#NEXUS [written Tue Aug 10 15:54:18 BST 2010 by Mesquite version 2.6 (build 486) at casewell-PC/138.253.249.145] BEGIN TAXA; TITLE Elapid; DIMENSIONS NTAX=40; TAXLABELS Acanthophis_antarcticus_P01434 Aipysurus_laevis_P19958 Aipysurus_laevis_P19959 Aipysurus_laevis_P19960 Aipysurus_laevis_P32879 Astrotia_stokesii_P01438 Naja_annulata_P34075 Boulengerina_christyi_P34076 Bungarus_fasciatus_P10808 Enhydrina_schistosa_P25492 Enhydrina_schistosa_P25493 Hemachatus_haemachatus_P01425 Hemachatus_haemachatus_P01433 Hydrophis_cyanocinctus_P25494 Hydrophis_lapemoides_P01437 Laticauda_colubrina_P10455 Laticauda_colubrina_P10456 Laticauda_colubrina_P10457 Laticauda_crockeri_P10458 Laticauda_crockeri_P25495 Laticauda_crockeri_P25496 Laticauda_laticaudata_P10459 Laticauda_laticaudata_P10460 Laticauda_semifasciata_P01435 Naja_atra_P01430 Naja_haje_P01420 Naja_haje_P01421 Naja_haje_P01422 Naja_haje_P01429 Naja_haje_P25675 Naja_kaouthia_P14613 Naja_melanoleuca_P01424 Naja_mossambica_P01431 Naja_mossambica_P01432 Naja_nigricollis_P01423 Naja_oxiana_P01427 Naja_pallida_P01426 Naja_philippiensis_P01428 Pseudechis_australis_P25497 Dendroaspis_polylepis_P01416_outgroup ; END; BEGIN CHARACTERS; TITLE 'Slowinski et al''s (1997) Elapid neurotoxin amino acid dataset alignment'; DIMENSIONS NCHAR=65; FORMAT DATATYPE = Protein INTERLEAVE GAP = - MISSING = ?; MATRIX Acanthophis_antarcticus_P01434 MQCCNQQSSQP---KTTTTCPGGVSSCYKKTWRDHRGTIIERGCGCPRVKPGIRLICCKTDECNN Aipysurus_laevis_P19958 LTCCNQQSSQP---KTTTDCA--DNSCYKKTWKDHRGTRIERGCGCPQVKPGIKLECCKTNECNN Aipysurus_laevis_P19959 LTCCNQQSSQP---KTTTDCA--DNSCYKMTWRDHRGTRIERGCGCPQVKPGIKLECCKTNECNN Aipysurus_laevis_P19960 LTCCNQQSSQP---KTTTDCA--DDSCYKKTWKDHRGTRIERGCGCPQVKPGIKLECCKTNECNN Aipysurus_laevis_P32879 LTCCNQQSSQP---KTTTDCA--DNSCYKKTWQDHRGTRIERGCGCPQVKPGIKLECCKTNECNN Astrotia_stokesii_P01438 MTCCNQQSSQP---KTTTNCA--GNSCYKKTWSDHRGTIIERGCGCPQVKSGIKLECCHTNECNN Naja_annulata_P34075 KICYNQPSSQH---PTTKACP-GEKNCYRKQWSDHRGTIIERGCGCPTVKPGVKLHCCTTEKCNN Boulengerina_christyi_P34076 MECHNQQSSQP---PTTTHCSGGETNCYEKRWHDHRGTIIERGCGCPTVKPGVKLNCCTTDKCNN Bungarus_fasciatus_P10808 RICLNQQQSTPEDQPTNGQCYI-KTDCQNKTWNTHRGSRTDRGCGCPKVKPGINLRCCKTDKCNE Enhydrina_schistosa_P25492 MTCCNQQSSQP---KTTTNCA--ESSCYKKTWSDHRGTRIERGCGCPQVKPGIKLECCHTNECNN Enhydrina_schistosa_P25493 MTCCNQQSSQP---KTTTNCA--ESSCYKKTWSDHRGTRIERGCGCPQVKSGIKLECCHTNECNN Hemachatus_haemachatus_P01425 LECHNQQSSQP---PTTKSCP-GDTNCYNKRWRDHRGTIIERGCGCPTVKPGINLKCCTTDRCNN Hemachatus_haemachatus_P01433 LECHNQQSSQT---PTTQTCP-GETNCYKKQWSDHRGSRTERGCGCPTVKPGIKLKCCTTDRCNK Hydrophis_cyanocinctus_P25494 MTCCNQQSSQP---KTTTNCA--ESSCYKKTWSDHRGTRIERGCGCPQVKKGIKLECCHTNECNN Hydrophis_lapemoides_P01437 MTCCNQQSSQP---KTTTNCA--ESSCYKKTWRDFRGTRIERGCGCPQVKPGIKLECCHTNECNN