#NEXUS BEGIN DATA; DIMENSIONS NTAX=32 NCHAR=348; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4"; MATRIX Sphenodon_punctatus 000?0110000000000000000??000000001200000000010001?0000000000000?210????0001?0000001000000?001???0?01000100001000000?0001000000101000000?02020000?1?0000000000000000010?000000000?000?0?0?1000002200201????00100?100?0001010?01?????010020001?10??01?100001000020110000?????0000?00?00000000?00000000??1001?00000?000?0?00000??000000000?00010000000000000000 Kallimodon_pulchellus 000??0100000??00?00000????0000000020000??0??10?01?0000000?0??0????0?????0????0000??00??00??01???0?0?0?????????????????????????1??00?000?020200???1????0???????????0????????1????????????????00??20?2?1????00?0??0?0?00??01??0100??00??000001010??????????0000010100????????1?00?01?0?00??0???0?00??0??1?0????????00000?000?1??000000000?0??????????????????? Gephyrosaurus_bridensis 000?00100000?0000?10000??000000000100000000001000?0000100000010?100????000000000010100?00?001???0?00000?10????0??0????00000?00001000000?00010000?00?00010?00???00?0??????00?01?0001???????00001210?201????0000?0000?00?0001?0000000011042200000?????????????00001000???????0?0000??00000000?00000100??0?00???????????0?0?0?1????1??????????????????????????? Paramacellodus 10?0200000011?000?0?010??00000???????????????1?20010?01100012110000????10????00?00?100????0???????????0???????????????0???????????01101?0100?????0?10200011????1????????????????????????????00220100002?00??0011????1????????0????010003100000100???????????????????????????????????????????????????????????????????????????????2??????????????????????????? Parmeosaurus_scutatus 10001?00000???00000101022000?11001000000???1010000010011000?21??0000???100???00120???1??????0???1?10120??????01?00??2?0???11?01????1001?01001??0?0?10200011??0?11?0?0000?00?01?10?0?????0??1?02101000030000100?11?2?10001000000001010003110000100???????????0?21??0????????0?????????????????0?????0??1?0????????????0?1????????212211?01??????????????????? Tepexisaurus_tepexii 100???0?????????????0?023?0??1?1????0002?1?1???2??????11??0?????010??????????00??01???0??0?101001??0120?????????????????????????0?????1?011??2???1?1120010???0???????1????????0?????????????002201?01000?00100101?201???10?010???00?00?4210000100????????2000021????0??????0001?1??0??1??0???0?????0????0111?1???00010??1110??00??00000?0??????????????????? Cricosaura_typica 100?000100?211??0111330220101111??0??0021111?102000011111201211100011111111?20100012?000100101?0101012122300001100102120101000111110001?011?121011111300101010011101110001020001001011?000110022011222?11?1???11101?101010100000000000130100000??1111013020000210001001000000011101011111010101100101?1001011111120010011010{0 1}1002000000?010101122??1110??110 Palepidophyma_paradisa 10??000?00????????0??????12????????????????????????????????????121?1111???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????2?????22?????????????????????????????1?0?30?0000211???????????????????????????????????????????????????????????????????????????????{2 3}??????????????????????????? Lepidophyma_flavimaculatum 100?0000000210120001040??1202111??0??0020201?012001011111201201121011111011?100001110001111101?0101011122400001101102120101001112100001?011?1110012113001010000111111100121201011000110000110022010222?1011???1010211010101010000001000300000022111110130200002100010011??0000111{0 1}1021011010{1 2}01110101?1001111{1 2}11100010011010010030?0000?010101122011110?1111 Palaeoxantusia_CG 10??0?0?10????????0???????1????????????????????????????????????1?1?1111?????????????????????????1?10??1?2???????????????????????????????????????01????????????????????????????????????????????2???0?220?00??????1??????????????????1?013?00000100???????????????????????????????????????????????????????????????????????????????{2 3}??????????????????????????? Palaeoxantusia_amara 10??0?0?10????????0???????1????1000?000{1 2}???1??1????????????????1?1?1111?????????????????????????????????????????????????????????????????????????11????????????????????????????????????????????22??0?220?1????????????????????????????013?00000100???????????????????????????????????????????????????????????????????????????????