#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 19, 2025; 20:59 GMT TreeBASE (cc) 1994-2008 Study reference: Casewell N.R., Wagstaff S.C., Harrison R.A., & Wuster W. 2010. Gene tree parsimony of multi-locus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss. Molecular Biology and Evolution, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10791] [ The following blocks are input data for analysis step 6346 ] BEGIN TAXA; TITLE TaxaForAnalysisStep6346; DIMENSIONS NTAX=40; TAXLABELS Acanthophis_antarcticus_P01434 Aipysurus_laevis_P19958 Aipysurus_laevis_P19959 Aipysurus_laevis_P19960 Aipysurus_laevis_P32879 Astrotia_stokesii_P01438 Boulengerina_christyi_P34076 Bungarus_fasciatus_P10808 Dendroaspis_polylepis_P01416_outgroup 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_annulata_P34075 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_philippinensis_P01428 Pseudechis_australis_P25497 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M6415] TITLE 'Slowinski et al''s (1997) Elapid neurotoxin amino acid dataset alignment'; LINK TAXA = TaxaForAnalysisStep6346; DIMENSIONS NCHAR=65; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 ] [ . . . . . . ] 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 Boulengerina_christyi_P34076 MECHNQQSSQP---PTTTHCSGGETNCYEKRWHDHRGTIIERGCGCPTVKPGVKLNCCTTDKCNN Bungarus_fasciatus_P10808 RICLNQQQSTPEDQPTNGQCYI-KTDCQNKTWNTHRGSRTDRGCGCPKVKPGINLRCCKTDKCNE Dendroaspis_polylepis_P01416_outgroup RICYNHQSTTR---ATTKSCE--ENSCYKKYWRDHRGTIIERGCGCPKVKPGVGIHCCQSDKCNY 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_annulata_P34075 KICYNQPSSQH---PTTKACP-GEKNCYRKQWSDHRGTIIERGCGCPTVKPGVKLHCCTTEKCNN 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_philippinensis_P01428 LECHNQQSSQA---PTTKTCS-GETNCYKKWWSDHRGTIIERGCGCPKVKPGVKLNCCRTDRCNN Pseudechis_australis_P25497 MTCCNQQSSQP---KTTTICAGGESSCYKKTWSDHRGSRTERGCGCPHVKPGIKLTCCKTDECNN ; END; [ The following blocks are output data for analysis step 6346 ] BEGIN TREES; TITLE 'Slowinski et al''s (1997) Elapid nerotoxin amino acid dataset TB'; LINK TAXA = TaxaForAnalysisStep6346; TREE Elapid_NXS = [&R] (Dendroaspis_polylepis_P01416_outgroup:0.331877,(((((Acanthophis_antarcticus_P01434:0.079835,(((((Aipysurus_laevis_P19958:0.017492,Aipysurus_laevis_P19960:0.033566)0.46:0.026895,Aipysurus_laevis_P32879:0.030095)0.45:0.028204,Aipysurus_laevis_P19959:0.039921)1.00:0.094489,((((Astrotia_stokesii_P01438:0.065043,Enhydrina_schistosa_P25493:0.016765)0.60:0.027142,Hydrophis_cyanocinctus_P25494:0.030692)0.66:0.029574,Enhydrina_schistosa_P25492:0.015976)0.68:0.0305,Hydrophis_lapemoides_P01437:0.038049)0.79:0.036267)0.91:0.071804,Pseudechis_australis_P25497:0.099991)0.97:0.111935)0.97:0.201162,Boulengerina_christyi_P34076:0.110276)0.30:0.043848,(((((Bungarus_fasciatus_P10808:0.672306,Hemachatus_haemachatus_P01433:0.083993)0.76:0.113254,(((Naja_atra_P01430:0.015845,Naja_kaouthia_P14613:0.031636)1.00:0.088219,(Naja_mossambica_P01431:0.033687,Naja_mossambica_P01432:0.204271)0.59:0.041996)1.00:0.114665,Naja_haje_P01429:0.056086)0.49:0.076548)0.54:0.064471,Hemachatus_haemachatus_P01425:0.107288)0.15:0.025006,Naja_pallida_P01426:0.038154)0.23:0.039198,(Naja_oxiana_P01427:0.031214,Naja_philippinensis_P01428:0.03606)1.00:0.120909)0.14:0.041245)0.14:0.054247,(((Naja_haje_P01420:0.016616,Naja_haje_P01421:0.03171)1.00:0.233649,((Naja_haje_P01422:0.03415,Naja_nigricollis_P01423:0.035068)0.83:0.032794,Naja_haje_P25675:0.020156)1.00:0.105552)0.95:0.065749,Naja_melanoleuca_P01424:0.043246)0.72:0.068306)0.55:0.14528,Naja_annulata_P34075:0.180325)0.98:0.174144,((((Laticauda_colubrina_P10455:0.017674,Laticauda_colubrina_P10456:0.028281)0.74:0.032462,Laticauda_colubrina_P10457:0.021048)1.00:0.090187,((Laticauda_crockeri_P10458:0.016331,Laticauda_laticaudata_P10460:0.032416)0.95:0.038763,(Laticauda_crockeri_P25495:0.01621,(Laticauda_crockeri_P25496:0.015664,Laticauda_laticaudata_P10459:0.049791)1.00:0.050386)1.00:0.055989)0.58:0.046511)0.62:0.072464,Laticauda_semifasciata_P01435:0.165152)0.61:0.112639); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr21140] END;