#NEXUS [written Thu Sep 24 16:52:27 JST 2020 by Mesquite version 3.61 (build 927) at tsutsumichie-no-iMac.local/202.220.64.189] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS Osmunda_japonica_J1J2J3J4J5J6J7J8 Osmunda_lancea_L1L2 Osmunda_lancea_L3 Osmunda_regalis_R13R14R15R16R17R18USA Osmunda_regalis_R10 Osmunda_regalis_R5R6R7R8R9NI Osmunda_regalis_Ger Osmunda_regalis_R11R12 Osmunda_regalis_R4 Osmunda_regalis_R1R2R3H2H3H5 Osmunda_hybrida_H1H4 Plenasium_banksiifolium Plenasium_javanicum Plenasium_vachellii Claytosmunda_claytoniana_CL1 Claytosmunda_claytoniana_CL2_USA_Japan ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=413; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Osmunda_japonica_J1J2J3J4J5J6J7J8 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATTTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_lancea_L1L2 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATTTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAATAGCTTTCCCAATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_lancea_L3 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAAATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATTTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_regalis_R13R14R15R16R17R18USA AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATTTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-CCGGATATCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_regalis_R10 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCCGGCAGATTCTCTGGTACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTAGAATACAATATA Osmunda_regalis_R5R6R7R8R9NI AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCCGGCAGATTCTCTGGTACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_regalis_Ger AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCCGGCAGATTCTCTGGTACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTC------------------------------------ Osmunda_regalis_R11R12 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGGCAGATTCTCTGGTACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCT-ATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_regalis_R4 -----------------------------------------------------------------------------------------------------------------------------AATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_regalis_R1R2R3H2H3H5 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAATTAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCCGATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Osmunda_hybrida_H1H4 AACTGAGCAAGACGAATATCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGAACTCGGAATTGGGGCTATAGAATCTGGATCTCCATAT-TATTTCTTCTATTTTCCCTATCTAAAATCTATCTAAAATGCACGTTCAATCTCTTCACTCATTGCTCCATCAAATGGAAATAATAACTCGTTCTCTTCTTTCTAC-CCGGATGTCCCACAAATGAACCATTAGGAAAATCCACAAGATTCTATCAATGGTTCATTTATGGATTCTGGATAAGGAATAATAGCTTTCCCAATATGTTTCTCATTCTCCGTCTGATTGACAGAGAACAAGAATTTATAATACAATATA Plenasium_banksiifolium AACTGAGCAAGATGAATCTCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAAATTCATTTAATAGTAGTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGTACTTGGAGTTGGGGCTATAGAATCTAGATCTCCATCTATATTTCTTCTATTTCCCG---------TGTATCTAGAATACACGTTCATTTTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-TCGGATATCCCACAAATGAACCATTAGGAAAATCTACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAAGAGCTTTCCCAATATGTTTCTCATTCGCCCTATGATTGACGGAGAACAGGAATTTCTAATACAATAAA Plenasium_javanicum AACTGAGCAAGATGAATCTCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAAATTCATTTAATAGTAGTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGTACTTGGAGTTGGGGCTATAGAATCTAGATCTCCATCTATATTTCTTCTATTTCCCG---------TGTATCTAGAATACACGTTCATTTTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-TCGGATATCCCACAAATGAACCATTAGGAAAATCTACAAGATTCTATCAATGGTTCATTTATGGATTCTCGAGAAGGAATAAGAGCTTTCCCAATATGTTTCTCATTCGCCCTATGATTGACGGAGAACAGGAATTTCTAATACAATAAA