#NEXUS [written Fri Jul 19 11:16:43 CEST 2013 by Mesquite version 2.75 (build 566) at Mac-Intel-de-Michel-Laurin-2.local/10.8.65.5] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=82; TAXLABELS Alytes Arariphrynus Arthroleptis_p Bombina Ceratophrys Chiromantis Conraua Cratia Dermatonotus Discoglossus Eurycephalella Gastrotheca Guibemantis Heleophryne Hylarana Hyperolius Hypsiboas Lepidobatrachus Leptodactylus Leptopelis Litoria Megophrys Melanophryniscus Mixophyes Nannophryne Pelobates Pelodytes Phlyctimantis Phrynobatrachus Phrynomantis Phyllomedusa Platyplectrum Pleurodema Pristimantis Ptychadena Rana Scaphiopus Scinax Sooglossus Telmatobius Telmatobufo Thoropa Beelzebufo Afrana Afrixalus Allophryne Amnirana Callulops Astylosternus Aubria Batrachophrynus Bufo_granulosus Bufo_viridis Cardioglossa Calyptocephalella Ceratobatrachus Chacophrys Cyclorana Dendrosophus Dyscophus Flectonotus Heleioporus Hemiphractus Hoplobatrachus Hymenochirus Isthmohyla Kassina Limnodynastes Odontophrynus Opisthohylax Osteopilus Physalaemus Pseudis Pyxicephalus Rhinoderma Spea Schoudedenella Thaumastosaurus Triprion Xenopus Baurubatrachus Wawelia ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=74; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4"; MATRIX Alytes 000111000110110001000010001211100101010000001000--000000100010000110011000 Arariphrynus ?01111????1?1?????101??0????????02?1?111?01?0??????????20?0?????1?0?11?04? Arthroleptis_p 10221010111011001110001001120100021100112010000110011112010210111000110022 Bombina 1001110001101100000000000012121001000200010110010-00000010002000001?012001 Ceratophrys 012010012211111000101011000-120000111001101000110-01000201022001001?113002 Chiromantis 1002110011101100011000000111120002210001201000011011111201123031101?102032 Conraua 10201000111011000110???00111110102210011201000011011111111022021100?112022 Cratia 1000?1?0111?11?????????0?????????????00?1??1???????00??10????????????????? Dermatonotus 00221010000-110011000200001212010221020100110000--011111010210010000111002 Discoglossus 00011000121011000101?0000012111001000100100010010-000000100010001110011001 Eurycephalella 1?21?10??210110???1??????????????1?????????????????000?2010?20??????11?11? Gastrotheca 10010100111?110001100010????????021??0011010000?????000???121101?????????2 Guibemantis 10021100111011000110001001110100021100012010000110111112011210310010112032 Heleophryne 100101001110110001110000011?120011110001101001010-000001010020210010112020 Hylarana 10021100111011000110002001111100022100112010000110?11112010210210000112022 Hyperolius 100110101110110011100010011100000221010120110001100011110112111100111111?2 Hypsiboas 00??1100111011000111???00011120002110110101000010-000001011231?10010111102 Lepidobatrachus 012010012211111100101021100-121101111101101100110-01000201021001001?113100 Leptodactylus 0000110011101100001100100012120002110111101000010-000001010220011000112102 Leptopelis 10021100111011000010011001110100022100112010000111011112011211?11011100100 Litoria 1011110010101?0001111010????????021101011010000????000?102122101000?11??02 Megophrys 10121100211?110000011110210-110001100011010001011?1?0001?1002?010?00112?00 Melanophryniscus 00221000100-100011100??0011201000111010010010000--010001010210010010111002 Mixophyes 0010110011101100011100200110110001110111201001010-?0000201011001101?111000 Nannophryne 00211100110-0-0011100??0001111000111000110110000--01000201022001001?11?002 Pelobates 0122210022101100000010102110120001100201011101010-11000111001001000?003000 