#NEXUS [written Wed Jun 20 15:45:26 EDT 2012 by Mesquite version 2.75 (build 564) at Robert-Baratheons-MacBook.local/10.0.1.25] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=21; TAXLABELS Armigatus Clupea Denticeps Diplomystus Ellimma Ellimmichthys Elops Knightia Paraclupea Onchorhynchus Santanaclupea Ellimma_branneri Diplomystus_shengliensis Paraclupea_chetungensis Diplomystus_dentatus Clupea_harengus Onchorhynchus_mykiss Armigatus_brevissimus Ellimma_riacensis Ellimmichthys_longicostatus Knightia_bohaiensis ; IDS _ _ _ _ _ _ _ _ _ _ _ 2cb8c6cb - 7b1d -4280 - bd45 - 5d188533f5e5 298f4a73 -6942 ; END; BEGIN CHARACTERS; TITLE ';'; DIMENSIONS NCHAR=30; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2"; CHARSTATELABELS 1 Recessus_lateralis, 2 Otophysic_connection_involving_a_diverticulum_of_the_swimbladder_that_penetrates_the_exoccipital_and_extends_into_the_prootic_within_the_lateral_wall_of_the_braincase, 3 Preepiotic_fossa, 4 Parietals, 5 Frontal_fontanelle, 6 Supratemporal_commissure, 7 Anterodorsal_process_of_hyomandibular, 8 Supramaxillae, 9 Teeth_on_entopterygoid, 10 Tooth_patch_on_posterior_part_of_parasphenoid, 11 Basipterygoid_process, 12 Bericiform_foramen_in_anterior_ceratohyal, 13 Angular, 14 Dorsal_scutes, 15 Ornamentation_on_dorsal_scutes, 16 Abdominal_scutes, 17 Caudal_scutes, 18 First_ural_centrum, 19 Neural_spine_of_first_preural_centrum, 20 Parhypural, 21 Number_of_hypurals, 22 Second_hypural, 23 Number_of_epurals, 24 First_uroneural, 25 First_uroneural, 26 Third_hypural, 27 First_hypural, 28 'Semicircular to almost vertical fine surface ridges (circuli) on scales', 29 Lateral_line_scales, 30 Neural_spines_of_a_few_posterior_preurals ; MATRIX Armigatus ?????????????????????????????? Clupea ?????????????????????????????? Denticeps 11010101011110-110011110100000 Diplomystus ?????????????????????????????? Ellimma ?????????????????????????????? Ellimmichthys ?????????????????????????????? Elops 00000000001100-000000000000000 Knightia ?????????????????????????????? Paraclupea ?????????????????????????????? Onchorhynchus ?????????????????????????????? Santanaclupea 0111?1001100?0-100010100101000 Ellimma_branneri 0??0010001?01211000101000000?0 Diplomystus_shengliensis 001001001000120100010100010100 Paraclupea_chetungensis 0??0110001001211000101000000?0 Diplomystus_dentatus 001001001000120100010100010100 Clupea_harengus 11111110011110-111000111101110 Onchorhynchus_mykiss 00000000011110-010100000000001 Armigatus_brevissimus 0010010010001101000101000100?0 Ellimma_riacensis 0??0010001?01211000101000000?0 Ellimmichthys_longicostatus 0??001?001?01211000101000000?0 Knightia_bohaiensis 11?111110111120101000101101110 ; BLOCKID d95d4879; END; BEGIN TREES; Title Trees; LINK Taxa = Taxa; TRANSLATE 1 Armigatus, 2 Clupea, 3 Denticeps, 4 Diplomystus, 5 Ellimma, 6 Ellimmichthys, 7 Elops, 8 Knightia, 9 Paraclupea, 10 Onchorhynchus, 11 Santanaclupea, 12 Ellimma_branneri, 13 Diplomystus_shengliensis, 14 Paraclupea_chetungensis, 15 Diplomystus_dentatus, 16 Clupea_harengus, 17 Onchorhynchus_mykiss, 18 Armigatus_brevissimus, 19 Ellimma_riacensis, 20 Ellimmichthys_longicostatus, 21 Knightia_bohaiensis; TREE 'Figure 13A+' = (((((1,4),(5,6,9)),(((2,8),11),3)),10),7); TREE 'Figure 13B+' = (((((1,4),(5,6,9)),(((2,8),3),11)),10),7); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 30; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 30; END; BEGIN NOTES; SUT TAXA = Taxa TAXON = 12 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 13 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 14 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 15 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 16 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 17 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 18 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 19 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 20 NAME = color INTEGER = 8; SUT TAXA = Taxa TAXON = 21 NAME = color INTEGER = 8; TEXT FILE TEXT = 'Note: Student Michael Jones has modified some of the taxa labels to link with the appropriate NCBI and UBio entries.^n^n^nTaxon List: Ericka Grey^nMatrix: unknown^nMerge: Ericka Grey^nFree text description: Du, Rui'; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1340221527052; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 384668901062605310; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4697084321078831105 d95d4879; mqVersion 275; checksumv 0 3 1288835082 d95d4879 getNumChars 30 numChars 30 getNumTaxa 21 numTaxa 21 short true bits 7 states 7 sumSquaresStatesOnly 866.0 sumSquares 866.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1076 488; setLocation 7 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #384668901062605310 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1075.1234982801398.6945987771268036546; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 976 421; setLocation 7 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; 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; orientRight; 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 2; setTree '(((((1,4),(5,6,9)),(((2,8),3),11)),10),7);'; 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 on; 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 #4697084321078831105 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 976 421; setLocation 7 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; 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; 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; getEmployee #mesquite.basic.ManageFileComments.ManageFileComments; tell It; editFileComment 0; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 976 471; setLocation 7 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; showWindow; endTell; endTell; endTell; end;