Plenasium_vachellii AACTGAGCAAGATGAATCTCGTTCGGAAGATTGATTCTGAGTCATGATGGATCAAATTCATTTAATAGTAGTTATTCAATCCATCAGATTCTCTGG------------TACATAAGGGTACTTGGAGTTGGGGCTATAGAATCTAGATCTCCATCTATATTTCTTCTATTTCCCG---------TGTATCTAGAATACACGTTCATTTTCTTCACTCATTGCTCCATCAAATGGAATTAATACCTCGTTCTCTTCTTTCTAC-TCGGATATCCCACAAATGAACCATTAGGAAAATCTACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAAAAGCTTTCCCAATATGTTTCTCATTCGCCCTATGATTGACGGAGAACAGGAATTTCTAATACAATGAA Claytosmunda_claytoniana_CL1 --------AAGATGAATCTCGTTCGGAAGATTCATTTTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TATATA---GAACTCGGAATTGGGGCTATAGAATCTGGATTTCTATATATATTTCTTCTATTTCCCC-----------TATCTAAAATGCACGTTCATCTTCTTCACTCATTTCTGCATCAAATGGAATTAATAACTCGTTCTATTCTTTCTACACCAAATGTACCACAAATGAACCATTAGGTAAATCTACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAATAGCTTTCCCAATATGTTTCTCATTCTCCCTCTGATTGACGGAAAACAGGAATTTGTAATACAATATA Claytosmunda_claytoniana_CL2_USA_Japan AACTGAGCAAGATGAATCTCGTTCGGAAGATTCATTTTGAGTCATGATGGATCAGATTCATTCAATAGTATTTATTCAATCCATCAGATTCTCTGG------------TATATA---GAACTCGGAATTGGGGCTATAGAATCTGGATTTCTATATATATTTCTTCTATTTCCCC-----------TATCTAAAATGCACGTTCATCTTCTTCACTCATTTCTGCATCAAATGGAATTAATAACTCGTTCTATTCTTTCTACACCAAATGTACCACAAATGAACCATTAGGTAAATCTACAAGATTCTATCAATGGTTCATTTATGGATTCTGGAGAAGGAATAATAGCTTTCCCAATATGTTTCTCATTCTCCCTCTGATTGACGGAAAACAGGAATTTGTAATACAATATA ; END; BEGIN MRBAYES; Lset nst = 6 rates = propinv; Prset statefreqpr = dirichlet ( 1 , 1 , 1 , 1 ); log start filename = OtrnLFnewfortree.log replace; mcmcp ngen = 10000000 printfreq = 1000 samplefreq = 100 nchains = 4 savebrlens = yes filename = OtrnLFnewfortree; mcmc; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 413; END; BEGIN NOTES; TEXT TAXON = 7 TEXT = 5R6R7R8R9; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 413; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 413; END; BEGIN TREES; Title trnLF; ID 0174befff24f16; LINK Taxa = Taxa; TRANSLATE [0] 1 Osmunda_japonica_J1J2J3J4J5J6J7J8, [1] 2 Osmunda_lancea_L1L2, [2] 3 Osmunda_lancea_L3, [3] 4 Osmunda_regalis_R13R14R15R16R17R18USA, [4] 5 Osmunda_regalis_R10, [5] 6 Osmunda_regalis_R5R6R7R8R9NI, [6] 7 Osmunda_regalis_Ger, [7] 8 Osmunda_regalis_R11R12, [8] 9 Osmunda_regalis_R4, [9] 10 Osmunda_regalis_R1R2R3H2H3H5, [10] 11 Osmunda_hybrida_H1H4, [11] 12 Plenasium_banksiifolium, [12] 13 Plenasium_javanicum, [13] 14 Plenasium_vachellii, [14] 15 Claytosmunda_claytoniana_CL1, [15] 16 Claytosmunda_claytoniana_CL2_USA_Japan; TREE con_50_majrule = ((15:0.001256508,16:0.001244996):0.015333745,((12:0.001196249,13:0.002906157,14:0.004444161):0.03561354,(2:0.001516412,(1:0.001201305,3:0.002864073,4:0.002845157,(8:0.002841207,9:0.001472584,10:0.001191858,11:0.004428353,(5:0.002442265,6:0.001176128,7:0.001242997):0.002614556):0.006282358):0.002798969):0.01916109):0.015333745); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1600933947192; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8310719888148997260; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3968535014462870848; mqVersion 361; checksumv 0 3 1021742045 null getNumChars 413 numChars 413 getNumTaxa 16 numTaxa 16 short true bits 15 states 15 sumSquaresStatesOnly 157495.0 sumSquares 157495.0 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 1858 1054; setLocation 551 287; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3968535014462870848 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 551 287; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; 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;