{2 3}??????????????????????????? Palaeoxantusia_borealis 100?0?001001????0001030220101111????00020201?0?2001011111?0?211101011111011?1010011100011111?10?1?1012?0????????10??2?1???10??1?2110001?011?1?1?11111300101??0?11?1??1???00?0101??1?1???0011002201122201101?011010211010101010???0010023000000100????????2000021???????????0?????????????????0?????0??1?????????????????????????3000000?0??????????????????? Xantusia_vigilis 100?0100100111110001030210101011000000020?21?012000011110201211100011111011?10100012?001101101?010101213?3000011101?2120101001111110001?011?12101111130010101001111111000102000100?011?000110022011222?1101???111021101010100000000100230000000??11110120200002100010011??000011111021111010101100101?100111111100001001101010002000000?010111122011110?1111 Platysaurus_imperator 10012100000110000001030100001110000000021221010200121111010131100100000100?100000011010111010100101012022300001101101101101100100211001?011?121011011200011010011111000010000101000?11000011002201020010000101111020101000100011010100031100000??11?10001200102111010000000000111?10001110101001001000000101?111?00010?110?0??00201110001?010111201101001?10 Smaug_mossambicus 100120002002110000100302000011101000000212210102001211111211311001000101000100000011010111010100101012022200001101111101101100100211001?011?121001011200001000011111000010000001000?110000110022010200200001011110201000001000110101000311000010011?100??20?002111010000000000111?100011101010111010001001011211?00010?11010??002011111011?10111201101001111 Zonosaurus_ornatus 10001000010111000000030220001110?000000211110102011221110101311001010001000100000011010111010100101012012300101100102101101100110101001?011?12100001120001100001111100001010010100011100001100220101002000010120102011101010000001010003100000?001101{0 1}?004000021110100101000001110102111101110111010011001011{1 2}110200101110101000?112112011010112201101001110 Cordylosaurus_subtessellatus 100010000001110000000302000010100000000211110102011221111001311?00110013000100000?110101110?01001010120?2300001100102101101100100101001?111?121000011200?21110011111000010100101010?110000110022011100100001011110211120?0100000010000131100000??12?11?1?400?021?02?0??????0????1??0?????????0?????0????0??11????????0?11?1??????11212201?00011220110100?110 Myrmecodaptria_microphagosa 00012?00000??00?00110111000011?1????1000?1?1?1?200000011020?21??010???010?1??00100020010100100101?10??0?????????????????????????0??1??????1?1?10?1?10100011?????1?0??????00?010?0???????????01?20101001?000100111?2?10?00010000000??000???00??0?????????????????????????????????????????????????????????????????????????????????2??????0???????????????????? Carusia_intermedia 00012?0000010000001101100000?1?1????10000121?1?202000011020?21??010???01001?0001000100101001????1?101?0?????????00????????1????????1?01?02???2??1??10?00011????11?0??????00?01??0?????????1?002?01?10020??0?01111?2?1???0?1010??000?000411?00???????????????0??1????????????????????????????????????????????????????????????????30000??0???????????????????? Globaura_venusta 000020000001110001110101000021?00001200101?101?201110011000?21??011???1200??000100011010100101001010120???????????????0????11?1001010?1?011?1210000101000110?0??1?0?00???00?01010???????0??1?02?01000020010100?01?2?100010100000110000121?0000100???????????????????????????????????????????????????????????????????????????????20000??????????????????????? Hymenosaurus_clarki ??????????????????0?0?023?00???0000120?????1?1?20111001100??21??011???0?1????00100?110?010010??01010120???????????????????????????????????10?2??00010?00011?10?1?????0?1?00?01??0?1011?????100220100001001010121110010001010000011??001??000??100???????????????????????????????????????????????????????????????????????????????2??????????????????????????? Eoxanta_lacertifrons 