#NEXUS [written Mon Jan 25 12:51:07 MST 2016 by Mesquite version 3.04 (build 725) at EBIO-C105-3M/10.200.164.73] BEGIN TAXA; TITLE Lecania_combined; DIMENSIONS NTAX=34; TAXLABELS Bacidina_ramea Bilimbia_lobulata Bilimbia_microcarpa Bilimbia_sabuletorum Bacidia_fuscoviridis Catillaria_aphana Catillaria_croatica Catillaria_scotinodes Cliostomum_tenerum Lecania_aipospila Lecania_atrynoides Lecania_brialmontii Lecania_cyrtella Lecania_cyrtellina Lecania_dubitans Lecania_erysibe Lecania_furfuracea Lecania_fuscella Lecania_gerlachei Lecania_glauca Lecania_hutchinsiae Lecania_inundata Lecania_naegelii Lecania_nylanderiana Lecania_rabenhorstii Lecania_racovitzae Lecania_sambucina Lecania_sp1 Lecania_sp2 Lecania_sylvestris Lecania_turicensis Lecidea_sphaerella Mycobilimbia_pilularis Mycobilimbia_tetramera ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=1; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1"; CHARSTATELABELS 1 'Reprod_Mode' ; MATRIX Bacidina_ramea 0 Bilimbia_lobulata 0 Bilimbia_microcarpa 0 Bilimbia_sabuletorum 0 Bacidia_fuscoviridis 0 Catillaria_aphana 0 Catillaria_croatica 1 Catillaria_scotinodes 0 Cliostomum_tenerum 0 Lecania_aipospila 0 Lecania_atrynoides 0 Lecania_brialmontii 0 Lecania_cyrtella 0 Lecania_cyrtellina 0 Lecania_dubitans 0 Lecania_erysibe 0 Lecania_furfuracea 0 Lecania_fuscella 0 Lecania_gerlachei 0 Lecania_glauca 1 Lecania_hutchinsiae 0 Lecania_inundata 0 Lecania_naegelii 0 Lecania_nylanderiana 0 Lecania_rabenhorstii 0 Lecania_racovitzae 0 Lecania_sambucina 0 Lecania_sp1 0 Lecania_sp2 0 Lecania_sylvestris 0 Lecania_turicensis 0 Lecidea_sphaerella 0 Mycobilimbia_pilularis 0 Mycobilimbia_tetramera 0 ; END; BEGIN TREES; Title Tb8211; LINK Taxa = Lecania_combined; TRANSLATE [0] n0 Bacidina_ramea, [1] n1 Bilimbia_lobulata, [2] n2 Bilimbia_microcarpa, [3] n3 Bilimbia_sabuletorum, [4] n4 Bacidia_fuscoviridis, [5] n5 Catillaria_aphana, [6] n6 Catillaria_croatica, [7] n7 Catillaria_scotinodes, [8] n8 Cliostomum_tenerum, [9] n9 Lecania_aipospila, [10] n10 Lecania_atrynoides, [11] n11 Lecania_brialmontii, [12] n12 Lecania_cyrtella, [13] n13 Lecania_cyrtellina, [14] n14 Lecania_dubitans, [15] n15 Lecania_erysibe, [16] n16 Lecania_furfuracea, [17] n17 Lecania_fuscella, [18] n18 Lecania_gerlachei, [19] n19 Lecania_glauca, [20] n20 Lecania_hutchinsiae, [21] n21 Lecania_inundata, [22] n22 Lecania_naegelii, [23] n23 Lecania_nylanderiana, [24] n24 Lecania_rabenhorstii, [25] n25 Lecania_racovitzae, [26] n26 Lecania_sambucina, [27] n27 Lecania_sp1, [28] n28 Lecania_sp2, [29] n29 Lecania_sylvestris, [30] n30 Lecania_turicensis, [31] n31 Lecidea_sphaerella, [32] n32 Mycobilimbia_pilularis, [33] n33 Mycobilimbia_tetramera; TREE 'Figure 1++' = (((((((n9,(((n10,n27),n30),n21)),(n24,n23)),n17),((((((n12,(n15,n28)),n20),n26),n14),n29),n13))Lecania_s._str.,(((n22,(n16,n8)),(n7,n5)),((n4,((n1,n3),n2)Bilimbia_s._str.),(((n11,n25),n18)Thamnolecania,(n31,n6)))Bilimbia_s._lat.)),(n0,(n33,n32)Mycobilimbia)),n19); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Asymm. 2 param. (estimate)': 1; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1453751467871; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2979859318903015085; tell It; setDefaultOrder 2 7 8 9 0 10 11 13 14 15 16 18 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 9131751470117848035; mqVersion 304; checksumv 0 3 2596707217 null getNumChars 1 numChars 1 getNumTaxa 34 numTaxa 34 short true bits 3 states 3 sumSquaresStatesOnly 40.0 sumSquares 40.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 933 1185; setLocation 0 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2979859318903015085 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2979859318903015085; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 833 1113; setLocation 0 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #2979859318903015085 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 907.1453578664005.6158125856580105817; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 833 1113; setLocation 0 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.BallsNSticks.BallsNSticks; tell It; setSpotDiameter 10; setEdgeWidth 2; orientRight; useSquare; 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 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(20,((1,(33,34)Mycobilimbia),((((6,8),(23,(9,17))),((5,(3,(2,4))Bilimbia_s._str.),((7,32),(19,(12,26))Thamnolecania))Bilimbia_s._lat.),((18,((24,25),(10,(22,(31,(11,28)))))),(14,(30,(15,(27,(21,(13,(16,29))))))))Lecania_s._str.)));'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; 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 #9131751470117848035; 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 1; setMapping 1; toggleShowLegend on; setColorMode 0; toggleWeights on; setInitialOffsetX 20; setInitialOffsetY 4; setLegendWidth 142; setLegendHeight 161; resume ; endTell; 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 #9131751470117848035; 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 1; setMapping 1; toggleShowLegend on; setColorMode 0; toggleWeights on; setInitialOffsetX 34; setInitialOffsetY 132; setLegendWidth 193; setLegendHeight 161; 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; setDigits 4; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges 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; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #9131751470117848035 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 165; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 833 1113; setLocation 0 23; 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; toggleShowBoldCellText off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; 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;