#NEXUS [written Sat Nov 16 20:31:40 CET 2019 by Mesquite version 3.6 (build 917) at Agnese-laptop/192.168.1.39] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=101; TAXLABELS Aetiocetus Aglaocetus Agorophius Albertocetus Albireo Ambulocetus Archaeodelphis Artiocetus Atocetus Balaena Balaenoptera Basilosaurus Berardius Brachydelphis Caperea Cephalorhynchus Cetotherium Chonecetus Cophocetus Coronodon Cotylocara Delphinapterus Delphinus Diorocetus Dorudon Echovenator Eomysticetus Eschrichtioides Eschrichtius Eubalaena Feresa Fucaia Georgiacetus Globicephala Grampus Hyperoodon Indopacetus Inermorostrum Inia Isocetus Janjucetus Kentriodon Kogia Lagenodelphis Lagenorhynchus Lipotes Lissodelphis Llanocetus Maiacetus Mammalodon Matapanui Megaptera Mesoplodon Micromysticetus Mirocetus Mixocetus Monodon Morawanocetus Mystacodon Neophocaena Ninoziphius Notocetus Orcaella Orcinus Orycterocetus Pakicetus Parabalaenoptera Parapontoporia Parietobalaena Patriocetus Pelocetus Peponocephala Phocoena Phocoenoides Physeter Platanista Pliopontos Pontoporia Prosqualodon Protocetus Pseudorca Remingtonocetus Rodhocetus Simocetus Sotalia Sousa Squalodon Squaloziphius Stenella Steno Tasmacetus Tohoraata Tokarahia Tursiops Waharoa Waipatia Xenorophus Xiphiacetus Yamatocetus Zarhachis Ziphius ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=4; FORMAT DATATYPE = STANDARD RESPECTCASE GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A B C D"; CHARSTATELABELS 1 Habitat / Riverine 'Riv/Estuarine' 'Riv/Est/MarCos' 'Est/MC' MC 'MC/MarBenth' 'MarPel/MC' MP 'MP/MC/MB', 2 Prey_capture / 'Biting/crush' 'Bit/crush/Suction' 'Bit/crush/Filter' Suc 'Fil/Suc' Fil, 3 'Teeth+cusps' / Heterodont Homodont Reduced Absent, 4 Prey_type / Fish Squid 'Fis/Squ' Zooplkt BenthInv 'Zp/BI' 'Fis/BI' 'Fis/Zp(/BI)' 'Fis/Squ/BI' 'Fis/Tetrapods' ; MATRIX Aetiocetus 6407 Aglaocetus 6537 Agorophius 7102 Albertocetus 7102 Albireo 6112 Ambulocetus 3000 Archaeodelphis 61?2 Artiocetus 3000 Atocetus 7112 Balaena 7533 Balaenoptera 7537 Basilosaurus 6009 Berardius 7322 Brachydelphis 6112 Caperea 7533 Cephalorhynchus 4112 Cetotherium 6537 Chonecetus 64?7 Cophocetus 6537 Coronodon 6407 Cotylocara 6102 Delphinapterus 8316 Delphinus 6112 Diorocetus 6537 Dorudon 6009 Echovenator 6000 Eomysticetus 6537 Eschrichtioides 8535 Eschrichtius 8534 Eubalaena 7533 Feresa 7112 Fucaia 6407 Georgiacetus 6000 Globicephala 7312 Grampus 7311 Hyperoodon 7322 Indopacetus 7321 Inermorostrum 6332 Inia 0010 Isocetus 6537 Janjucetus 6000 Kentriodon 6112 Kogia 7312 Lagenodelphis 7112 Lagenorhynchus 6112 Lipotes 0010 Lissodelphis 7112 Llanocetus 6207 Maiacetus 3000 Mammalodon 5304 Matapanui 6537 Megaptera 7537 Mesoplodon 7322 Micromysticetus 6537 Mirocetus 6000 Mixocetus 6537 Monodon 6322 Morawanocetus 6407 Mystacodon 5304 Neophocaena 6112 Ninoziphius 6118 Notocetus 6112 Orcaella 3116 Orcinus 6019 Orycterocetus 6010 Pakicetus 1000 Parabalaenoptera 6537 