#NEXUS [written Wed Jul 20 12:43:26 ACST 2016 by Mesquite version 3.10 (build 765) at Elen/192.168.1.3] BEGIN TAXA; DIMENSIONS NTAX=42; TAXLABELS Anhima_cornuta Anseranas_semipalmata Dendrocygna_eytoni Cereopsis_novaehollandiae Anser_caerulescens Malacorhynchus Tadorna_tadornoides Leipoa_ocellata Megapodius_reinwardt Megapodius_eremita Alectura_lathami Latagallina_naracoortensis Latagallina_olsoni Progura_campestris Progura_gallinacea Talegalla_fuscirostris Macrocephalon Gallus_gallus Coturnix_pectoralis Acryllium_vulturinum Megavitiornis_altirostris Ortalis_vetula Sylviornis_neocaledonica Presbyornis_pervetus Dromaius_novaehollandiae Dinornis_robustus Tinamus_robustus Struthio Dromornis_planei Crax_rubra Eulipoa_wallacei Lithornis_promiscuus Chauna_torquata Lithornis_plebius Paracathartes_howardae Phasianus_colchicus Burhinus_grallarius Porphyrio_melanotus Grus_rubicunda Talegalla_jobiensis Aepypodius_bruijnii Aepypodius_arfakianus ; END; BEGIN CHARACTERS; DIMENSIONS NCHAR=285; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4"; MATRIX Anhima_cornuta 2000111000011010021101010001100101011111100101011110100010110003000102200100100001000210100001101100000000100110111-1000000000?00020-00100000011000110111101200100-01100011000110011001100000010001100100101001001011101000010100001101001101012102100002001100112002210010100000001010000001 Anseranas_semipalmata 0110121100011?1010110100100221021101111110221101101010000001011310011201011111001100001000000110020000001100011100001000000000000000-00000000011000000111001010110100000000001110011011100001100000000100100001000011100000001000001101000010011102100002000000000011110000100011000020000002 Dendrocygna_eytoni 211112111002021010110100100221021101111110221101111010001001011310011101001011111000011110002100110000111201011001011101010000100000-00010110011000000110001120200100000001101111012011000111000000000100100001011011001000011100001101000000012102100002001000021013110010111101001120000003 Cereopsis_novaehollandiae 211112111012211110110100000220021101111110021101110110001011011311011200001010111100021000001102110011011001011011001000000000100000-00000110011100000111011020101200101001200110102011001011000001001100110102001010000010011110001110010000012102100002000000012012110110111101101110000003 Anser_caerulescens 011112111002101010110101100221021101111110221101111010001001111311011201001010110110101010002102110001011000011011011000010000100000-00001110011000200110011120101101102000200120002021000011000001000100111002001011001010011100000100000001012102100000001000122003110010120102101110000003 Malacorhynchus 021112111102221010111101100221021101111110221101111010001101111310011101001110121000111011002100030010111101011001011110010000111220-00011120011100210110011120210111002001210120012021100111000001000110100002011010000000011110001101000000012102100001000000120003110000111102101120000?03 Tadorna_tadornoides 211112111002111010111100000221021101111110221111111010001101111311011101011010121000121011002100010001011001011001011100010010110110-00011120011100201110011120100110101010201120012021000011000001000100111002001010001010001110001111000001012102100001000000022003110000111102101120000003 Leipoa_ocellata 210010001000111001010101000120110000?010100200001101010111010002001100000101023221102201111120200111100000100002021-0102120121110011002100100100012000000120021010001012000000012111101100110010000010110100000001000000100000101001111000101112001011010001111110110001101100020000021000210 Megapodius_reinwardt 2100100010001010000101010001201100000010101200001101010111010002001100000101023221102201111120200111100000110002021-0102120121110011002100100101012000000120021010001012011000012011001100110010000010110100000001000000100000101001010000101112001011011001111110110001100100020000020000210 Megapodius_eremita 22001000100010100001010100012011000000101012000011010?01110100020?1100000101123221102201110120200111100000110002021-0102120121110011002100100101012000000120121000001012010000012001001100110010000010110100000001001000100000101001000000101112001011011001111110110001100100020000020000210 Alectura_lathami 