#NEXUS [written Thu Sep 24 17:28:26 JST 2020 by Mesquite version 3.61 (build 927) at tsutsumichie-no-iMac.local/202.220.64.189] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=17; TAXLABELS Osmunda_regalis_R10 Osmunda_japonica_J4J6J7J8 Osmunda_japonica_J1J3J5 Osmunda_japonica_J2 Osmunda_regalis_R15R17R18 Osmunda_regalis_R14 Osmunda_lancea_L1 Osmunda_regalis_R5R6R7R8R9 Osmunda_lancea_L2L3 Osmunda_regalis_R13 Osmunda_regalis_R1R4 Osmunda_regalis_R2R3 Osmunda_regalis_R11R12 Plenasium_banksiifolium Claytosmunda_claytoniana_CL1a Claytosmunda_claytoniana_CL1b Claytosmunda_claytoniana_CL2 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=353; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Osmunda_regalis_R10 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGGGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCATTGGTCTACCGTGATAGATTTTACTCGGGGGTTT--------------GTCACAAGTTTCT---CACTATTCGCC-TTTTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCATAAATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_japonica_J4J6J7J8 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATCCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTTCCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGTTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_japonica_J1J3J5 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATCCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_japonica_J2 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATCCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTTCCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTCGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R15R17R18 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCACTGGTCTACCGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTTTAACCTCTTT-GACCTGGGTGTAGAACGATGAATGGTATGGATACAGTGAGAGGACTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACCTAGCAGAGATTTGCGGACCCCTCTTCTGATTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R14 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGTGTTTTCATGTATTTCGAAGGTATGGAGTCTTCAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CAAATTTCCC----TTTAACCTCTTT-GACCTAGGTCTAGCACGATGAACGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_lancea_L1 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATCCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTCTAACCTCTTC-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R5R6R7R8R9 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCACTGGTCTACCGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTTTAACCTCTTT-GACCTGGGTCTAGAACGATGAATGGTACGGATACAGTGAGAGGCCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACCTAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_lancea_L2L3 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATCCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTGTCAGGGGGTTT--------------GTCACAAGTTTCT---CACAATTCCCCC-TTTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGAGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R13 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTCAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCAC--------CGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CAAATTTCCC----TTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R1R4 AAGTGATGCCTGCTGTGATTGTTCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCATTGGTCTACCGTGATAGATTTTACTAGGGGGTTT--------------GTCACAAGTTTCT---CACTATTCGCC-TTTTTAACCTCTTT-GACCTAGTTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R2R3 AAGTGATGCCTGCTGTGATTGTTCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCATTGGTCTACCGTGATAGATTTTACTAGGGG-TTT--------------GTCACAAGTTTCT---CACTATTCGCC-TTTTTAACCTCTTT-GACCTAGTTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCTGTGTTATATTGTCGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Osmunda_regalis_R11R12 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGCGTTTTCATGTATTTCGAAGGTATGGAGTCTTAAATTCTGGAGTAAGCCATTTCTT---------AAACATGTCATTGGTCTACCGTGATAGATTTTGCCAGGGGGTTT--------------GTCACAAGTTTCT---CACTATTCGCC-TTTTTAACCTCTTT-GACCTAGGTCTAGCACGATGAATGGTATGGATACAGTGAGAGGGCCGTGTTATATTGTTGCAGCAGAGACTTGCTGGACATAGCAGAGATTTGCTGACCCCTCTTCTGGTTTCTGATCGTTGCTGCAGATAA Plenasium_banksiifolium AAGTGATGCCTGCCGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGTGTTTTCATGTATTTCGAAGGTATGGAGTCTCAAATTCTGCAGTAAACTCTTTCTTGGATATTTACAATATGTCACTGA-----CGTGATAGATTTTATTAGGTAGTTTATTTATGTTATTTT-TCATAAGTTCCTGTACAACATTCCCCCTTTTTAACCTCTTTTGACCTT--------------AATGGTATGGATATAGTGACTGGACTGTGTTATATTGCTGTATCAGAGACTTGCTTGACCTATC----ATTTTACGCCCCTGCTTCTGATTTCTGATTGTTGCTGCAGATAA Claytosmunda_claytoniana_CL1a AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGTGTTTTCATGTATTTCGAAGGTATGGAGTCTCAAATTCTGGAGTAAGCCCTTTCTTGgATATTTACAATATGTCACTGGTCTACCGCGAtAGATTTtACCAGGGAGTTTCTTTATGTTATTTTATCACAGGTTTCTGTACAACATTCCCCC-TTTTAaCCTCTTTTGACCTGGGTCTAGAACGATGAATGTTATAGATACAGTGAGTGCACTGTGTTATATTGTTGCATCAGAGACTTGCTAGACCTATC----ATTTTACGCCCCTGCTTCTGATTTCTGATTATTGCTGCAGATAA Claytosmunda_claytoniana_CL1b AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGTGTTTTCATGTATTTCGAAGGTATGGAGTCTCAAATTCTGGAGTAAGCCCTTTCTTGcATATTTACAATATGTCACTGGTCTACCGCGAcAGATTTcACCAGGGAGTTTCTTTATGTTATTTTATCACAGGTTTCTGTACAACATTCCCCC-TTTTAgCCTCTTTTGACCTGGGTCTAGAACGATGAATGTTATAGATACAGTGAGTGCACTGTGTTATATTGTTGCATCAGAGACTTGCTAGACCTATC----ATTTTACGCCCCTGCTTCTGATTTCTGATTATTGCTGCAGATAA Claytosmunda_claytoniana_CL2 AAGTGATGCCTGCTGTGATTGTGCGCCAGCGCAAACCTTGGAGAAGAAAGGATGGTGTTTTCATGTACTTCGAAGGTATGGAGTCTCAAATTCTGGAGTAAGCCCTTTCTTGGATATTTACAATATGTCACTGGTCTACCGCGATAGATTTCACCAGGGAGTTTCTTTATGTTATTTTATCACAGGTTTCTGTACAACATTCCCCC-TTTTAACCTCTTTTGAGCTGGATCTAGAACGATGAATGGTATAGATACAGTGAGTGGACTGTGTTATATTGTTGCATCAGAGACTTGCTGGACCTATC----ATTTTACGCCCCTGCTTCTGATTTCTGATTATTGCTGCAGATAA ; END; BEGIN MRBAYES; Prset statefreqpr = dirichlet ( 1 , 1 , 1 , 1 ); Lset nst = 6 rates = propinv; log start filename = L258.log replace; mcmcp ngen = 10000000 printfreq = 1000 samplefreq = 100 nchains = 4 savebrlens = yes filename = L258; mcmc; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 353; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 353; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 353; END; BEGIN TREES; Title L258tree; ID 0174bf378fbb21; LINK Taxa = Taxa; TRANSLATE [0] 1 Osmunda_regalis_R10, [1] 2 Osmunda_japonica_J4J6J7J8, [2] 3 Osmunda_japonica_J1J3J5, [3] 4 Osmunda_japonica_J2, [4] 5 Osmunda_regalis_R15R17R18, [5] 6 Osmunda_regalis_R14, [6] 7 Osmunda_lancea_L1, [7] 8 Osmunda_regalis_R5R6R7R8R9, [8] 9 Osmunda_lancea_L2L3, [9] 10 Osmunda_regalis_R13, [10] 11 Osmunda_regalis_R1R4, [11] 12 Osmunda_regalis_R2R3, [12] 13 Osmunda_regalis_R11R12, [13] 14 Plenasium_banksiifolium, [14] 15 Claytosmunda_claytoniana_CL1a, [15] 16 Claytosmunda_claytoniana_CL1b, [16] 17 Claytosmunda_claytoniana_CL2; TREE con_50_majrule = ((17:0.013897,(15:0.004449,16:0.013946)1.00:0.012768)0.93:0.0081975,(14:0.069131,(5:0.009474,(8:0.008484,((6:0.010027,10:0.003388)1.00:0.014184,(13:0.006439,(1:0.017149,(11:0.00335,12:0.006546)1.00:0.010318):0.010034)0.99:0.014026,(3:0.003324,7:0.009845,9:0.010149,(2:0.006836,4:0.006731)0.95:0.006779)0.80:0.006549)1.00:0.016455)1.00:0.009871)0.89:0.084514)1.00:0.0081975)[% ] [% ] [% setBetweenBits = selected ]; TREE con_50_majrule = (1:0.017149,(11:0.00335,12:0.006546):0.010318,((((2:0.006836,4:0.006731):0.006779,3:0.003324,7:0.009845,9:0.010149):0.006549,((5:0.009474,(14:0.069131,((15:0.004449,16:0.013946):0.012768,17:0.013897):0.016395):0.084514):0.009871,8:0.008484):0.016455,(6:0.010027,10:0.003388):0.014184):0.014026,13:0.006439):0.010034); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1600936106302; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4686034940565267892; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5785744700121514794; mqVersion 361; checksumv 0 3 282442941 null getNumChars 353 numChars 353 getNumTaxa 17 numTaxa 17 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 142722.0 sumSquares -2.30584300921364275E18 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 296; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1361 1119; setLocation 949 71; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #5785744700121514794 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 949 71; 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; toggleReduceCellBorders off; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; togglePaleMissing off; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; 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 16 6 1 1; 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;