Pelodytes 1001010011101100010000102111111001110201001101010-100001110110010010011000 Phlyctimantis 1021110011101100011000100111000002200001201?000110001112011210?100111110?0 Phrynobatrachus 10021100111011001110000001111201022100112010000111111111010210211001112022 Phrynomantis 10220110000-110011000000001212010221020100110000--00--110-1211310000111132 Phyllomedusa 101111001010110001110100010-12010211011112100000--01000201121101001?111100 Platyplectrum 10201100111011000111?0100111110011110111201001010-00000201011001101?113002 Pleurodema 0020110010100-00011000100011110102110111201000010-100001010220010000112102 Pristimantis 100111001110110001110010010-110002110011201000010-00000201021121001?111122 Ptychadena 1020110011101100010001200011110122-111112010000110111111020210011000112102 Rana 1021110011101100011000100111110002210011201000?11111111101021001100?112002 Scaphiopus 0121100022100-00000010102110120001100201020101010-00000201002001001?013000 Scinax 10??1100111011000111???00111120002110111101000010-000001011220010010112002 Sooglossus 00010000111?1101111?1110?11212000211010?010?01010-000001?1001001?0?1111002 Telmatobius 1020110000101100011000100?11120001110100201000010-00000112021041000?111042 Telmatobufo 10011100111011000111102001101?0011100000100000010-00000101001001000?111000 Thoropa 001011001110110001100??00?11120002110111101000010-0?0??20102?0?10000???022 Beelzebufo ?12?1??122111110????1??????????0?11?1???101??0???????????????????????????? Afrana 100?11011110110001100120001011000220101?201?0?011111110??10210411000112102 Afrixalus 002?21101110110111101120011100000221021?101?00011000111??11111110000111110 Allophryne 10222100110-0-1-11010000001111000211000110100000--000102010200210010100022 Amnirana 10021100111011000110012001101100021000012???0?0111111102?10210111000112022 Callulops 002120?0010-110?1110???0000-0100022102?110100000--00--1??-0220311?0?112132 Astylosternus 00002100111011000111002001111100021100??201?0?0110011112?10210111001113102 Aubria 010?20002211110000101021001111000220101?201?0?01101???0??10210111000111142 Batrachophrynus 00010100000-100010101110??????000110021?200?0?010-0?110??102?0110?0?1??042 Bufo_granulosus 01220001200-111011101100001111000110100110110000--1?1102010220110010112042 Bufo_viridis 100101?0100-0-011110011000111100011002??101?0000--1???0??10220110010112042 Cardioglossa (0 1)00?21(0 1)0110-11?0011101100112010002(1 2)10?1?201?0?0110011112?10100111001010042 Calyptocephalella 012220?122101101001011200?????000111120?10??0?010-0?0002?10210011010110000 Ceratobatrachus 0122000002101101001001110111110002201011201000011011111??20210011?00101002 Chacophrys 0120200122111110?010???1000-12100010020?101?0?010-0?0?02?10210411010113042 Cyclorana 0(0 1)0011101210110100101110??10?2000211000?101?0?010-0?1?02?102?0411?1?1??042 Dendrosophus 00??01?01010110??110???000101100021102??101?0?010-0???02?11231010000112102 Dyscophus 00??20?00010110??010???00?????00022102??101?0001110???12?