2200100010001010010101010001201100000010101200001101010111010002001100000101023211102201111120200111100000100002021-0102110121110111002100100101012000000120021010001012010000012111101100110010000010110100000001000000100000101001110000101012001011011000111110110000101100021000020000210 Latagallina_naracoortensis ??0?????100?11100?0?01???00120???????????????0???????????????????????????????232211022?1111120200111100000100??2?21?02121101211100010021011001010110000001201210000010110000??????????????1100(0 1)01000001101001000010110001000001010011110001011120010110101011111211101111011000200000210????? Latagallina_olsoni ??0?1????????????????????????????????????????????????????????0????????0??????2????????????????????????????????????1?01121101211100010021011001000???0000012012100000101100000001211????1??1100101000001101001000010110101000001010011100001001120010110101011111111101101011000200000200????? Progura_campestris ??0????1100011100?01010100012011????????????00?????????????????????????????1??????102?11111?2020111110000010001?021?0???1?0??????????02101100?000?????????200210000010130000??????????????11001000000011010000000100001010000?10??011110101011120010110111011111201100100001000200100210????? Progura_gallinacea ???????????????????????????????????????????????????????????????????????????????????????1?11??0201?11?00?????0?????????????????????????????????????????????2012?0000?101?0?10?????????????????????????????????????????????????????????????????????????????1011111001100100021000200100210????? Talegalla_fuscirostris 220010011000101000010100000120110000????100200001101010111010002001100000101023211102201111120210111000000100002021-0202110121110211002100100101012000000120021000001011010000012111001100110000100010110100000001001000100010101001101000101112001011011000111120110001001100020000011000010 Macrocephalon 120010012000101001010100100120110000001010120000110101111101000200?100000101023221102201101120210111000000110012021-0102110121110211002100100100012000000110021010001012010000012101?011?0110000000000100100000101001000100010001001000000101012001011011000111110111110000100021000021000010 Gallus_gallus 200010000101121001010101010120110000001010120000110101011111000300210000(0 1)10102(2 3)221102201110120201111101000110002021-110212112111022111210001110101200001012002101000101211000001200010100011000000100011010000101101000011000010100110(1 2)000101011001011010001110110111100001101011000021000000 Coturnix_pectoralis 210010000001111001010101010120110000???0101200001101010111110003002100000101?22221102200110120200311101100100002031-1312121121110011112100100101012001010120021020001012100000022010101000100000001000110100001100000000110000001001101001101012001011010001111110112100001101101000020000000 Acryllium_vulturinum 210010000101001010010101000120110000????101200001101010111110003000100001101123221102201110120200311101100100002021-12021211011001111121000001010120000101200210000010110000000120100010001100000010011101000000010010001000000010011010001010120010110(0 1)1001110110111100000110011000020000000 Megavitiornis_altirostris ?22010?21000?0?0000?0????0012011??00????1????0001101000100(0 1)1000200010?0001?1?2321?01???011012020---1---10-1-0?????--0---1----1--0--1-00100----------010---2002?-000-1---0-01000??01??0?1??1000000000101101001000010101011200000011011110000010120010110100001111101111101011000201000100100?? Ortalis_vetula 2000100000020110010101000101201100000011101200111101010111110003002100000101123021102201111120200111101000110002031-12021201211102211121000001000020010001201210001010121000000120001010101100000010001101000000010110001000000000010110011010120010100110011101101101?0001100020000021000001 Sylviornis_neocaledonica ?22010022000001000010100100120110001????100210001101?001010100?200?100001101?2??2??????11111202-----------1-0?????1--10--2---1--0----02100----------010---200211001-10110102?0???????211??1000100010101001000000010000001100000011011010000000120020110101001111121111101000000001010220001?? Presbyornis_pervetus 00111?110112?11010110?01??0221??1000????1???1100111011011101110310011?1??????0???1000000110001001300010110000??1?1001000000000101010-00000100011100300111002110210101001011201020??10011000001000011001001011010010110001100010000012000001110111021000020001001200011100100110020010200????3 Dromaius_novaehollandiae 00010000110220100000001001000002000000000-331010001000010100000100100301011100222101102--1--0----------1----1-------------------0----00--------------1--------?