#NEXUS [written Tue Sep 16 11:18:19 CEST 2025 by Mesquite version 3.61 (build 927) at LAPTOP-52QPPEIL/192.168.118.7] BEGIN TAXA; TITLE taxa; DIMENSIONS NTAX=10; TAXLABELS Hyopsodus Tapirus_terrestris Equus_caballus Anchitherium_aurelianense_NMB.San.15063 Hipparion_concudense_NMB.Ccd.3 Hipparion_depereti_NMB.A.Mo.655 Equus_stenonis_NMB.V.A.2753 Equus_przewalskii Equus_senezensis_NMB.Se.554 Equus_senezensis_NMB.Se.141 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=50; FORMAT DATATYPE = STANDARD RESPECTCASE GAP = - MISSING = ? SYMBOLS = " 0 1"; CHARSTATELABELS 1 Texture_of_area_around_internal_acoustic_meatus / rough smooth, 2 Subarcuate_fossa__ / present absent, 3 Subarcuate_fossa_depth / deep shallow, 4 Petromastoid_canal_in_subarcuate_fossa / absent present, 5 Hiatus_Fallopii_distinct_anterior_hole / present absent, 6 'Hiatus Fallopii size, if foramen is position anteriorly' / small large, 7 Prefacial_commissure_fossa_of_the_petrosal / 'absent (convex, flat or a bump)' 'present (concave)', 8 Shape_of_tegmen_tympani / flat pronounced_convexity, 9 Inflation_of_the_tegmen_tympani / absent present, 10 Degree_of_inflation_of_the_tegmen_tympani / 'hyperinflation (transverse width > or = width of promontorium)' 'moderate (1/2-1/4 width of promontorium)', 11 Anterior_process_of_the_tegmen_tympani / absent present, 12 Size_of_anterior_process_of_the_tegmen_tympani / small 'large, projects anterior to promontorium', 13 'Apex of anterior process of tegmen tympani - shape' / pointed blunt, 14 Vascular_groove_on_the_lateral_surface_of_the_tegmen_tympani / present absent, 15 Distinct_fossa_for_the_head_of_the_malleus_on_petrosal / absent present, 16 Ventrolateral_tuberosity_of_petrosal / absent present, 17 Shape_of_ventrolateral_tuberosity_of_petrosal / 'bump/knob' spike, 18 Fossa_for_tensor_tympani_muscle_round_or_oval_depression / present absent, 19 'Fossa for tensor tympani (if round or oval) extends into an excavated portion of the tegmen tympani' / absent present, 20 Transpromontorial_sulcus_ / present absent, 21 Double_transpromontorial_sulci / absent present, 22 Sulcus_for_stapedial_artery_on_promontorium / present absent, 23 Pars_cochlearis_protrudes_ventromedially / absent present, 24 Mastoid_region_size_relative_to_promontorium / 'small (~ 50%)' 'large (~100% or more)', 25 Shape_of_bone_of_mastoid_region_of_the_petrosal / 'square, robust knob' wedge 'convex dorsally, flat/irregular ventrally', 26 Epitympanic_wing / absent present, 27 Posteromedial_flange_of_promontorium / absent present, 28 Shape_of_promontorium / 'hemi-ellipsoid' 'hemi-spherical' 'almond-shaped', 29 Caudal_tympanic_process_shape / 'mediolaterally narrow, bar of bone medial to stapedial muscle fossa' 'mediolaterally broad, sometimes with irregular projections or knobs', 30 Mastoid_plate / absent present, 31 Basicapsular_groove_on_pars_cochlearis_of_the_petrosal / present absent, 32 Position_of_basicapsular_groove_ / ventral dorsal, 33 'Secondary facial foramen position (relative to fenestra cochleae and fenestra vestibuli)' / Anterior Posterior, 34 'Stapes: presence of stapedial foramen' / present absent, 35 'Stapes: width of crura relative to size of foramen' / narrower_than_stapedial_foramen_width Wider_than_stapedial_foramen_width, 36 Posterior_Entry_of_Lateral_Semicircular_Canal / Secondary_Common_Crus Posterior_Ampulla Vestibule, 37 Largest_Semicircular_Arc_Radius_of_Curvatue / Anterior_Semicircular_Canal Lateral_Semicircular_Canal Posterior_Semicircular_Canal, 38 Position_of_the_Lateral_Semicircular_Canal_with_respect_to_Posterior_Semicircular_Canal / Low High, 39 Shape_of_Cochlear_Spiral / Low High, 40 Coiling_of_the_Cochlea / '1-2 Turns' '2-3 Turns' '3+ Turns', 41 Percent_Volume_of_the_Cochlea / ?50% '51-75%' '>75%', 42 Caudal_Tympanic_Process_Extension / 'short (not exceeding the posterior process of the crista parotica)' 'long (exceeds the posterior process of the crista parotica)', 43 Caudal_Typmpanic_Process_Position / Ventral_to_fenestra_cochleae Dorsal_to_fenestra_cochleae, 44 Hiatus_Fallopii / 'Terminally (anterior edge of the petrosal)' 'Ventral Side (tympanic)', 45 Promontorial_Surface / Smooth Not_Smooth, 46 Subarcuate_Fossa_Size / small Wide, 47 Epitympanic_Recess / Large Small, 48 Secondary_Facial_Foramen / lateral_to_fenestra_vestibuli anterior_to_fenestra_vestibuli, 49 Cochlear_Aqueduct_Position / In_ventromedial_face In_ventral_face, 50 Cochlear_Aqueduct_Slit / present absent ; MATRIX Hyopsodus 100000001110110??00001000100000?0????????010001101 Tapirus_terrestris 1010000011101100-011-1011110100100010001?000001100 Equus_caballus 10100000111101010011-11111101001000101011100011110 Anchitherium_aurelianense_NMB.San.15063 101000000-0--1?1?001-10111101?000????????000001?10 