-02?041000?112040 Flectonotus 100001?011101000?111111000101100021102??101?0?010-0???0??11211010000111102 Heleioporus 100111100010110100101010011111000111?20?10??01010-0???0??1?2??410???1???40 Hemiphractus 010221?122111101001010210?????00021110??201?0?010-0???02?112?0410???100042 Hoplobatrachus 000?20012110110001110120001111000221121?201?0?0110111102?10210410001112142 Hymenochirus 00??20?1010-0-1????1???00????10?110002??02??0000--0???1??20?00401001110042 Isthmohyla 000100?011101001?111???00010110002100???101?0?00--0???0??11211010000113102 Kassina 002?21001110110111100120011000000220021?101?000110001112?11111310001111112 Limnodynastes 10001100001011110110101001111100111002??10??01010-000002?10?10010?1?11?002 Odontophrynus 00212100(0 1)010110100100000011011000110120?10??0?00--0???02?10210410011113042 Opisthohylax 10??11?01110110??110???001100000022100??201?0001100???12?11111010010111102 Osteopilus 0122200(0 1)12101101001111000?????00021102?1101?0?010?0???02?112?001001?1??002 Physalaemus 00221100101011011010001001121100021002??101?0?010-100002?10210410000113042 Pseudis 00??21?01210110??010???0001111001110121?101?00010-0???0??10210410001111042 Pyxicephalus 011?200022111100001010210011110002201211201?0?0110111112?10210411010112042 Rhinoderma 100201?0110-100?-100?000001011001111021?201?00010-0???0??10200410000110042 Spea 10??01?011100-0??000???0?0121100001012??02??00010-0?110??10010410010013040 Schoudedenella 002?1100000-1110?1110120011201000211021?201?0?011001??12?10100311001110012 Thaumastosaurus 11022100121?110100101010????????00211011201?000110111??201?2???11????????? Triprion 0102210102101100001101000?????00021002??001?0?010-0???0???1210010?0?1??002 Xenopus 0000200021110-0???00???000???1000100120?02-010010-000000??00004001001111?0 Baurubatrachus 01???0??221?11?????01???????????0010000?10??0?0?????00??????????1????????? Wawelia ????????????????????????????????0??000??101?0???????????????????1????????? ; END; BEGIN TREES; Title 'Trees, 703 (TNT), 709 (PAUP)'; LINK Taxa = Taxa; TRANSLATE 1 Alytes, 2 Arariphrynus, 3 Arthroleptis_p, 4 Bombina, 5 Ceratophrys, 6 Chiromantis, 7 Conraua, 8 Cratia, 9 Dermatonotus, 10 Discoglossus, 11 Eurycephalella, 12 Gastrotheca, 13 Guibemantis, 14 Heleophryne, 15 Hylarana, 16 Hyperolius, 17 Hypsiboas, 18 Lepidobatrachus, 19 Leptodactylus, 20 Leptopelis, 21 Litoria, 22 Megophrys, 23 Melanophryniscus, 24 Mixophyes, 25 Nannophryne, 26 Pelobates, 27 Pelodytes, 28 Phlyctimantis, 29 Phrynobatrachus, 30 Phrynomantis, 31 Phyllomedusa, 32 Platyplectrum, 33 Pleurodema, 34 Pristimantis, 35 Ptychadena, 36 Rana, 37 Scaphiopus, 38 Scinax, 39 Sooglossus, 40 Telmatobius, 41 Telmatobufo, 42 Thoropa, 43 Beelzebufo, 44 Afrana, 45 Afrixalus, 46 Allophryne, 47 Amnirana, 48 Callulops, 49 Astylosternus, 50 Aubria, 51 Batrachophrynus, 52 Bufo_granulosus, 53 Bufo_viridis, 54 Cardioglossa, 55 Calyptocephalella, 56 Ceratobatrachus, 57 Chacophrys, 58 Cyclorana, 59 Dendrosophus, 60 Dyscophus, 61 Flectonotus, 62 Heleioporus, 63 Hemiphractus, 64 Hoplobatrachus, 65 Hymenochirus, 66 Isthmohyla, 67 Kassina, 68 Limnodynastes, 69 Odontophrynus, 70 Opisthohylax, 71 Osteopilus, 72 Physalaemus, 73 Pseudis, 74 Pyxicephalus, 75 Rhinoderma, 76 Spea, 77 Schoudedenella, 78 Thaumastosaurus, 79 Triprion, 80 Xenopus, 81 Baurubatrachus, 82 Wawelia; TREE 'tnt 1, 709' = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((5,(18,43)),(82,(57,81)))))))))),(((40,(72,(69,73))),(11,((46,75),((52,(51,53)),(25,(23,(9,30))))))),((34,(31,(17,(21,(38,(19,(33,42))))))),(12,(70,((16,28),(20,((49,((54,77),(64,((45,67),(48,60))))),(3,((6,13),((15,(29,(7,(35,36)))),((44,47),(2,(78,(56,(50,74))))))))))))))))))))); TREE tnt_2 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((5,(18,43)),(82,(57,81)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((34,(31,(17,(21,(38,(19,(33,42))))))),(12,(70,((16,28),(20,((49,((54,77),(64,(60,(48,(45,67)))))),(3,((6,13),((15,(29,(7,(35,36)))),((44,47),(2,(78,(56,(50,74))))))))))))))))))))); TREE tnt_3 