absent present, 42 Cerebral_commissures / four none, 43 Nuchal_commissures / absent present, 44 Commissural_ganglion / absent present, 45 Dorsal_ganglia / absent present, 46 Phaosomes / absent present, 47 Eyes / present absent, 48 Multiciliary_eye / absent present, 49 Number_of_multiciliary_eyes / 1_pair 2_pairs, 50 'Spionidan/protodrilidan light-sensitive "statocysts"' / absent present, 51 Chaetae / absent present calcified, 52 Internatized_supporting_chaetae / absent present, 53 Compound_chaetae / absent with_one_ligament with_two_ligaments with_a_fold, 54 'Uncini/hooks' / absent present, 55 'Shape of uncini/hooks' / absent 'present, simple, with intermediate filaments' hooded bearded, 56 'Lyrate/forked chaetae' / absent present, 57 Chaetal_arrangement / transversal_rows notopodial_bundles additional_short_rows, 58 Neuropodial_chaetal_turnover / ventrad dorsad chaetal_inversion, 59 Fine_silk_notochaetae / absent present, 60 Stomodaeum / 'absent/occluded' ventral_buccal_organ axial_muscular_proboscis axial_simple_proboscis ventral_muscular_proboscis dorsal_pharynx, 61 Dorsolateral_folds / absent present modified_into_tentacular_crown, 62 'Axial-stomodaeum jaws' / no_jaws lateral_pairs_of_jaws DV_pairs cross_or_circle_of_jaws, 63 Jaw_venom_glands / absent present, 64 Proventricle / absent present, 65 Eversibility_of_ventral_buccal_organ / eversible 'non-eversible', 66 'Ventral-proboscis jaws' / ctenognath prionognath labidognath absent, 67 Gular_membrane / absent present, 68 Gut / straight lateral_folds side_branches coiled occluded coiled_with_anterior_anus, 69 Trophosome / absent present, 70 Adult_nephridia / protonephridia metanephridia 'protonephridia with funnel (protonephromixia)', 71 Terminal_cell / monociliate multiciliate, 72 Filter_of_terminal_cells_with_clefts / absent present, 73 Microvillar_filter / absent present, 74 Ciliophagocytal_organ / absent present, 75 Distribution_of_segmental_organs / in_most_segments anterior_sterile_nephridia_and_posterior_gonoducts 'one pair of anterior nephridia, posterior gonoducts', 76 Clitellum / absent present, 77 '"Head kidneys"' / protonephridia metanephridia, 78 Nephridial_podocyte_lining / absent present, 79 Metanephridial_mantle_cell / absent present, 80 Metanephridial_duct / paired unpaired_dorsal, 81 Gonoducts / 'nephridial/coelomoduct' separate 'with distal prostate-glandular part', 82 Hermaphroditism / absent present, 83 Sperm_mitochondrial_interpolation / absent present, 84 Sperm_flagellum / posterior anterior absent two, 85 Acrosome / absent present acrosomal_tube, 86 Prototroch / absent present, 87 Metatroch / absent present, 88 Food_groove / absent present, 89 Oral_brush / absent present, 90 Akrotroch / absent present, 91 Meniscotroch / absent present, 92 Telotroch / absent present, 93 Neurotroch / absent present, 94 Apical_tuft / absent present, 95 'Building/cementing organ' / absent present, 96 Tube / absent 'sediment/mucuos' calcareous 'chitin-proteinaceous', 97 Gene_order_1 / absent present, 98 Gene_order_2 / absent present, 99 Gene_order_3 / absent present ; MATRIX Clitellata 11010000000---000-0------00000-00010000-010??100-0100000??050-00--0001???0?1101011102?0??000?000??? Pectinariidae 1101?0020?20--000-111100021000-20011001101000000-010011010011-001-1101???01001000000110000011111??? Alvinellidae 1?0100020021--000-1211?002?000-000110?0-0????01--010011010010-001-1101???010?0000010110??00???01??? Arenicolidae 11010000000---000-111100101000-0001000100????01--010013011031-00--1001???010?0000000110000011100??? Opheliidae 11110000003---000-11100010100110201000100???0000-0100000??031-00--1001???000???00000111?00011100??? Spionidae 11110000001-1000011(1 2)(1 2)00001110110001?001100011000-110012020031-000-0001???01010000000110000010101??? Serpulidae 11010000001-010001121100000000-?0011011010011000-0100110?2000-00--000110102001010000111100001102??? Echiuridae ?001?00??00---000-0------00000-00000000-0?0??01--0100000??0?0-00--03010?00?00000000011110??11100101 Capitellidae 11010000000---000-111100??1000-0000?00100????000-010012000030-00--1001???0?000001000110000011100??? Flabelligeridae 11010100001-10000111100001?010-00011001000011?00-0103000??011-000-0101???020?0000000110??0010?00??? Cirratulidae 11010000001-1100011110?0010000-0001100100?000000-010000000011-000-0001???020?0000000110000011000??? Siboglinidae 1101?003101-?10000111100000000-00011100?0????01--01001100?000-0?--041????020?00(0 1)0000110??0011?03111 Glyceridae 11012010001-00010012201110000100000?00100011101--0111000??020310--0002001100?0??00???10000101100??? Phyllodocidae 11112000011-00110012201100000100000?00100010000100111000??0200?0--000200100000??0000110000111100??? Nereiididae 11012000011-00010012201100000100001001100011100110111000??020100--0001???100?0001000110????10100111 Syllidae 11012000011-00110011201100?00100001000100001110110111000??020001--00011??0000??00000110??1011100??? Lumbrineridae 11011000000---000-122000(0 1)010010000??00100?????1--0112000??041-00-20001???000?0000000111??1010100??? Onuphidae 11010000001-001110112011101001000010001000111?0100112000??041-00-20001???000?0000000111001010101??? Sigalionidae 11112001011-001100122021000001000010011000011?0110111000??020210--0201???000?00000001100101??100??? Orbiniidae 11010000000---000-12200001110110001?001000100001001100012?011-000-000111?000000020??111??1011000111 Amphinomidae 11012000001-00110012201110?00100001000120010100110210000??041-00-30001???000?0000000111100011100??? Sipuncula 0001?10??00-----0-0------00000-0000?00??0?0??000-00--------12-00--0501???0?0?1000000111000000100?10 Chaetopteridae 11010000001-100?0112110000?000-00011001101001000-?1101100?00?