#NEXUS [written Wed Oct 19 15:36:15 EDT 2005 by Mesquite version 1.06 (build g97) at gisella-caccones-Computer.local/192.168.1.100] BEGIN TAXA; TITLE Untitled_Block_of_Taxa; DIMENSIONS NTAX=38; TAXLABELS Endomyzostoma_n.__sp._1 Endomyzostoma_cysticolum Endomyzostoma_deformator Endomyzostoma_n._sp._3 Endomyzostoma_tenuispinum Endomyzostoma_clarki Endomyzostoma_n._sp._2 Pulvinomyzostomum_pulvinar Myzostoma_cirriferum Myzostoma_glabrum Myzostoma_alatum Contramyzostoma_sphaera Myzostoma_capitocutis Myzostoma_nigromaculatum Myzostoma_coriaceum Myzostoma_ambiguum Myzostoma_mortenseni Myzostoma_polycyclus Myzostoma_toliarense Notopharyngoides_aruensis Myzostoma_cuniculus Myzostoma_pseudocuniculus Myzostoma_laingense Myzostoma_furcatum Myzostoma_fissum Hypomyzostoma_n._sp._1 Mesomyzostoma_n._sp._2 Mesomyzostoma_n._sp._3b Mesomyzostoma_n._sp._3a Mesomyzostoma_katoi Mesomyzostoma_n._sp._1b Mesomyzostoma_n._sp._1a Mesomyzostoma_reichenspergi Mesomyzostoma_n._sp._4b Mesomyzostoma_n._sp._4a Hypomyzostoma_sp._aff._crosslandi_b Hypomyzostoma_fasciatum Hypomyzostoma_sp._aff._crosslandi_ba ; END; BEGIN CHARACTERS; TITLE Matrix_from_clipboard; DIMENSIONS NCHAR=2; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7"; CHARSTATELABELS 1 Lifestyle_ / General_Ectocommensal Arm_ectocommensal Fixed_ectoparasite Soft_Cysticolous_Parasite Gallicolous_Parasite Anterior_Digestive_System_Endoparasite Endoparasite_of_coelomic_cavities Calcified_Cysticolous, 2 Host / comatulid stalked ; MATRIX Endomyzostoma_n.__sp._1 30 Endomyzostoma_cysticolum 70 Endomyzostoma_deformator 41 Endomyzostoma_n._sp._3 01 Endomyzostoma_tenuispinum 41 Endomyzostoma_clarki 41 Endomyzostoma_n._sp._2 41 Pulvinomyzostomum_pulvinar 50 Myzostoma_cirriferum 00 Myzostoma_glabrum 20 Myzostoma_alatum 20 Contramyzostoma_sphaera 30 Myzostoma_capitocutis 00 Myzostoma_nigromaculatum 00 Myzostoma_coriaceum 00 Myzostoma_ambiguum 00 Myzostoma_mortenseni 00 Myzostoma_polycyclus 00 Myzostoma_toliarense 30 Notopharyngoides_aruensis 50 Myzostoma_cuniculus 10 Myzostoma_pseudocuniculus 10 Myzostoma_laingense 10 Myzostoma_furcatum 10 Myzostoma_fissum 10 Hypomyzostoma_n._sp._1 10 Mesomyzostoma_n._sp._2 60 Mesomyzostoma_n._sp._3b 60 Mesomyzostoma_n._sp._3a 60 Mesomyzostoma_katoi 60 Mesomyzostoma_n._sp._1b 60 Mesomyzostoma_n._sp._1a 60 Mesomyzostoma_reichenspergi 60 Mesomyzostoma_n._sp._4b 60 Mesomyzostoma_n._sp._4a 60 Hypomyzostoma_sp._aff._crosslandi_b 10 Hypomyzostoma_fasciatum 10 Hypomyzostoma_sp._aff._crosslandi_ba 10 ; END; BEGIN TREES; Title 'Trees from "consensus tree"'; LINK Taxa = Untitled_Block_of_Taxa; TRANSLATE 1 Endomyzostoma_n.__sp._1, 2 Endomyzostoma_cysticolum, 3 Endomyzostoma_deformator, 4 Endomyzostoma_n._sp._3, 5 Endomyzostoma_tenuispinum, 6 Endomyzostoma_clarki, 7 Endomyzostoma_n._sp._2, 8 Pulvinomyzostomum_pulvinar, 9 Myzostoma_cirriferum, 10 Myzostoma_glabrum, 11 Myzostoma_alatum, 12 Contramyzostoma_sphaera, 13 Myzostoma_capitocutis, 14 Myzostoma_nigromaculatum, 15 Myzostoma_coriaceum, 16 Myzostoma_ambiguum, 17 Myzostoma_mortenseni, 18 Myzostoma_polycyclus, 19 Myzostoma_toliarense, 20 Notopharyngoides_aruensis, 21 Myzostoma_cuniculus, 22 Myzostoma_pseudocuniculus, 23 Myzostoma_laingense, 24 Myzostoma_furcatum, 25 Myzostoma_fissum, 26 Hypomyzostoma_n._sp._1, 27 Mesomyzostoma_n._sp._2, 28 Mesomyzostoma_n._sp._3b, 29 Mesomyzostoma_n._sp._3a, 30 Mesomyzostoma_katoi, 31 