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((43,(5,18)),(81,(57,82)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((34,(31,(17,(21,(38,(19,(33,42))))))),(12,(70,((16,28),(20,((49,((54,77),(64,((45,67),(48,60))))),(3,((29,(7,(35,36))),((15,(44,47)),((6,13),(2,(78,(56,(50,74))))))))))))))))))))); TREE tnt_4 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((5,(18,43)),(57,(81,82)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((34,(31,(21,(17,(38,(19,(33,42))))))),(12,(70,((16,28),(20,((49,((54,77),(64,(60,(48,(45,67)))))),(3,((47,(6,13)),((2,(78,(56,(50,74)))),(15,(29,(7,(36,(35,44))))))))))))))))))))); TREE tnt_5 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((18,(5,43)),(82,(57,81)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((34,(31,(38,(21,(17,(19,(33,42))))))),(12,(70,(28,(16,(20,((49,((54,77),(64,(60,(48,(45,67)))))),(3,((44,47),((2,(78,(56,(50,74)))),((15,(6,13)),(29,(7,(35,36))))))))))))))))))))); TREE tnt_6 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((5,(18,43)),(81,(57,82)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((34,(31,(38,(21,(17,(19,(33,42))))))),(12,(70,((16,28),(20,((49,((54,77),(64,((45,67),(48,60))))),(3,((47,(6,13)),((2,(78,(56,(50,74)))),(15,(29,(7,(36,(35,44))))))))))))))))))))); TREE tnt_7 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((43,(5,18)),(81,(57,82)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((34,(31,(17,(38,(21,(19,(33,42))))))),(12,(70,((16,28),(20,((49,((54,77),(64,(60,(48,(45,67)))))),(3,((2,(78,(56,(50,74)))),((6,13),((15,(44,47)),(29,(7,(35,36)))))))))))))))))))); TREE tnt_8 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((18,(5,43)),(81,(57,82)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),((12,(34,(31,((17,21),(38,(19,(33,42))))))),(70,((16,28),(20,((49,((54,77),(64,((45,67),(48,60))))),(3,((47,(6,13)),((2,(78,(56,(50,74)))),(15,(29,(7,(36,(35,44)))))))))))))))))))); TREE tnt_9 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((5,(18,43)),(57,(81,82)))))))))),(((40,(72,(69,73))),(11,((46,75),((52,(51,53)),(25,(23,(9,30))))))),(12,((31,(21,(17,(38,(19,(33,42)))))),(34,(70,((16,28),(20,((49,((54,77),(64,(60,(48,(45,67)))))),(3,(((6,13),(2,(78,(56,(50,74))))),((44,47),(15,(29,(7,(35,36))))))))))))))))))))); TREE tnt_10 = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((43,(5,18)),(82,(57,81)))))))))),(((40,(72,(69,73))),(11,((46,75),(25,((23,(9,30)),(52,(51,53))))))),(12,((31,(21,(17,(38,(19,(33,42)))))),(34,(70,((16,28),(20,((49,((54,77),(64,((45,67),(48,60))))),(3,((44,47),((2,(78,(56,(50,74)))),(15,((6,13),(29,(7,(35,36)))))))))))))))))))))); TREE 'Strict onsensus tree of 10 trees ("Trees, 703 (TNT), 709 (PAUP)"' = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((62,68),(39,((59,(61,66)),(58,((71,79),(55,(63,((5,18,43),(57,81,82))))))))),(((40,(72,(69,73))),(11,((46,75),(25,(23,(9,30)),(52,(51,53)))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74)))))))))))))))))); TREE 'PAUP 1 of 100000, 709 steps' = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(((68,(62,(40,(72,(69,73))))),(39,((59,(61,66)),(58,((71,79),(55,(63,((18,(5,43)),(82,(57,81)))))))))),((11,(46,(25,((23,(9,30)),((51,75),(52,53)))))),((12,(34,(31,(21,(17,(38,(19,(33,42)))))))),(70,((16,28),(20,((49,((54,77),(64,((45,67),(48,60))))),(3,((47,(6,13)),((2,(78,(56,(50,74)))),(15,(29,(7,(36,(35,44)))))))))))))))))))); TREE 'PAUP, Strict cons of 100000 tr 709 steps, 1st batch' = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); TREE 