-------------10120012020000011000101001100000104001001001101100001111101110120101-101211-2110011102303220010121101101012110200 Dinornis_robustus 22000000100220100000001011000011000000000-3310000010?001?10000000010030100?100222100021--1------------------1-------------------------------------------------?-------------10120012020110001001000011001010113201100111100000001000111011020000-001211021101111122031202-00001001-1-130101?0 Tinamus_robustus 20001000100220000000000001000012000000000-330000000?001111100001001001000000022221100211111001200311100110010010021-1102120121100121211110101101011300010100021000001010010000022002120000100000000010110100011100001000220000001001011000110011000101110001100122003110210100101101011000200 Struthio 00010000010210100000000001000002000000000-331010000020010100000101100300000000221101011--1-------------1-0--1-------------------------------------------------?-------------10101002020000011000101000000000104001021001100000101021021111120001-1-021--211011010230221111012110--0-1-1210200 Dromornis_planei 022110222002?01102110100100120110???????100211002101110010010022010?0?00010??0222101012--1-------------1----1----------------1-------0------------------------?-------------111?00?2021110001000010110001?111?3201100011121011001011102-000100020010210110010101023031201010001010110121112?? Crax_rubra 2100100000020110010101000001201100000011101200011101110111110003000100000(0 1)01123021102201111120200311100000110002021-1202120121110111112100010100002200000120121000101012100000012000101110100000001000100100000001010000110000001001022-00101012001010011001111120110100001100020000021000001 Eulipoa_wallacei 010010002000101000010101000120110000001010120000110101011101000200?100000101?23221102201101120210111000000110112021-0102120121110111002100100101012000000111021020001012010000022000101100110110001000100100000101001000010010101101010000101011001011011001111010111001100100020000021000110 Lithornis_promiscuus 000000000102200?000?0?????00001?000000000033?0100010?0010100010100100?200101100111001220110101030300100100010100021-0000000000100120-0220010102100030100112002?1100010000101000?200212011?1110000000001100000111000010002210000011010110111110111100000-00001111223011200001000010000200????? Chauna_torquata 2000111100011011021101011001101111011111100101011110100000010003000102200010100001001011000021001000000010010110111-1000000000100000-00000(0 1)00011000110111101200200-01000001101100000001100000010001001000101000000111000010001100001101000001012102100002001100012202110010100001001020000001 Lithornis_plebius ??????????????000000?0100000001?????????00331?0000000011010???????????2?010?10?????????0110101030300110101210???0?1-1000000000100120-0211010102100030000112002?2100010100101?00??00??200??1110000000001100000111010010002210000010011110101110111100000-00011111223011200101000010000200????? Paracathartes_howardae 00000?????????000000???000???????????????033?000?000?0110100??????1?????0??0?????????????10101020300100100210???0???1000000000?00120-022101000?100000000111202121010101001????????????????1110000010001100020111010010??2210000010011110001110111100000-10000111222011200101000010000200000?? Phasianus_colchicus 210010000101011001010101000120110000????101200002101000111110003000100001111020221102201110120200111100000100002031-1102121121110021112100111101012001010120121120001012110000112010101000110010001000120100001111000001120000101001111001101011001011010001110110112110011101001000020000000 Burhinus_grallarius 000110000112021001100110001--0120110001111000010100020101100000000000010011101221100120001000100030011110221011102001000000000001110-00200111021001300010020020200201000011100020012001100100000001110100200000001010010111000100002202-00010011101011102000100122103210010111101111021100000 Porphyrio_melanotus 010110010002201001000100001--0020110001111000010110120100100000001000100111101221101121001000100000000010001000003021002020000001000-002111200000000011111201102001000000012001000001010001000000000101200000111100110001100000000021010001000120021000020011000101001100101010111-0010000000 Grus_rubicunda 100110000102101001000100011--002011000111100001011002010010000000000020?101000000100002001000120100000000010000-031-1000000000000000-10200021021000000110101110110110000001100100010101110100000001000100000010010011000110011000002101000001011001100102001100122112210010111102000020000000 Talegalla_jobiensis ??0???????????????????????0??