Parapontoporia 3010 Parietobalaena 6537 Patriocetus 6000 Pelocetus 6537 Peponocephala 7112 Phocoena 6112 Phocoenoides 6112 Physeter 7312 Platanista 0016 Pliopontos 6112 Pontoporia 1012 Prosqualodon 6000 Protocetus 6000 Pseudorca 6112 Remingtonocetus 4000 Rodhocetus 4000 Simocetus 6000 Sotalia 2116 Sousa 3110 Squalodon 6000 Squaloziphius 60?0 Stenella 7112 Steno 7112 Tasmacetus 7322 Tohoraata 6537 Tokarahia 6537 Tursiops 6112 Waharoa 6533 Waipatia 6000 Xenorophus 6000 Xiphiacetus 3010 Yamatocetus 6537 Zarhachis 6010 Ziphius 7322 ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 4; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1- 4; END; BEGIN TREES; Title 'Trees from "tree cetacea.tre"'; ID 0163ae2518572; LINK Taxa = Taxa; TRANSLATE [0] 20 Aetiocetus, [1] 28 Aglaocetus, [2] 51 Agorophius, [3] 46 Albertocetus, [4] 81 Albireo, [5] 2 Ambulocetus, [6] 44 Archaeodelphis, [7] 6 Artiocetus, [8] 80 Atocetus, [9] 36 Balaena, [10] 42 Balaenoptera, [11] 11 Basilosaurus, [12] 67 Berardius, [13] 75 Brachydelphis, [14] 38 Caperea, [15] 90 Cephalorhynchus, [16] 32 Cetotherium, [17] 18 Chonecetus, [18] 34 Cophocetus, [19] 12 Coronodon, [20] 48 Cotylocara, [21] 83 Delphinapterus, [22] 101 Delphinus, [23] 29 Diorocetus, [24] 10 Dorudon, [25] 49 Echovenator, [26] 22 Eomysticetus, [27] 40 Eschrichtioides, [28] 39 Eschrichtius, [29] 37 Eubalaena, [30] 95 Feresa, [31] 19 Fucaia, [32] 8 Georgiacetus, [33] 97 Globicephala, [34] 93 Grampus, [35] 70 Hyperoodon, [36] 71 Indopacetus, [37] 47 Inermorostrum, [38] 77 Inia, [39] 31 Isocetus, [40] 15 Janjucetus, [41] 79 Kentriodon, [42] 60 Kogia, [43] 100 Lagenodelphis, [44] 88 Lagenorhynchus, [45] 73 Lipotes, [46] 89 Lissodelphis, [47] 13 Llanocetus, [48] 4 Maiacetus, [49] 16 Mammalodon, [50] 24 Matapanui, [51] 43 Megaptera, [52] 72 Mesoplodon, [53] 21 Micromysticetus, [54] 50 Mirocetus, [55] 33 Mixocetus, [56] 82 Monodon, [57] 17 Morawanocetus, [58] 14 Mystacodon, [59] 84 Neophocaena, [60] 66 Ninoziphius, [61] 63 Notocetus, [62] 91 Orcaella, [63] 87 Orcinus, [64] 59 Orycterocetus, [65] 54 Pakicetus, [66] 1 Parabalaenoptera, [67] 41 Parapontoporia, [68] 74 Parietobalaena, [69] 30 Patriocetus, [70] 52 Pelocetus, [71] 35 Peponocephala, [72] 96 Phocoena, [73] 85 Phocoenoides, [74] 86 Physeter, [75] 61 Platanista, [76] 65 Pliopontos, [77] 76 Pontoporia, [78] 78 Prosqualodon, [79] 57 Protocetus, [80] 7 Pseudorca, [81] 94 Remingtonocetus, [82] 3 Rodhocetus, [83] 5 Simocetus, [84] 53 Sotalia, [85] 98 Sousa, [86] 99 Squalodon, [87] 56 Squaloziphius, [88] 58 Stenella, [89] 102 Steno, [90] 92 Tasmacetus, [91] 69 Tohoraata, [92] 25 Tokarahia, [93] 26 Tursiops, [94] 103 Waharoa, [95] 27 Waipatia, [96] 55 Xenorophus, [97] 45 Xiphiacetus, [98] 62 Yamatocetus, [99] 23 Zarhachis, [100] 64 Ziphius; TREE branch_lenghts_tree = (54:1.5[%color = 1 ],(2:2[%color = 1 ],(94:5[%color = 1 ],(4:1[%color = 1 ],(3:1.5[%color = 1 ],(6:0.5[%color = 1 ],(57:0.5[%color = 1 ],(8:1[%color = 1 ],(10:1.2[%color = 1 ],(11:0.7[%color = 1 ],((12:7.8[%color = 8 ],((13:1.7[%color = 8 ],14:1.7[%color = 8 ]):0.1[%color = 8 ],((15:8.5[%color = 8 ],16:7.5[%color = 8 ]):0.5[%color = 8 ],(17:9[%color = 8 ],((18:8.8[%color = 8 ],(19:0.2[%color = 8 ],20:8.7[%color = 8 ]):0.1[%color = 8 ]):0.1[%color = 8 ],(((21:2.6[%color = 8 ],(22:0.2[%color = 8 ],62:1[%color = 8 ]):0.1[%color = 8 ]):0.1[%color = 8 ],(24:0.9[%color = 8 ],(69:2.1[%color = 8 ],(25:2[%color = 8 ],103:2[%color = 8 ]):0.1[%color = 8 ]):0.9[%color = 8 ]):1.2[%color = 8 ]):0.1[%color = 8 ],((28:10[%color = 13 ],(29:7.4[%color = 13 ],(74:7[%color = 13 ],(31:1.5[%color = 13 ],((32:7.5[%color = 13 ],33:9.5[%color = 13 ]):0.5[%color = 13 ],(34:0.5[%color = 13 ],52:5[%color = 13 ]):0.5[%color = 13 ]):1[%color = 13 ]):0.5[%color = 13 ]):0.4[%color = 13 ]):0.1[%color = 13 ]):5[%color = 13 ],((36:17[%color = 16 ],37:17[%color = 16 ]):10.5[%color = 16 ],(38:23.5[%color = 13 ],(39:21[%color = 11 ],(40:15.9[%color = 11 ],(1:11.8[%color = 11 ],(42:16[%color = 11 ],43:16[%color = 11 ]):4.3[%color = 11 ]):0.4[%color = 11 ]):0.3[%color = 11 ]):2.5[%color = 11 ]):4[%color = 16 ]):0.5[%color = 16 ]):1.5[%color = 13 ]):2.4[%color = 8 ]):0.1[%color = 8 ]):1[%color = 8 ]):2.8[%color = 8 ]):0.1[%color = 8 ]):0.1[%color = 8 ],((44:10.3[%color = 5 ],(55:0.5[%color = 5 ],(46:2.8[%color = 5 ],(47:0.2[%color = 5 ],(48:3[%color = 5 ],49:3[%color = 5 ]):1.9[%color = 5 ]):0.1[%color = 5 ]):1.5[%color = 5 ]):5.3[%color = 5 ]):0.1[%color = 5 ],(50:5.9[%color = 5 ],((51:7[%color = 5 ],30:3.5[%color = 5 ]):3.9[%color = 5 ],(5:2.7[%color = 5 ],((27:0.5[%color = 5 ],99:7[%color = 5 ]):8.5[%color = 5 ],(78:10.3[%color = 5 ],(56:11.6[%color = 5 ],((59:9[%color = 14 ],(60:24.5[%color = 14 ],86:24.5[%color = 14 ]):0.5[%color = 14 ]):7[%color = 14 ],((45:5[%color = 9 ],(63:1[%color = 9 ],(23:1.5[%color = 9 ],61:20[%color = 9 ]):3[%color = 9 ]):0.5[%color = 9 ]):8.4[%color = 9 ],((66:17.2[%color = 11 ],(67:22[%color = 11 ],(92:20.3[%color = 11 ],(64:18.6[%color = 11 ],(70:17.1[%color = 11 ],(71:15.9[%color = 11 ],72:15.9[%color = 11 ]):1.2[%color = 11 ]):1.5[%color = 11 ]):1.7[%color = 11 ]):1.7[%color = 11 ]):0.2[%color = 11 ]):9.3[%color = 11 ],(((73:7[%color = 6 ],41:4.4[%color = 6 ]):15[%color = 6 ],(75:5.5[%color = 6 ],(65:12[%color = 6 ],(77:16.5[%color = 6 ],76:16.5[%color = 6 ]):0.5[%color = 6 ]):0.5[%color = 6 ]):4.5[%color = 6 ]):3[%color = 6 ],(79:0.5,(80:10,(81:10.5,(((82:6.3,83:6.3):9.2,(84:8.5,(96:7,85:7):1.5):7):3,(87:10,((88:7.5,(89:4.3,90:4.3):3.2):1.4,((91:8,(102:7.3,(93:4.2,(7:3.7,(95:2.9,(35:2.1,97:2.1):0.8):0.8):0.4):3.1):0.7):0.4,(53:7,(98:3.8,(100:3.5,(101:2.2,(58:2,26:2):0.2):1.3):0.3):3.2):1.4):0.5):1.1):8.5):0.5):0.5):0.5):5):6.5[%color = 6 ]):0.4[%color = 11 ]):0.1[%color = 9 ]):1.1[%color = 14 ]):0.2[%color = 5 ]):0.2[%color = 5 ]):0.2[%color = 5 ]):0.2[%color = 5 ]):0.1[%color = 5 ]):1.9[%color = 5 ]):0.1[%color = 5 ]):4.5):0.5):1):1.5):4):1):0.5):1):1):1)[% ] [% ] [% setBetweenLong = color ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1573932700258; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7956429934027931330; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 660872237150309389; mqVersion 360; checksumv 0 3 3173008445 null getNumChars 4 numChars 4 getNumTaxa 101 numTaxa 101 short true bits 1023 states 1023 sumSquaresStatesOnly 2098094.0 sumSquares 2098094.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 276; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1920 940; setLocation -9 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7956429934027931330 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 0163ae2518572; toggleUseWeights off; endTell; setAssignedID 1972.1573152852267.7288337668865556299; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1644 868; setLocation -9 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.BallsNSticks.BallsNSticks; tell It; setSpotDiameter 22; setEdgeWidth 2; orientUp; useDiagonal; toggleBallsInternal on; toggleCosmic off; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; setFixedTaxonDistance 0; endTell; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors off; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; setSelectedTaxonHighlightMode 1; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; setTaxonNameStyler #mesquite.trees.NoColorForTaxon.NoColorForTaxon; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName off; showWindow; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; togglePredictions off; toggleGray off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #660872237150309389; endTell; endTell; setMethod #mesquite.stochchar.MargProbAncStates.MargProbAncStates; tell It; setModelSource #mesquite.stochchar.CurrentProbModels.CurrentProbModels; getEmployee #mesquite.stochchar.zMargLikeCateg.zMargLikeCateg; tell It; setReportMode Proportional_Likelihoods; setRootMode Use_Root_State_Frequencies_as_Prior; setDecision 2.0; setUnderflowCheckFreq 2; endTell; endTell; toggleShowSelectedOnly off; endTell; setCharacter 3; setMapping 1; toggleShowLegend on; setColorMode 0; toggleWeights on; setInitialOffsetX 4; setInitialOffsetY -327; setLegendWidth 142; setLegendHeight 196; resume ; 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; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #660872237150309389 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1644 868; setLocation -9 0; 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; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; togglePaleMissing off; toggleShowBoldCellText off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; endTell; getEmployee #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; 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.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;