'PAUP, Strict cons of 100000 tr 709 steps, 2nd batch' = (((1,10),4),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); TREE 'PAUP, Strict cons of 150 000 tr 709 steps' = (((1,10),4),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); END; BEGIN TREES; Title Consensus_trees; LINK Taxa = Taxa; TRANSLATE 1 Alytes, 2 Arariphrynus, 3 Arthroleptis_p, 4 Bombina, 5 Ceratophrys, 6 Chiromantis, 7 Conraua, 8 Cratia, 9 Dermatonotus, 10 Discoglossus, 11 Eurycephalella, 12 Gastrotheca, 13 Guibemantis, 14 Heleophryne, 15 Hylarana, 16 Hyperolius, 17 Hypsiboas, 18 Lepidobatrachus, 19 Leptodactylus, 20 Leptopelis, 21 Litoria, 22 Megophrys, 23 Melanophryniscus, 24 Mixophyes, 25 Nannophryne, 26 Pelobates, 27 Pelodytes, 28 Phlyctimantis, 29 Phrynobatrachus, 30 Phrynomantis, 31 Phyllomedusa, 32 Platyplectrum, 33 Pleurodema, 34 Pristimantis, 35 Ptychadena, 36 Rana, 37 Scaphiopus, 38 Scinax, 39 Sooglossus, 40 Telmatobius, 41 Telmatobufo, 42 Thoropa, 43 Beelzebufo, 44 Afrana, 45 Afrixalus, 46 Allophryne, 47 Amnirana, 48 Callulops, 49 Astylosternus, 50 Aubria, 51 Batrachophrynus, 52 Bufo_granulosus, 53 Bufo_viridis, 54 Cardioglossa, 55 Calyptocephalella, 56 Ceratobatrachus, 57 Chacophrys, 58 Cyclorana, 59 Dendrosophus, 60 Dyscophus, 61 Flectonotus, 62 Heleioporus, 63 Hemiphractus, 64 Hoplobatrachus, 65 Hymenochirus, 66 Isthmohyla, 67 Kassina, 68 Limnodynastes, 69 Odontophrynus, 70 Opisthohylax, 71 Osteopilus, 72 Physalaemus, 73 Pseudis, 74 Pyxicephalus, 75 Rhinoderma, 76 Spea, 77 Schoudedenella, 78 Thaumastosaurus, 79 Triprion, 80 Xenopus, 81 Baurubatrachus, 82 Wawelia; TREE 'PAUP, Strict cons of 100000 tr 709 steps, 1st batch' = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); TREE 'PAUP, Strict cons of 100000 tr 709 steps, 2nd batch' = (((1,10),4),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); TREE 'PAUP, Strict cons of 150 000 tr 709 steps' = (((1,10),4),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); TREE Strict_consensus_tree_of_3_Consensus_Trees = ((4,(1,10)),((76,(65,80)),((22,(26,37)),(27,(((14,41),(8,(24,32))),(62,68,(40,(72,(69,73))),(11,(25,46,51,52,53,75,(23,(9,30)))),(39,((59,(61,66)),(58,((71,79),(55,(63,(5,18,43,(57,81,82)))))))),(12,34,(31,(17,21,38,(19,(33,42)))),(70,(16,28,(20,((49,((54,77),(64,(48,60,(45,67))))),(3,(7,15,29,35,36,44,47,(6,13),(2,(78,(56,(50,74))))))))))))))))); TREE 'Majority rule onsensus tree of 136211, 709' = ((4,(1[%consensusFrequency = 1.0 ],10)[%consensusFrequency = 1.0 ]),((76,(65,80)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],((22,(26,37)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(27,(((14,41)[%consensusFrequency = 1.0 ],(8,(24,32)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(((68,(62,(40,(72,(69,73)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 0.66573918 ])[%consensusFrequency = 0.66573918 ],(39,((59,(61,66)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(58,((71,79)[%consensusFrequency = 1.0 ],(55,(63,((5,18,43)[%consensusFrequency = 0.87307193 ],(57,81,82)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 0.66573918 ],((11,((46,75)[%consensusFrequency = 0.65262717 ],(25,((23,(9,30)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(52,(51,53)[%consensusFrequency = 0.65262717 ])[%consensusFrequency = 0.65262717 ])[%consensusFrequency = 0.54215886 ])[%consensusFrequency = 0.65262717 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(12,(34,(31,(17,21,38,(19,(33,42)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 