-00--0001???010000000001?1000000101??? Brachiopoda 00?1-0---00---???-0------0000--0?01?100-0????000-0100000??0?0-00--0?01???0?0?0000000?00000000000000 Gastropoda 000?-0---00---???-0------0000--0?00?000-0????100-00--------?0-00--00011110?000000000111100000100000 Bivalvia 000?-0---00---???-0------0000--0?00?000-0????000-00--------?0-00--00011110?000000000111000000000000 Myzostomidae ?000?00?000---000-102011?00000-0000?000-0?????1--0110000??0??-00--020011100000?0110101100??10100111 Nemertea 0111-0---00---???-0------0?00--0?01?000-0?011000-00--------00-00--0000111?-0----?0?0110000000100000 Bryozoa 0001-1---00---???-0------0000--0?000000-0000001--00--------?0-00--050?---?-0----?102000000000100000 Acrocirridae 1??10000001-10000111100001?010000-1100100?????00-0103000??01?-000-??0????020???000001?????????00??? Eunicidae 11011000001-001110112011101001000-1000100010100100112??0??041-00-20001???000?0000000111??1011100??? Magelonidae 11112000001-100000122000001001000-11000-000110100110012020011-000-000?????100????000110000000100??? Nephtyidae 11112000011-0001001220111?0001000-1001100?????01(0 1)011000???020100--0002001100?0??00???100?0110100??? Oweniidae 1111?000001-?00001111100000000100-10100-0????000-010011000011-000-00010000?001000000111100000101??? Polynoidae 11112001011-001100122021000001000-1001100001100110110000??020210--020101100000000000110010101100??? Sabellidae 11010000001-010001111100000000100-10001010010000-0100110?2000-00--0001???020?1010000111?00001001??? Sabellariidae 11012002001-100001112100010000000-11001000010000-0100110??000-00--000101102000000000110000011111??? Tomopteridae 1??12000011-000000122000??0000000-0?00100?????01001?0000??0200?0--0002101000?0??0003010??0000000??? ; END; BEGIN TREES; Title Imported_trees; LINK Taxa = Taxa; TRANSLATE 1 Clitellata, 2 Pectinariidae, 3 Alvinellidae, 4 Arenicolidae, 5 Opheliidae, 6 Spionidae, 7 Serpulidae, 8 Echiuridae, 9 Capitellidae, 10 Flabelligeridae, 11 Cirratulidae, 12 Siboglinidae, 13 Glyceridae, 14 Phyllodocidae, 15 Nereiididae, 16 Syllidae, 17 Lumbrineridae, 18 Onuphidae, 19 Sigalionidae, 20 Orbiniidae, 21 Amphinomidae, 22 Sipuncula, 23 Chaetopteridae, 24 Brachiopoda, 25 Gastropoda, 26 Bivalvia, 27 Myzostomidae, 28 Nemertea, 29 Bryozoa, 30 Acrocirridae, 31 Eunicidae, 32 Magelonidae, 33 Nephtyidae, 34 Oweniidae, 35 Polynoidae, 36 Sabellidae, 37 Sabellariidae, 38 Tomopteridae; TREE Imported_tree_0 = ((((((((((((1,((3,2),4)),((8,9),5)),((6,37),(36,7))),((((10,30),11),12),20)),((((((38,13),14),(33,15)),((35,19),16)),((31,18),17)),27)),(22,21)),23),(34,32)),28),(25,26)),24),29); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 99; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 99; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1373574023844; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7783031546635512659; tell It; setDefaultOrder 7 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 31 32 33 34 35 37 38 40 39 41 42 43 44 45 46 47; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2019260048541132220; checksumv 0 2 199546791 null numChars 99 short true bits 63 states 63 sumSquaresStatesOnly 12198.0 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 459; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 716; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7783031546635512659 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1033.1370514497666.2166782243770248317; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 649; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '((((((((((((1,((3,2),4)),((8,9),5)),((6,37),(36,7))),((((10,30),11),12),20)),((((((38,13),14),(33,15)),((35,19),16)),((31,18),17)),27)),(22,21)),23),(34,32)),28),(25,26)),24),29);'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; newAssistant #mesquite.ancstates.TraceCharOverTrees.TraceCharOverTrees; tell It; suppress ; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #2019260048541132220; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; toggleMPRsMode off; endTell; endTell; setCharacter 5; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setNumTrees 100; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; toggleGray off; endTell; toggleShowLegend on; toggleShowNodeAbsent on; toggleShowEquivocal on; setMode Count_Trees_with_Uniquely_Best_States; setInitialOffsetX 4; setInitialOffsetY -252; setLegendWidth 142; setLegendHeight 236; desuppress ; endTell; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2019260048541132220 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 50; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 629; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; colorCells #mesquite.charMatrices.NoColor.NoColor; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 649; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam; endTell; rowsAreCharacters on; toggleConstrainChar on; toggleConstrainCharNum 3; togglePanel off; toggleSummaryPanel off; endTell; showWindow; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;