Hipparion_concudense_NMB.Ccd.3 10100000110--1010001-11111101?0100010101?100011110 Hipparion_depereti_NMB.A.Mo.655 10100000110--1010011-11111101?01???10101?100011110 Equus_stenonis_NMB.V.A.2753 10100000111001010011-11111101?01?0010111?100011?10 Equus_przewalskii 10100000111101010011-111111010??0??1?1???100011110 Equus_senezensis_NMB.Se.554 10100000111101010011-11111101?0100010111?100011110 Equus_senezensis_NMB.Se.141 10100000111101010011-11111101?010??10101?100011110 ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 50; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1- 50; END; BEGIN TREES; Title 'Trees from "matrix(1).tre"'; ID 01994e0b54911; LINK Taxa = taxa; TRANSLATE [0] 1 Hyopsodus, [1] 2 Tapirus_terrestris, [2] 3 Equus_caballus, [3] 4 Anchitherium_aurelianense_NMB.San.15063, [4] 5 Hipparion_concudense_NMB.Ccd.3, [5] 6 Hipparion_depereti_NMB.A.Mo.655, [6] 7 Equus_stenonis_NMB.V.A.2753, [7] 8 Equus_przewalskii, [8] 9 Equus_senezensis_NMB.Se.554, [9] 10 Equus_senezensis_NMB.Se.141; TREE 'PAUP_1' = (1:7,(2:1,((((3:0.0,(7:1,9:0.0):1,8:0.0,10:0.0):1,6:0.0):1,5:0.0):3,4:2):6):0.0):0.0; TREE 'PAUP_2' = (1:7,(2:1,((((3:0.0,(7:1,8:0.0,9:0.0):1,10:0.0):1,6:0.0):1,5:0.0):3,4:2):6):0.0):0.0; TREE 'PAUP_3' = (1:7,(2:1,(((((3:0.0,10:0.0):0.0,(7:1,(8:0.0,9:0.0):0.0):1):1,6:0.0):1,5:0.0):3,4:2):6):0.0):0.0; TREE 'PAUP_4' = (1:7,(2:1,((((3:0.0,((7:1,9:0.0):0.0,8:0.0):1,10:0.0):1,6:0.0):1,5:0.0):3,4:2):6):0.0):0.0; TREE 'PAUP_5' = (1:7,(2:1,(((((3:0.0,8:0.0,10:0.0):0.0,(7:1,9:0.0):1):1,6:0.0):1,5:0.0):3,4:2):6):0.0):0.0; TREE 'PAUP_6' = (1:7,(2:1,(((((3:0.0,8:0.0,9:1,10:0.0):1,7:1):1,6:0.0):1,5:0.0):3,4:2):5):0.0):0.0; TREE 'PAUP_7' = (1:7,(2:1,((((((3:0.0,8:0.0,10:0.0):1,9:0.0):1,7:0.0):2,6:0.0):1,5:0.0):3,4:2):5):0.0):0.0; TREE 'PAUP_8' = (1:7,(2:1,(((((((3:0.0,10:0.0):0.0,8:0.0):1,9:0.0):1,7:0.0):2,6:0.0):1,5:0.0):3,4:2):5):0.0):0.0; TREE 'PAUP_9' = (1:7,(2:1,(((((3:0.0,(8:0.0,9:0.0):1,10:0.0):1,7:1):1,6:0.0):1,5:0.0):3,4:2):5):0.0):0.0; TREE 'PAUP_10' = (1:7,(2:1,((((((3:0.0,10:0.0):1,(8:0.0,9:0.0):0.0):1,7:0.0):2,6:0.0):1,5:0.0):3,4:2):5):0.0):0.0; TREE 'PAUP_11' = (1:7,(2:1,((((((3:0.0,10:0.0):1,8:0.0,9:0.0):1,7:0.0):2,6:0.0):1,5:0.0):3,4:2):5):0.0):0.0; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1758014299480; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7752128649643291418; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7008424866247100619; mqVersion 361; checksumv 0 3 2443438168 null getNumChars 50 numChars 50 getNumTaxa 10 numTaxa 10 short true bits 3 states 3 sumSquaresStatesOnly 1097.0 sumSquares 1097.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 186; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1920 973; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #7752128649643291418 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #7752128649643291418; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1734 901; setLocation -8 0; 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 #7752128649643291418 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 01994e0b54911; toggleUseWeights off; endTell; setAssignedID 966.1757950999929.8103672449824613824; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1734 901; setLocation -8 0; 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.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; orientRight; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; 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; 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 #7008424866247100619 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 244; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1734 901; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; endTell; setActive; 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; toggleReduceCellBorders off; 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 156; 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.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1734 901; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.categ.StateNamesEditor.StateNamesWindow.arrow; endTell; rowsAreCharacters on; toggleConstrainChar on; toggleConstrainCharNum 3; togglePanel off; toggleSummaryPanel off; endTell; showWindow; 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.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #7008424866247100619 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.DefaultCharOrder.DefaultCharOrder; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.lists.CharListPartition.CharListPartition; newAssistant #mesquite.parsimony.CharListParsModels.CharListParsModels; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1734 901; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;