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????1200?0001???????????????????????????????????????????????????????????????????010100110100010101200101101?000111110110110001100020000020000010 Aepypodius_bruijnii ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????1200?0001????????????????????????????????????????????????????????????????????101?0?011000101011001011012001111110110010100100020000020000110 Aepypodius_arfakianus ??0???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????10001010120010110120011111201100001?0100020000021000110 ; END; BEGIN PAUP; SET MAXTREES = 10000 ROOT = OUTGROUP OUTROOT = monophyl CRITERION = parsimony tcompress = yes torder = left; PSET opt = AccTran; OUTGROUP Lithornis_promiscuus Lithornis_plebius Paracathartes_howardae Dromaius_novaehollandiae Dinornis_robustus Struthio Tinamus_robustus / only; LOG start file = Megapod_log.txt replace = yes; TYPESET * Morphoclines = ord : 1 2 6 7 8 12 -14 18 28 29 32 49 64 70 78 80 81 95 98 106 112 116 122 130 131 140 156 160 161 172 176 177 180 182 200 202 217 227 -231 236 240 243 249 257 260 -263 269 272 273 278 -280 283 285; DELETE Aepypodius_arfakianus Talegalla_jobiensis; CONSTRAINTS FullBackbone ( backbone ) = ( ( ( ( ( ( Crax_rubra , Ortalis_vetula ) , ( Acryllium_vulturinum , ( Coturnix_pectoralis , ( Gallus_gallus , Phasianus_colchicus ) ) ) ) , ( ( ( ( Megapodius_eremita , Megapodius_reinwardt ) , Eulipoa_wallacei ) , Macrocephalon ) , ( Talegalla_fuscirostris , ( Leipoa_ocellata , ( Aepypodius_bruijnii , Alectura_lathami ) ) ) ) ) , ( ( Anhima_cornuta , Chauna_torquata ) , ( ( Dendrocygna_eytoni , ( ( Tadorna_tadornoides , Malacorhynchus ) , ( Cereopsis_novaehollandiae , Anser_caerulescens ) ) ) , Anseranas_semipalmata ) ) ) , ( ( Grus_rubicunda , Porphyrio_melanotus ) , Burhinus_grallarius ) ) , ( Struthio , ( Dromaius_novaehollandiae , ( Dinornis_robustus , Tinamus_robustus ) ) ) ); HSEARCH addseq = random nreps = 1000 rstatus = yes nchuck = 2000 chuckscore = 1 enforce = yes constraints = FullBackbone; SAVETREES File = Megapod_MP.trees brlens = yes replace = yes; CONTREE / treefile = Megapod_MP_con.tree root = outgroup outroot = monophyl replace = yes; [BOOTSTRAP nreps = 1000 conlevel = 50 grpfreq = yes keepall = yes brlens = yes treefile = Megapod_boot.trees replace = yes search = heuristic / addseq = random nreps = 100 nchuck = 1000 chuckscore = 1 enforce = yes constraints = FullBackbone;] SAVETREES from = 1 to = 1 file = Megapod_boot_con1.tree savebootp = nodelabels; CONTREE / treefile = Megapod_boot_con2.tree root = outgroup outroot = monophyl LE50 = yes GRPFREQ = yes; LOG stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 285; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 285; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1468984407008; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8434822446211192167; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3274983745572812866; mqVersion 310; checksumv 0 3 4035674338 null getNumChars 285 numChars 285 getNumTaxa 46 numTaxa 46 short true bits 31 states 31 sumSquaresStatesOnly 41317.0 sumSquares 41317.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 127; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1366 659; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3274983745572812866 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1239 587; setLocation -8 -8; 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; toggleAutoWCharNames on; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded 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.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.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;