#NEXUS [written Wed Dec 15 15:35:29 CST 2010 by Mesquite version 2.74 (build 550) at David-Gernandts-MacBook-Pro-2.local/10.1.3.189] BEGIN TAXA; TITLE Taxa4; DIMENSIONS NTAX=50; TAXLABELS Abies Cathaya_argyrophylla Cedrus Larix Keteleeria Picea Pinus_belgica Pinus_ponderosa Pinus_nelsonii Pseudolarix_amabilis Pseudotsuga Tsuga Pseudoaraucaria_arnoldii Pseudoaraucaria_benstedi Pseudoaraucaria_gibbosa Pseudoaraucaria_heeri Pseudoaraucaria_loppineti Pseudoaraucaria_major Obirastrobus_kokubunii Obirastrobus_nihongii Pityostrobus_andraei Pityostrobus_argonnensis Pityostrobus_beardii Pityostrobus_bernissartensis Pityostrobus_californiensis Pityostrobus_cliffwoodensis Pityostrobus_corneti Pityostrobus_hallii Pityostrobus_hautrageanus Pityostrobus_hokodzensis Pityostrobus_hueberi Pityostrobus_jacksonii Pityostrobus_kayeii Pityostrobus_leckenbyi Pityostrobus_lynnii Pityostrobus_macrocephalus Pityostrobus_makahensis Pityostrobus_mcmurrayensis Pityostrobus_matsubarae Pityostrobus_milleri Pityostrobus_oblongus Pityostrobus_palmeri Pityostrobus_pubescens Pityostrobus_ramentosa Pityostrobus_shastaensis Pityostrobus_villerotensis Pityostrobus_virginiana Cryptomeria_japonica Pararaucaria_patagonica Sciadopitys_verticillata ; END; BEGIN CHARACTERS; TITLE ConeMorphologyDG; DIMENSIONS NCHAR=54; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7"; CHARSTATELABELS 1 Pith_sclerenchyma / absent present, 2 Pith_resin_canals / absent present, 3 Secondary_xylem_continuity / forming_a_continuous_cylinder_or_little_dissected in_separate_strands, 4 Secondary_xylem_resin_canals / absent present, 5 Secondary_xylem_growth_increments / one two, 6 Inner_cortex_sclerenchyma_ / absent present, 7 Sclerenchyma_in_outer_cortex / absent present, 8 Cortical_resin_canal_diameter / uniform dilated_markedly_near_points_of_branching, 9 Axis_scale_or_bract_base_trichomes / absent present, 10 Bract_and_scale_trace_origin / separate united, 11 Scale_trace_derivation / from_two_lateral_strands single_abaxially_concave_strand, 12 Scale_trace_shape / abaxially_concave becoming_cylindrical_after_divergence, 13 Resin_canals_to_cone_scale_complex_arising_from_cortical_canals / as_a_single_branch two_origins three_separate_origins four_separate_origins more_than_four_separate_origins, 14 Bract_and_ovuliferous_scale_separation / fused separating, 15 Bract_and_ovuliferous_scale_manner_of_separation / laterally_first medially_first all_at_once, 16 Bract_length_relative_to_ovuliferous_scale / shorter equal longer, 17 Abaxial_lobe_of_bract_base_or_cone_scale_complex / absent present, 18 Bract_apex_shape / simple tridentate, 19 Bract_sclerenchyma / absent present, 20 Bract_resin_canals_ / absent present, 21 Bract_resin_canal_number / two more_than_two, 22 Bract_trace / entering_bract terminating_before_entering_free_part_of_bract, 23 Bract_trace_vascular_ray / absent present, 24 Ovuliferous_scale_vascular_bundles_distal_to_seed / straight abaxially_concave, 25 Ovuliferous_scale_resin_canals / absent present, 26 Resin_canals_abaxial_to_ovuliferous_scales_at_scale_base / absent present, 27 Resin_canals_adaxial_to_ovuliferous_scales_at_scale_base / absent present, 28 Resin_canals_to_ovuliferous_scales_abaxial_at_level_of_seed_body / absent present, 29 Resin_canals_to_ovuliferous_scales_between_vascular_tissue_at_level_of_seed_body / absent present, 30 Resin_canals_to_ovuliferous_scales_adaxial_to_vascular_tissue_at_level_of_seed_body / absent present, 31 Resin_canals_to_ovuliferous_scale_distal_to_seed_body_including_under_wing_and_more_distal_sections_abaxial / absent present, 32 Resin_canals_to_ovuliferous_scale_distal_to_seed_body_including_under_wing_and_more_distal_sections_between / absent present, 33 Resin_canals_to_ovuliferous_scale_distal_to_seed_body_including_under_wing_and_more_distal_sections_adaxial / absent present, 34 Sclerenchyma_in_ovuliferous_scale_abaxial_to_vascular_tissue / absent present, 35 Sclerenchyma_in_ovuliferous_scale_between_vascular_tissue / absent present, 36 Sclerenchyma_in_ovuliferous_scale._adaxial_to_vascular_tissue / absent present, 37 Ovuliferous_scale_shape / flabellate_or_broad_at_apex round_to_rhomboid_or_broad_in_middle tongue_shaped subcordate deltate_triangular, 38 Ovuliferous_scale_base / pedicillate broad, 39 Ovuliferous_scale_apex / thinning_distally thickening_distally_into_an_apophysis, 40 Umbo / absent present, 41 Umbo_position / dorsal terminal, 42 Interseminal_ridge / absent present, 43 Interseminal_ridge_extension / extending_less_than_half_of_seed_diameter extending_more_than_half_of_seed_diameter extending_between_and_overarching, 44 Scale_at_right_angles_to_cone_axis_for_length_of_seed_body_with_sharply_upturned_distal_portion / absent present, 45 Method_of_cone_seed_release / cone_spreading scale_abscission_from_cone_axis, 46 Seed_wings_formed_from_ovuliferous_scale_tissue / absent present, 47 Seed_wings_formed_from_sarcotestal / absent present, 48 Resin_vesicles_or_cavities_in_integument / absent present, 49 Ridged_sclerotesta / absent present, 50 Enlarged_parenchyma_pad_or_cushion_at_chalazal_end_of_seed / absent present, 51 Number_of_ovules_per_ovuliferous_scale / one two three_or_more, 52 Seed_body_shape / ovoid_obovate triangular_cuneate_oblong, 53 Vascular_strand_entering_seed / absent present, 54 Seed_wing_attachment / deep_cup shallow_cup claws ; MATRIX Abies 101(0 1)011(0 1)(0 1)(0 1)10111(0 2)(0 1)(0 1)1100001010010111010000-0-11101001110 Cathaya_argyrophylla 000000100010???01001010?111???1111011100-10001000010?1 Cedrus 00101(0 1)10(0 1)01031000010-1001111001001110000-(0 1)011101001110 Larix 100(0 1)0(0 1)101010111(0 2)(0 1)101(0 1)(0 1)(0 1)11010011111011100-1(0 1)00100001001 Keteleeria 00000011(0 1)011110(0 2)111101(0 1)11111011??1013000-1010101001110 Picea (0 1)0(0 1)(0 1)0(0 1)10(0 1)01011001001(0 1)0(0 1)0101101(0 1)111111100-1(0 1)00100001001 Pinus_belgica 100100000110110000?100?111011011110021110100010000100? Pinus_ponderosa ?0010000011011?000110??1110111111111211101000100001002 Pinus_nelsonii 0001100001101100100100?1110111111000211101200100001002 Pseudolarix_amabilis 101001101010?100001100?01111111110114000-1001101001010 Pseudotsuga 10010(0 1)10(0 1)0101102010100(0 1)11010011111011100-1000100001001 Tsuga 10000(0 1)(0 1)0(0 1)010311(0 2)(0 1)0110000101001111101(0 1)000-1000101001010 Pseudoaraucaria_arnoldii 001000110000110000011(0 1)001010011111100?011121010101111? Pseudoaraucaria_benstedi 00100?1?0000?10000?1000?1??001???100?????1210101011??? Pseudoaraucaria_gibbosa 101001110000310000?1000011100111110110011121010001111? Pseudoaraucaria_heeri 0010001000001100001100001010011011010001112101010111?? Pseudoaraucaria_loppineti 001000100000110000010010101001???100??0111210100011110 Pseudoaraucaria_major 001000100000110000010110101001111111?00111210101011??? Obirastrobus_kokubunii 0011011100(0 1)03110000110001111111111010100-11001000010?? Obirastrobus_nihongii 000101110(0 1)104110100110001111011111011?00-1100100001?1? Pityostrobus_andraei 000?01?1001011?000????01110100111101211100-00100001002 Pityostrobus_argonnensis 10000110001010-000???1011101001111012?10-10001000010?2 Pityostrobus_beardii 10100110101011000001100?110100111111??11?1000100101??? Pityostrobus_bernissartensis 110000000010110000?0-101110100101100210110-001000010?2 Pityostrobus_californiensis 1101011100101100000100101111111111010000-1100100001??? Pityostrobus_cliffwoodensis 000100100010???000?100001101111111001?00?1000100001??? Pityostrobus_corneti 100001100011?100001101001111111111000000-0-00101001??? Pityostrobus_hallii 0000001001101110000100001101101111111100-??00100001??? Pityostrobus_hautrageanus 100001100000???0000??101110110111100211110-001001010?? Pityostrobus_hokodzensis 10100110101011200001010?1101001111110000-1000100101??? Pityostrobus_hueberi 10000100101111000010-1001101101011000100-100010000100? Pityostrobus_jacksonii 000100000010?10000?11000110???11110021110100010??01??? Pityostrobus_kayeii 1001000000001100000100011101001111012?1100-00100001??? Pityostrobus_leckenbyi 00000???011021000?0101001010011111000000-100010100101? Pityostrobus_lynnii 0001001101101110000??