000?0?0000011110010111021?00211000012001?1?10102000000110?012110011????2000100010001101010?1????1??0?2002????01?001?2?0???1110??11010110011?121?01011100011??0?11?0?00???00?01010?1011?00?1100220100001001010011?120100010?000??01000012000000100???????????00?1???????????0????????????????????????????????????????????????????2??????????????????????????? Plestiodon_fasciatus 000?000000021100000102021000111000013011112101020111001102012110010000120001000100110111100101001110120?23000011001021011011101101010210011?1210000101010110000111010100100?0101010011000011002201010020000100111120100010110000010100031100000??1101001020000211002011000100011111021111011101100101?110101111110001001101011002122122111010112101001101100 Scincus_scincus ?100{1 2}000?002101000010202000011110?0120110121?1020111001102012110010000021001000110010111100101001110120121000011001021011011001121010210001?121000010101011000011101000010010101010011000011102201010010000100111100100010100000011000121000000??11?100103001021100?001010100011101021011011101100101?0101{0 1}112111021000110101{0 1}?12122122111010112001001101100 Brachymeles_gracilis 000?0000000212000001030??0001111??0?201?0121?1010111001112013110010000022001000000110?11100101001110120222000011001021011011101111010211011?121001010101?21000011101000010010101000001100011002201120010000100211120100010110000010100131100000??110100104001021010200100{0 1 2}110011111021111011101100101?11000112110110000110101{0 1}1021221221120101120010?11??10? Acontias_percivali 00101000000110000001230??10011100001?1???????10102100111020121100000000320010010?012?00?1?010100111112002211011100112101111?1012210102110?1?121001011101?211101111012?1201?21101?01011?01011002201022000000100111000100010?10000010000120000000??10?01???4211111000?1?????02???????1?????1???0?????0????1????????????1??????????002212211??10112011001101101 Brachyseps_splendidus 0000100000021100000103020000111000013011012101010111001102013110010000032001000000110?111001010011101201220000110010211110111?1011010211011?121001010101?21000011101000010000101010011010011002201020010000100211120100010?10000010100131100000??11010030410?021?00?0{0 1}1010100010110021111011101110101?100101111103001001101010002122122111010????????????10? Feylinia_polylepis 10001000001210001001020??00111?0000??????????10001110011120131100?110003201?01????????1?1001010011111201231111110010211111111012?10103110?1?121101111?1???1011011101101101?10101?00?010?1011002201120010000101111021100010110000010000220010100??{1 2}1?01???4202111?01?1?????2110??0??0000201???1?????1??1?1????????????1??????????102212211?110????????????1?? Trachylepis_quinquetaeniata 000?0000000210000011010100001111??0?30111121?102011100110201211?010000130001000000010111100101001110120?22000011001?212110111011110103120?1?121001010101?21010011101000010000101000011020011102201012010000100201120100010110000010000031100000??1111003020010211002001010000111101021111011101100101?1001?11211?000101110111?002022122111010112001001101100 Sphenomorphus_solomonis 000?0000000111000011110220001110000130110121010201110011020131100101000320010000001101111001010010101202220000110010212110111012210103120?1?111001010101?210000111010000100?0111001?11020011002201022000000101111120100010100000010100131100000??120100302002021?00?011010110111111021111011101110101?1001111111120010111010110021221221110101121010?111?10? Eugongylus_rufescens 100?00000002110000110102000011110?0130111121?10201000011020121100100001310010000001101111001010011101202220000110011212110111011010103120?1?111001010101?21000011101000010000101000111010011002201122000000100111120100010100000010000041100000??110100304002021100?0010101000111{0 1}1021111011101110101?1001011{1 2}11100010011010110021221221110101120010?111?100 Tiliqua_scincoides 001?0000000011000011010200001111??0?30111121?102001000110201311?110????3201?0000010101111001010111101202220010110010212110111012210103120?1?1011?1110101?21000011101000010010101101011020011002012022000000100211110100010100000000100030000000??110100304102021100?0010101001111010{1 2}1111011{1 2}011{0 1}0101?10010112111200{0 1}0?11010111020221221110101120010011011?1 ; END; begin mrbayes; constraint trachygylus partial = Trachylepis_quinquetaeniata Eugongylus_rufescens : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Sphenomorphus_solomonis Tiliqua_scincoides ; constraint lygosominae partial = Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis ; constraint lygomeles partial = Brachymeles_gracilis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Acontias_percivali Brachyseps_splendidus Feylinia_polylepis ; constraint scincbrachylinia partial = Scincus_scincus Brachyseps_splendidus Feylinia_polylepis : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Brachymeles_gracilis Acontias_percivali Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint brachylinia partial = Brachyseps_splendidus Feylinia_polylepis : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint higherscincidae partial = Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Acontias_percivali ; constraint scincidae partial = Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus ; constraint gerrhosauridae partial = Zonosaurus_ornatus Cordylosaurus_subtessellatus : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint cordylidae partial = Platysaurus_imperator Smaug_mossambicus : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint cordyliformes partial = Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus : Sphenodon_punctatus Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint xantusioidea partial = Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus : Sphenodon_punctatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint xantophyma partial = Lepidophyma_flavimaculatum Xantusia_vigilis : Sphenodon_punctatus Cricosaura_typica Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint xantusiidae partial = Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis : Sphenodon_punctatus Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides ; constraint scincoidea partial = Cricosaura_typica Lepidophyma_flavimaculatum Xantusia_vigilis Platysaurus_imperator Smaug_mossambicus Zonosaurus_ornatus Cordylosaurus_subtessellatus Plestiodon_fasciatus Scincus_scincus Brachymeles_gracilis Acontias_percivali Brachyseps_splendidus Feylinia_polylepis Trachylepis_quinquetaeniata Sphenomorphus_solomonis Eugongylus_rufescens Tiliqua_scincoides : Sphenodon_punctatus ; calibrate Kallimodon_pulchellus = Unif(150.94, 153.96) Gephyrosaurus_bridensis = Unif(174.1, 208.5) Paramacellodus = Unif(148.1, 150.3) Parmeosaurus_scutatus = Unif(72.1, 83.6) Tepexisaurus_tepexii = Unif(100.5, 113.0) Palepidophyma_paradisa = Unif(53.5, 56.0) Palaeoxantusia_CG = Unif(55.8, 56.0) Palaeoxantusia_amara = Unif(52.5, 54.0) Palaeoxantusia_borealis = Unif(35, 36) Myrmecodaptria_microphagosa = Unif(71.1, 83.6) Carusia_intermedia = Unif(66.0, 83.6) Globaura_venusta = Unif(66.0, 83.6) Hymenosaurus_clarki = Unif(72.1, 83.6) Eoxanta_lacertifrons = Unif(66.0, 83.6) ; outgroup Sphenodon_punctatus; ctype ord: 5 12 16 21 22 24 25 27 29 35 37 43 48 52 53 58 61 65 72 73 77 81 84 102 104-106 117 128 136 140 142 147 154 168 172 184 191-193 196 197 199 211 215 231-234 239 240 243 250 251 255 260 266-268 302 321 330 337; set autoclose=yes nowarn=yes; lset nst=1 rates=gamma; prset clockvarpr = tk02; prset tk02varpr = exp(10); [default] prset clockratepr = lognormal(-6, 1); prset topologypr = constraints (trachygylus, lygosominae, lygomeles, scincbrachylinia, brachylinia, higherscincidae, scincidae, gerrhosauridae, cordylidae, cordyliformes, xantusioidea, xantophyma, xantusiidae, scincoidea) ; prset brlenspr = clock:fossilization; prset nodeagepr = calibrated; prset samplestrat = diversity; prset sampleprob = 0.01; [= 18/ c. 1857 species] prset speciationpr = uniform(0,10); prset extinctionpr = beta(1,1); prset fossilizationpr = beta(1,1); prset treeagepr = offsetexp(150,277); [Paramacellodus, Zheng-Wiens] mcmcp ngen= 20000000 relburnin=yes burninfrac=0.25 printfreq=5000 samplefreq=5000 nchains=4 savebrlens=yes; mcmc; sump; sumt; end;