0.95604613 ],(70,(16,28,(20,((49,((54,77)[%consensusFrequency = 1.0 ],(64,((45,67)[%consensusFrequency = 1.0 ],(48,60)[%consensusFrequency = 0.66873454 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(3,((6,13)[%consensusFrequency = 1.0 ],(44,47)[%consensusFrequency = 0.92243651 ],(2,(78,(56,(50,74)[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ],(15,(29,(7,(35,36)[%consensusFrequency = 0.92243651 ])[%consensusFrequency = 0.92243651 ])[%consensusFrequency = 0.92243651 ])[%consensusFrequency = 0.52577986 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 0.66573918 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ])[%consensusFrequency = 1.0 ] [% ] [% setBetweenDouble = consensusFrequency ]; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 74; END; BEGIN MacClade; Version 4.0 87; LastModified -857547917; FileSettings editor '0' '0' '1' '1'; Singles 100; Editor 00011001111111100100010010 '0' '24' Geneva '9' '100' '1' all; EditorPosition '49' '501' '675' '1371'; TreeWindowPosition '46' '6' '1139' '1870'; ListWindow Characters open Geneva '9' '282' '48' '705' '352' 000; ListWindow Taxa closed Geneva '9' '50' '10' '276' '490' 100000000; ListWindow Trees closed Geneva '9' '50' '10' '276' '490'; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ListWindow ExSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharSets closed Geneva '9' '50' '10' '276' '490'; ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ChartWindowPosition '52' '30' '1118' '1860'; StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220'; WindowOrder List Characters Data; OtherSymbols & / 00 ? -; Correlation '0' '0' '1000' '0' '0' 10011010; Salmo 00000001; EditorFile '2'; ExportHTML _ MOSS '100' 110000; PrettyPrint 10; EditorToolsPosition '1009' '46' '115' '165'; TreeWindowProgram 10; TreeWindow 0000; Continuous '1' '3' 1; Calculations 0000001; SummaryMode '0' '0' 0; Charts Geneva '9' ( normal ) 0010; NexusOptions '0' '0' '50' 001010001; TipLabel '1'; TreeFont Geneva '9' ( normal ); TreeShape 1.0 1.0 0100; TraceLabels 0101; ChartColors '0' '0' '65535' '9' '0' 1; ChartBiggestSpot 1; ChartPercent 10; ChartBarWidth '10' 1; ChartVerticalAxis 10101; ChartMinMax '0'; TraceAllChangesDisplay '0' 1; BarsOnBranchesDisplay '0' '0' '60000' '10000' '10000' '10000' '10000' '60000' '65000' '65000' '65000' '6' '1' 0000101; ContinuousBranchLabels 0; AllStatesBranchLabels 1; IndexNotation '2' 1; PrintTree 10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' ( normal ) Geneva '10' ( normal ) Geneva '9' ( normal ) Geneva '9' ( normal ) Geneva '9' ( bold ) Geneva '9' ( normal ) Geneva '9' ( normal ) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '2' '15395' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000; MatchChar 00 .; EntryInterpretation 01; ColorOptions 00; TreeTools '0' '5' '4' '0' '10' '4' '0' 00100111111101110; EditorTools '0' '0' '0' '1000' '0' '0' '6' '3' '1' 100010101110011; PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010; BothTools '1'; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 3 6 - 8 11 - 22 24 - 27 29 31 - 33 35 - 40 43 - 55 57 59 61 - 74, ord: 4 - 5 9 - 10 23 28 30 34 41 - 42 56 58 60; END; BEGIN NOTES; TEXT TAXON = 78 CHARACTER = 1 TEXT = Changed_to_reflect_the_mummy.; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374225403727; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5763510104795268614; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8549327182252021983; mqVersion 275; checksumv 0 3 222380395 null getNumChars 74 numChars 74 getNumTaxa 82 numTaxa 82 short true bits 31 states 31 sumSquaresStatesOnly 29683.0 sumSquares 29683.