#NEXUS [written Tue Jun 30 12:45:30 CEST 2015 by Mesquite version 3.03 (build 702) at belinda-HP/141.48.90.85] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=14; TAXLABELS Apis_andreniformis Apis_florea Apis_cerana Apis_mellifera_ligustica Apis_mellifera_mellifera Apis_mellifera_scutellata Bombus_hypocrita_sapporensis Bombus_ignitus Philanthus_triangulum Melipona_bicolor Polistes_sp. Rediviva_intermixta Hylaeus_dilatatus Colletes_gigas ; END; BEGIN CHARACTERS; TITLE Character_Matrix; LINK TAXA = Taxa; DIMENSIONS NCHAR=332; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Apis_andreniformis ATAATTTTAGTTTTTATTATTTCATTTATTTTAATAATAATT---AATAAATTTATTTCAATAAATAAAAGTATAGATTTTGAAAAAAGATCTCCATTTGAATGTGGATTTAATCCAATTACTAAATCTTATTTACCATTTTCTTTACCTTTTTATTTAATTACAATAATATTTTTAATTTTTGATGTAGAAATTATTTTATTTTTACCTTTAATTTTTTATTT----AAAGTCAATAAATTCAATTTGTACATTTATATTAATTTCGATATTTTTAA-TTTTATTAATTTTTACTTTAGTTTTTGAATGAATAAATAGATATTTAAATTGA Apis_florea TTTATTTTAATTTTTATTATTTCATTTATTTTATTATTAATT---AATAAATTTATTTCAATAAAAAAAAAAATAGATTTTGAAAAAAGATCACCATTTGAATGCGGATTTAACCCAATTACAAAATCTAATTTACCATTTTCTCTCCCATTTTATTTAATTACTATAATATTTTTAATTTTTGATGTAGAAATTATTTTATTTTTACCAATAATTTTTTATTT----AAAATCAATTAATTCAATTATTACATTCTTATTAATTTCATTATTTCTAA-TTTTATTAATTATTACCTTAATTTTTGAATGAATAAATAATTACTTAAATTGA Apis_cerana TTTATTGTTATTATCTTAGTTTCTTCAATTCTTTTAATATTA---AATAAAGCTATTTCAATAATTAAAAAAAAAGATTATGAAAAAAGATCACCATTTGAATGTGGTTTTAATCCAATTACTAAAGCTAATTTACCATTTTCATTACCTTTTTTCTTAATTACAATAATATTTTTAATTTTTGATGTTGAAATTATTTTATTTACACCAATTATTTTATATAT----AAAATCTTATAGAACAATACTCTCATTTATATTAATTTCCCTATTTCTTA-TTCTTTTAATTTTAACACTTATATTTGAATGAATAAATAATTATTTAAATTGA Apis_mellifera_ligustica TTTATTTTTATTATTTTAATCTCATCAATTTTATTATTATTA---AATAAATTTATTTCAATTTATAAAAAAAAAGATTATGAAAAAAGTTCACCATTTGAATGTGGATTTAATCCAATTACAAAAGCAAATTTACCATTTTCTTTACCTTTTTTTCTAATAACAATAATATTTTTAATTTTTGACGTTGAAATTATTTTATTTCTACCAATTATTTTTTATCT----AAAATCATCAAGAACAATAATTTCATATTTAATAATTTCAATTTTTCTTA-TCTTATTAATTACCACATTAATTTTAGAATGAATAAATAATTATTTAAATTGA Apis_mellifera_mellifera TTTATTTTTATTATTTTAATCTCATCAATTTTATTATTATTA---AATAAATTTATTTCAATTTATAAAAAAAAAGATTATGAAAAAAGTTCACCATTTGAATGTGGATTTAATCCAATTACAAAAGCAAATTTACCATTTTCTTTACCTTTTTTTCTAATAACAATAATATTCTTAATTTTTGACGTTGAAATCATTTTATTTCTACCAATTATTTTTTATTT----AAAATCATCAAGAACAATAATTTCATATTTAATAATCTCAATTTTTCTTA-TCTTATTAATTGCCACACTAATTTTAGAATGAATAAATAATTATTTAAATTGA Apis_mellifera_scutellata TTTATTTTTATTATTTTAATCTCATCAATTTTATTATTATTA---AATAAATTTATTTCAATTTATAAAAAAAAAGATTATGAAAAAAGTTCACCATTTGAATGTGGATTTAATCCAATTACAAAAGCAAATTTACCATTTTCTTTACCTTTCTTTTTAATAACAATAATATTCTTAATTTTTGACGTTGAAATTATTTTATTTCTACCAATTATTTTTTATTT----AAAATCATCAAGAACAATAATTTCATACTTAATAATTTCAATTTTCCTTA-TCTTATTAATTGCCACATTAATTTTAGAATGAATAAATAATTATTTAAATTGA Bombus_hypocrita_sapporensis