Mesomyzostoma_n._sp._1b, 32 Mesomyzostoma_n._sp._1a, 33 Mesomyzostoma_reichenspergi, 34 Mesomyzostoma_n._sp._4b, 35 Mesomyzostoma_n._sp._4a, 36 Hypomyzostoma_sp._aff._crosslandi_b, 37 Hypomyzostoma_fasciatum, 38 Hypomyzostoma_sp._aff._crosslandi_ba; TREE 'Bayesian tree (18S+16S+COI)' = ((((((((((((((31:0.3039,32:0.2779):5.9636,30:21.6378):1.6739000000000002,((34:0.06470000000000001,35:0.10200000000000001):3.2229,33:6.280900000000001):1.0339):0.8681,(28:0.12639999999999998,29:0.11720000000000001):2.1696999999999997):5.876200000000001,27:5.9858):3.3350999999999997,((37:4.400500000000001,38:3.1655999999999995):3.3577999999999997,36:3.7678999999999996):2.3925):1.1351,26:7.1482):1.0875,(24:4.5245,25:4.5407):1.9695):1.0522999999999998,23:10.607):3.5983,((22:3.4992,21:5.21):2.3958000000000004,20:5.9877):2.1132):0.8295999999999999,(((18:0.11939999999999999,19:0.1899):6.2901,17:0.5812999999999999):0.6874,16:0.5277999999999999):2.8432000000000004):1.0482,(((14:1.2255,15:1.5718999999999999):2.4515,13:3.9418):4.2803,12:5.4401):1.1732):4.7473,((10:1.683,11:0.5599):7.1278,9:4.571):4.4366):14.6297700002,((((6:0.0588,(5:0.1429,4:0.07830000000000001):0.10239999999999999):2.2082999999999995,((1:5.168699999999999,2:3.5148):12.048399999999999,3:5.0159):1.9893999999999998):17.8558,7:6.631399999999999):12.322199999999999,8:24.866600000000002):10.81293); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 2; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 21721721224609191; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 12985681851996670; tell It; setDefaultOrder 20 18; attachments ; endTell; checksum 0 3786470345; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #21721721224609191 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 503.1086699706969.266561715281103184; getTreeWindow; tell It; setSize 1027 593; setLocation 25 53; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setEdgeWidth 6; orientRight; toggleCorners off; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale off; toggleCenter on; toggleEven on; namesAngle ?; endTell; endTell; setBackground White; setBranchColor Black; showNodeNumbers on; labelBranchLengths off; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleShowNames on; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree on; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #12985681851996670; 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 Sum_Likelihoods; setDecision 2.0; setUnderflowCheckFreq 2; endTell; endTell; endTell; setCharacter 2; toggleShowLegend on; toggleGray off; toggleWeights off; setInitialOffsetX 21; setInitialOffsetY -553; setLegendWidth 211; setLegendHeight 159; resume ; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 49 361 100 137; setOffsetX 49; setOffsetY 361; setNote 'node 2: ^n0:0.383563154, ^n1:0.06300002, ^n2:0.067006649, ^n3:0.059889455, ^n4:0.19772878, ^n5:0.111302454, ^n6:0.05874699, ^n7:0.05876251'; setOffsetX 49; setOffsetY 361; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 10 539 873 35; setOffsetX 10; setOffsetY 539; setNote ' ML reconstruction on the Bayesian phylogram of Figure 5, obtained from analyses of the combined (18S + COI + 16S) data set (PP threshold of 90%). '; setOffsetX 10; setOffsetY 539; endTell; endTell; endTell; showWindow; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; endTell; endTell; endTell; end;