(0 1)0111010011110021110100010??01??? Pityostrobus_macrocephalus 10000110000?1??000?10100110???111101211??0-00100101??2 Pityostrobus_makahensis 10010011001011100001(0 1)0001101011111010000-1000101001??? Pityostrobus_mcmurrayensis 10100110001011001?01000?110101???001??00-10001000010?? Pityostrobus_matsubarae 10000110000011000001000?1111111111011000-10001000010?? Pityostrobus_milleri 00110011101010-0??11010?11011011110101110100010??01??? Pityostrobus_oblongus 10000111011021000?0100001011011111010?00-1000101001?1? Pityostrobus_palmeri 100111100(0 1)001100000101001101011101112?11?100010000100? Pityostrobus_pubescens 001000001010110010010000110001?101110000-11001?0001??? Pityostrobus_ramentosa 000000111110?100000100001111011111012?00-110010??01??? Pityostrobus_shastaensis 10010110001011000001010?110???111101?????1000100001??? Pityostrobus_villerotensis 000000000110111000?100011101111111112100-10001000010?? Pityostrobus_virginiana 000?00001100?100000100011101001001010000-1000100001?0? Cryptomeria_japonica 1000011000??01010?0110?00--------1110000-0-0001000210- Pararaucaria_patagonica 10000?1-1010-1000000-00?0--------0110?10-0-1010000(0 1)?1? Sciadopitys_verticillata 0010000010001101000110001010010110010000-0-0001000201- ; END; begin paup; set maxtrees = 50000 increase = no; pset mstaxa = polymorph; hs / addseq = rand nreps = 50000 nchuck = 1 chuckscore = 1; des / plot = phylo; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 54; END; BEGIN TREES; Title 'Trees from "cones14decc.tre"'; LINK Taxa = Taxa4; TRANSLATE 1 Abies, 2 Cathaya_argyrophylla, 3 Cedrus, 4 Larix, 5 Keteleeria, 6 Picea, 7 Pinus_belgica, 8 Pinus_ponderosa, 9 Pinus_nelsonii, 10 Pseudolarix_amabilis, 11 Pseudotsuga, 12 Tsuga, 13 Pseudoaraucaria_arnoldii, 14 Pseudoaraucaria_benstedi, 15 Pseudoaraucaria_gibbosa, 16 Pseudoaraucaria_heeri, 17 Pseudoaraucaria_loppineti, 18 Pseudoaraucaria_major, 19 Obirastrobus_kokubunii, 20 Obirastrobus_nihongii, 21 Pityostrobus_andraei, 22 Pityostrobus_argonnensis, 23 Pityostrobus_beardii, 24 Pityostrobus_bernissartensis, 25 Pityostrobus_californiensis, 26 Pityostrobus_cliffwoodensis, 27 Pityostrobus_corneti, 28 Pityostrobus_hallii, 29 Pityostrobus_hautrageanus, 30 Pityostrobus_hokodzensis, 31 Pityostrobus_hueberi, 32 Pityostrobus_jacksonii, 33 Pityostrobus_kayeii, 34 Pityostrobus_leckenbyi, 35 Pityostrobus_lynnii, 36 Pityostrobus_macrocephalus, 37 Pityostrobus_makahensis, 38 Pityostrobus_mcmurrayensis, 39 Pityostrobus_matsubarae, 40 Pityostrobus_milleri, 41 Pityostrobus_oblongus, 42 Pityostrobus_palmeri, 43 Pityostrobus_pubescens, 44 Pityostrobus_ramentosa, 45 Pityostrobus_shastaensis, 46 Pityostrobus_villerotensis, 47 Pityostrobus_virginiana, 48 Cryptomeria_japonica, 49 Pararaucaria_patagonica, 50 Sciadopitys_verticillata; TREE Strict = ((((((((((1,(((13,14),(16,(17,18))),15)),(12,(34,41))),((((3,40),5),44),37)),((19,20),25)),39),(10,49)),(27,31)),((((2,6),((((((7,(((21,((((22,(42,45)),(29,36)),24),33)),32),35)),9),8),46),28),26)),(43,47)),((23,30),38))),(4,11)),(48,50)); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 54; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1292448929197; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5934962247983956501; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5258811732653770831; mqVersion 274; checksumv 0 2 1619684104 null getNumChars 54 numChars 54 getNumTaxa 50 numTaxa 50 short true bits 31 states 31 sumSquaresStatesOnly 7285.0 sumSquares 7285.0 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 1046 626; setLocation 46 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5934962247983956501 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1022.1292448878066.683870593661271308; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 946 559; setLocation 46 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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; orientUp; 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 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 on; toggleHorizontal 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 #5258811732653770831 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 946 559; setLocation 46 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; endTell; end;