TATTTATTAATTTTAATTATTATTTTTATTATTTTAACCTTA---AATAAATTTTTATCAATAATTAAAAAAATAAATTTTGAAAAAAATCTTCCATATGAATGTGGATTTTACCCAATTACAAAAATAAATTTACCATTTTCACTTCCATTTTATTTAATTTCATTAACATTTATAATCTTTGATATTGAAATTATCTTATTAATACCATTAATTTCATTTAT----TAAAACTCTAAATTTCTTATATTTATTTTTTATAATAATTTTTTTTTTTT-CAATATTAATTTTTTCATTAATCATAGAATGATTCTGCAATTATTTAAATTGA Bombus_ignitus TTTATAATTATTTTAATTATTATTTTTATTATTTTTATTTTA---AATAAATTTTTATCTATAACTAAAAAAATAAATTTTGAAAAAAACCTTCCATATGAATGTGGATTTAATCCAATTACAAAAATAAATTTACCTTTTTCATTACCATTTTATTTAATTTCACTAACATTTTTAATTTTTGATATCGAAATTATTTTATTAATTCCTCTTATTTCATTTAT----TAAAACTTTAAATTATATATATATATATATAATAATAATTTTTTTTTTTTATAATATTAATTTATTCATTAATTATA-AATGATTTTGTAGTTATTTAAATTGA Philanthus_triangulum AGATTTTTATTCATTATAATCTCAATTTTAATTTTAATATTA---AATTTACTATTTTCAAAAAAATCATCAAAAGATCGAGAAAAAATAACTCCATTTGAATGTGGATTTGACCCTTTAACTAATTCACGTTTACCATTTTCAATTCAATTTTTTTTAATTAGATTAATATTTTTAATTTTTGATATTGAAATTATTTTATTATTACCAATAATTTTTTTTAT----AAAAATAAAAATCAATTTAAATATTATTTTAATATTTATTACTTTTTTAA-GAATCTTAATTTTAAGAACTTATTTAGAATGATTAGAAAGAAATTTAAATTGA Melipona_bicolor ATAGCTTTCATTATATTAATTTCATATATTATTTATAATTTA---AATAAATATTTATCTATAAATAAAAAAATTAATTTAGAAAAAAAAATTCCATTTGAATATGGATTCAATCCAATCTCTAAATTTAATTTACCTTTTTCCATACCATTTTTTTTAATTAGATTATTATTCTTAATCTTTGATATTGAAATTACTATATTAATTCCAATAATTATATATTT----AAAATATTTAAATTTTTTAATTATAATTATTATTATTTTTTTATTTTTAT-ATATAATATTAATTACATTAATTATAGAATGAATATTAGGATACTTACATTGA Polistes_sp. TTATTTTTAATTCCAATTTTTTTAACTATAATTCTTTTTTTAATTAATTTAATCTCTCAAATTAAAATTTTTAAAGATCGAGAAAAACCTTCACCATATGAATGTGGTTTTAATCCATTAACATCTTCACGTTTACCTTTTTCTATTCAATTTTTTTTAATTGCTTTAATTTTTTTAATTTTTGATATTGAAATTATTTTATTATTTCCTCTAATCCCTTCAATCTTAAAAAATAATAATTTTTTTTATTGAATTTTTAATATATTAATTATTTATT--TATGTTTAGTTATCGGTTTAATTTATGAATGAAATGAACAATCAATTATTTGA Rediviva_intermixta GTGTTGGTGCTGCTGCTTATTCCCTCAATTATTGTTGCATTA---AATTATTGCCTGTCTGTTAATAAGTTAGATAGACGGGAAAAGTCTCTTCCCTTTGAATGCGGATTTGATCCTTTAACTAAAATTCGTCTTCCTTTTTCTATACAATTTTTTCTAATTACTTTAATGTTCTTGATTTTTGATGTTGAAATTATTTTAATATTACCTATGATTTTGTTATC----AAAGTATTTTTTGTCAATATGTATAATTATTGTATTTATATTGTTTTTGA-TTATTCTAATATATAGATTATGAATAGAATGAATAATAAATTATATTAAATGA Hylaeus_dilatatus CTATTAATTATATTAATTATTCCAATTATTATCATAATATTA---AACTTATTTTTTTCAATAAATATAAAAAAAAACCGAGAAAAAATATTACCTTTTGAATGCGGATTTGATCCATTAACCAATTCACGATTACCTTTTTCAATTCAATTTTATATAATTACATTAATATTTTTAATTTTCGATATTGAAATTATTTTAATAATTCCTTTTAT-------------AAAA--------------------------------------------------------------------------------------------TTAATTAA Colletes_gigas TTTTTTATTATTTTATTTATTTGTATTATACTTATTTTAATA---AATTTATATTTTAATATTATATTAAAAAAAAATCGAGAAAAAAGATTACCTGTTGAATGTGGATTTGATCCATTGATTAATAAACGATTACCTTTTTCTATTAATTTTTTTTTAATTTCATTAGTATTTTTAATTTTTGATGTTGAAATTGTTTTAATTATACCTATAATTTTTATTTT----GAAAAATATTATACCTTTAATTTCTTTAATTATATTTATTTATTTTTTAT-TTATATTACTTATTGGATTATTAATAGAATGATATTTAGGGTATTTAGAATGA ; END; BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=14; TAXLABELS Apis_andreniformis Apis_florea Apis_cerana Apis_mellifera_ligustica Apis_mellifera_mellifera Apis_mellifera_scutellata Bombus_hypocrita_sapporensis Bombus_ignitus Philanthus_triangulum