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 67; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1082 921; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.ManageTrees.ManageTrees; tell It; getTreeBlock 0; tell It; setSelected 13 - 15; attachments ; endTell; showTrees 1 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 2; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; getTable; tell It; rowNamesWidth 348; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.arrow; endTell; endTell; showWindow; endTell; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; endTell; showTreeBlocks #mesquite.lists.TreeblockList.TreeblockList; tell It; getWindow; tell It; newAssistant #mesquite.lists.TreeblocksListNumber.TreeblocksListNumber; newAssistant #mesquite.lists.TreeblocksListTaxa.TreeblocksListTaxa; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.lib.ListableVectorWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5763510104795268614 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1544.1354698534460.5489322033496135995; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; 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 3; 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; setFontSize 14; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 5; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 744; setOffsetsY 304; getLegendsVector; tell It; distributeCommands; setBounds 744 304 236 39; setOffsetX 744; setOffsetY 304; endDistributeCommands; endTell; newLegendItemNoCalc #mesquite.trees.TreeValueUsingMatrix.TreeValueUsingMatrix; tell It; getEmployee #mesquite.parsimony.TreelengthForMatrix.TreelengthForMatrix; tell It; getEmployee #mesquite.parsimony.ParsCharSteps.ParsCharSteps; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; endTell; endTell; getEmployee #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices; tell It; setDataSet #8549327182252021983; endTell; endTell; endTell; calculate; endTell; 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; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges 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; makeTreeWindow #5763510104795268614 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 2; toggleUseWeights off; endTell; setAssignedID 1083.1355002685296.1795619686478507269; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 4; setOffsetsY 4; getLegendsVector; tell It; distributeCommands; setBounds 4 4 289 22; setOffsetX 4; setOffsetY 4; endDistributeCommands; endTell; calculate; endTell; 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; toggleWhiteEdges 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 #8549327182252021983 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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.stratigraphictools.ColorScaleCells.ColorScaleCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #8549327182252021983 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.DefaultCharOrder.DefaultCharOrder; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.lists.CharListPartition.CharListPartition; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.parsimony.CharListParsModels.CharListParsModels; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1015 854; setLocation 46 46; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;