Laticauda_colubrina_P10455 RRCYNQQSSQP---KTTKSCPPGENSCYNKQWRDHRGSITERGCGCPKVKPGIKLRCCESEDCNN Laticauda_colubrina_P10456 RRCFNQQSSQP---KTTKSCPPGENSCYNKQWRDHRGSITERGCGCPKVKPGIKLRCCESEDCNN Laticauda_colubrina_P10457 RRCYNQQSSQP---KTTKSCPPGENSCYNKQWRDHRGSITERGCGCPTVKPGIKLRCCESEDCNN Laticauda_crockeri_P10458 RRCFNQQSSQP---QTNKSCPPGENSCYRKQWRDHRGTIIERGCGCPTVKPGIKLRCCQSEDCNN Laticauda_crockeri_P25495 RRCFNHPSSQP---QTNKSCPPGENSCYNKQWRDHRGTIIERGCGCPTVKPGIKLRCCQSDDCNN Laticauda_crockeri_P25496 RRCFNHPSSQP---QTNKSCPPGENSCYNKQWRDHRGTIIERGCGCPQVKSGIKLRCCQSDDCNN Laticauda_laticaudata_P10459 RRCFNHPSSQP---QTNKSCPPGENSCYNKQWRDHRGTITERGCGCPQVKSGIKLTCCQSDDCNN Laticauda_laticaudata_P10460 RRCFNQQSSQP---QTNKSCPPGENSCYRKQWRDHRGTIIERGCGCPTVKPGVKLRCCQSEDCNN Laticauda_semifasciata_P01435 RICFNHQSSQP---QTTKTCSPGESSCYNKQWSDFRGTIIERGCGCPTVKPGIKLSCCESEVCNN Naja_atra_P01430 LECHNQQSSQT---PTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN Naja_haje_P01420 MICYKQQSLQF---PITTVCP-GEKNCYKKQWSGHRGTIIERGCGCPSVKKGIEINCCTTDKCNR Naja_haje_P01421 MICYKQRSLQF---PITTVCP-GEKNCYKKQWSGHRGTIIERGCGCPSVKKGIEINCCTTDKCNR Naja_haje_P01422 MICHNQQSSQP---PTIKTCP-GETNCYKKRWRDHRGTIIERGCGCPSVKKGVGIYCCKTNKCNR Naja_haje_P01429 LECHNQQSSQP---PTTKTCP-GETNCYKKRWRDHRGSITERGCGCPSVKKGIEINCCTTDKCNN Naja_haje_P25675 MICHNQQSSQP---PTIKTCP-GETNCYKKQWRDHRGTIIERGCGCPSVKKGVGIYCCKTDKCNR Naja_kaouthia_P14613 LECHNQQSIQT---PTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN Naja_melanoleuca_P01424 MECHNQQSSQP---PTTKTCP-GETNCYKKQWSDHRGTIIERGCGCPSVKKGVKINCCTTDRCNN Naja_mossambica_P01431 LECHNQQSSEP---PTTTRCSGGETNCYKKRWRDHRGYRTERGCGCPTVKKGIELNCCTTDRCNN Naja_mossambica_P01432 LNCHNQMSAQP---PTTTRCSRWETNCYKKRWRDHRGYKTERGCGCPTVKKGIQLHCCTSDNCNN Naja_nigricollis_P01423 MICHNQQSSQR---PTIKTCP-GETNCYKKRWRDHRGTIIERGCGCPSVKKGVGIYCCKTDKCNR Naja_oxiana_P01427 LECHNQQSSQP---PTTKTCS-GETNCYKKWWSDHRGTIIERGCGCPKVKPGVNLNCCRTDRCNN Naja_pallida_P01426 LECHNQQSSQP---PTTKTCP-GETNCYKKVWRDHRGTIIERGCGCPTVKPGIKLNCCTTDKCNN Naja_philippiensis_P01428 LECHNQQSSQA---PTTKTCS-GETNCYKKWWSDHRGTIIERGCGCPKVKPGVKLNCCRTDRCNN Pseudechis_australis_P25497 MTCCNQQSSQP---KTTTICAGGESSCYKKTWSDHRGSRTERGCGCPHVKPGIKLTCCKTDECNN Dendroaspis_polylepis_P01416_outgroup RICYNHQSTTR---ATTKSCE--ENSCYKKYWRDHRGTIIERGCGCPKVKPGVGIHCCQSDKCNY ; END; begin mrbayes; set autoclose = yes nowarn = yes; mcmc nruns = 4 ngen = 5000000 nchains = 4 samplefreq = 500 printfreq = 500 savebrlens = yes filename = slowinski_NXS.nex; sumt burnin = 2000 contype = allcompat showtreeprobs = yes filename = slowinski_NXS.nex; END; Begin mrbayes; set autoclose = yes nowarn = yes; outgroup Dendroaspis_polylepis_P01416_outgroup; set autoclose = yes; begin mrbayes; set autoclose = yes nowarn = yes; prset aamodelpr = fixed ( WAG ); lset rates = gamma; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 65; END; BEGIN TREES; Title 'Slowinski et al''s (1997) Elapid nerotoxin amino acid dataset tree'; LINK Taxa = Elapid; TRANSLATE 1 Acanthophis_antarcticus_P01434, 2 Aipysurus_laevis_P19958, 3 Aipysurus_laevis_P19959, 4 Aipysurus_laevis_P19960, 5 Aipysurus_laevis_P32879, 6 Astrotia_stokesii_P01438, 7 Naja_annulata_P34075, 8 Boulengerina_christyi_P34076, 9 Bungarus_fasciatus_P10808, 10 Enhydrina_schistosa_P25492, 11 Enhydrina_schistosa_P25493, 12 Hemachatus_haemachatus_P01425, 13 Hemachatus_haemachatus_P01433, 14 Hydrophis_cyanocinctus_P25494, 15 Hydrophis_lapemoides_P01437, 16 Laticauda_colubrina_P10455, 17 Laticauda_colubrina_P10456, 18 Laticauda_colubrina_P10457, 19 Laticauda_crockeri_P10458, 20 Laticauda_crockeri_P25495, 21 Laticauda_crockeri_P25496, 22 Laticauda_laticaudata_P10459, 23 Laticauda_laticaudata_P10460, 24 Laticauda_semifasciata_P01435, 25 Naja_atra_P01430, 26 Naja_haje_P01420, 27 Naja_haje_P01421, 28 Naja_haje_P01422, 29 Naja_haje_P01429, 30 Naja_haje_P25675, 31 Naja_kaouthia_P14613, 32 Naja_melanoleuca_P01424, 33 Naja_mossambica_P01431, 34 Naja_mossambica_P01432, 35 Naja_nigricollis_P01423, 36 Naja_oxiana_P01427, 37 Naja_pallida_P01426, 38 Naja_philippiensis_P01428, 39 Pseudechis_australis_P25497, 40 Dendroaspis_polylepis_P01416_outgroup; TREE con_all_compat = (40:0.331877,(((((1:0.079835,(((((2:0.017492,4:0.033566)0.46:0.026895,5:0.030095)0.45:0.028204,3:0.039921)1.00:0.094489,((((6:0.065043,11:0.016765)0.60:0.027142,14:0.030692)0.66:0.029574,10:0.015976)0.68:0.0305,15:0.038049)0.79:0.036267)0.91:0.071804,39:0.099991)0.97:0.111935)0.97:0.201162,8:0.110276)0.30:0.043848,(((((9:0.672306,13:0.083993)0.76:0.113254,(((25:0.015845,31:0.031636)1.00:0.088219,(33:0.033687,34:0.204271)0.59:0.041996)1.00:0.114665,29:0.056086)0.49:0.076548)0.54:0.064471,12:0.107288)0.15:0.025006,37:0.038154)0.23:0.039198,(36:0.031214,38:0.03606)1.00:0.120909)0.14:0.041245)0.14:0.054247,(((26:0.016616,27:0.03171)1.00:0.233649,((28:0.03415,35:0.035068)0.83:0.032794,30:0.020156)1.00:0.105552)0.95:0.065749,32:0.043246)0.72:0.068306)0.55:0.14528,7:0.180325)0.98:0.174144,((((16:0.017674,17:0.028281)0.74:0.032462,18:0.021048)1.00:0.090187,((19:0.016331,23:0.032416)0.95:0.038763,(20:0.01621,(21:0.015664,22:0.049791)1.00:0.050386)1.00:0.055989)0.58:0.046511)0.62:0.072464,24:0.165152)0.61:0.112639); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 65; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 65; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8557220390959655963; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3444503507840760865; checksumv 0 2 291822855 null; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;