Melipona_bicolor Polistes_sp. Rediviva_intermixta Hylaeus_dilatatus Colletes_gigas ; END; BEGIN MRBAYES; log start filename = NAD3newLog.txt; set autoclose = yes; Lset nst = 6 rates = gamma; Prset statefreqpr = dirichlet ( 1 , 1 , 1 , 1 ); mcmc ngen = 10000000 nchains = 4 nruns = 2 samplefreq = 1000 printfreq = 1000 savebrlens = yes filename = NAD3new; sumt burnin = 2500; sump burnin = 2500; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 332; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 332; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 332; END; BEGIN TREES; Title 'Trees from "NAD3new2.con"'; LINK Taxa = Taxa2; TRANSLATE [0] 1 Apis_andreniformis, [1] 2 Apis_florea, [2] 3 Apis_cerana, [3] 4 Apis_mellifera_ligustica, [4] 5 Apis_mellifera_mellifera, [5] 6 Apis_mellifera_scutellata, [6] 7 Bombus_hypocrita_sapporensis, [7] 8 Bombus_ignitus, [8] 9 Philanthus_triangulum, [9] 10 Melipona_bicolor, [10] 11 Polistes_sp., [11] 12 Rediviva_intermixta, [12] 13 Hylaeus_dilatatus, [13] 14 Colletes_gigas; TREE con_50_majrule = (11:0.33837865,(9:0.3397577,(12:0.7975918,13:0.1109311,14:0.5503702):0.1328397,((10:0.4587125,(7:0.111879,8:0.06203717):0.2504344):0.139213,((1:0.1311895,2:0.03912118):0.08671496,(3:0.1743703,(4:0.006036084,(5:0.01081503,6:0.01497608):0.009745037):0.07012299):0.1046639):0.1929071):0.4146748):0.33837865[%selected = on ])[% ] [% ] [% setBetweenBits = selected ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1435661130565; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2238225143280417468; setID 1 6122736141247310826; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6640486091829217005; mqVersion 303; checksumv 0 3 3331758279 null getNumChars 332 numChars 332 getNumTaxa 14 numTaxa 14 short true bits 15 states 15 sumSquaresStatesOnly 144728.0 sumSquares 144728.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 175; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1045 765; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6122736141247310826 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #6122736141247310826; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2145.1435661077946.4450063541785980010; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 870 693; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; 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 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 #6640486091829217005 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 157; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 870 693; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; 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 off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; 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.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.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;