#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 May 10, 2024; 13:11 GMT

TreeBASE (cc) 1994-2008

Study reference:
Cacciali P., & Koehler G. 2018. Diversity of Tropidurus (Squamata: Tropiduridae)
in Paraguay – an integrative taxonomic approach based on morphological and molecular
genetic evidence. Zootaxa, 4375(4): 511-536.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S21797]

[ The following blocks are input data for analysis step 22361 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22361;
        DIMENSIONS NTAX=17;
        TAXLABELS
            Plica_plica_AMCC106953
            Tropidurus_catalanensis_SMF100090
            Tropidurus_catalanensis_SMF100093
            Tropidurus_catalanensis_UFRGST2890
            Tropidurus_etheridgei_LG1096
            Tropidurus_etheridgei_SMF101595
            Tropidurus_etheridgei_SMF101596
            Tropidurus_guarani_SMF100095
            Tropidurus_guarani_SMF100096
            Tropidurus_lagunablanca_SMF103320
            Tropidurus_spinulosus_AMCC204478
            Tropidurus_spinulosus_IIBPH3463
            Tropidurus_spinulosus_SMF100094
            Tropidurus_tarara_SMF103314
            Tropidurus_tarara_SMF103315
            Tropidurus_tarara_SMF103316
            Tropidurus_teyumirim_AMNHFS20281
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M44490]

	TITLE Tropidurus_16S_Matrix;
	LINK TAXA = TaxaForAnalysisStep22361;
	DIMENSIONS NCHAR=536;
	FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -;

MATRIX
[                                              10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530         ]
[                                               .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         ]
Plica_plica_AMCC106953                 ?????????????????????????????????TTCAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAA?CATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGCGGACCAATCTGTCTCCTTTAACCAACCAGTGAAACTGATCTACCAGTACAAAAGCTGGTATAGCAATATAAGACGAGAAGACCCTGTGGAGCTTAAAATTATAA-TCA-----------------CACCAACC--TCTAATCATTA---AGCC-TTGACCTATAATTTTCAGTTGGGGCGACTTTGGAACTAAGCCAAACTTCCAAGCAAAATAGACCTAAATCTTAACCAAGACCAACAAGTCT-AACAAAATGACCCAGTAAAACTGATCAACGAACCAAGTTACCCCAGGGATAACAG?GCAATCTTCTTCAAGAGTCCATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAA?????????????????????????????
Tropidurus_catalanensis_SMF100090      ??????????GGT-ACGCCTG-CCAGTG-AACTTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGAAATCATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGAGGGCTAACCTGTCTCCTTTAACCTATCAGTGAAACTGATCTACCAGTACAAAAGCTGGTATAACCCCATAAGACGAGAAGACCCTGTGGAGCTTTAAATTAAAAGTCAACGG-CAAC-------CTACCAACC--CCC-CCCGTTA-----TC-TTGACCCTAAGTTTTTAGTTGGGGCGACTTCGGAACCAAACCAAACTTCCGAGC-AAACGACCTTAAATCTCAA-AAAGACCCACAAGTCTAAACCAAATGACCCAGTAAGACTGATAAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTA-TAAAGGTCG????????????????????????
Tropidurus_catalanensis_SMF100093      AAGTATTAAAGGTAACGCCTGCCCAGTGAAACTTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGAAATCATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGAGGGCTAACCTGTCTCCTTTAACCTATCAGTGAAACTGATCTACCAGTACAAAAGCTGGTATAACCCCATAAGACGAGAAGACCCTGTGGAGCTTTAAATTAAAAGTCAACGG-CAAC-------CTACCAACC--CCC-CCCGTTA-----TC-TTGACCCTAAGTTTTTAGTTGGGGCGACTTCGGAACCAAACCAAACTTCCGAGC-AAACGACCTTAAATCTCAA-AAAGACCCACAAGTCTAAACCAAATGACCCAGTAAGACTGATAAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAATAGTCCT
Tropidurus_catalanensis_UFRGST2890     ????????????????????????????????TTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGAAATCATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGAGGGCTAACCTGTCTCCTTTAACCTATTAGTGAAACTGATCCACCAGTACAAAAGCTGGTATAACCCCATAAGACGAGAAGACCCTGTGGAGCTTTAAATTAAAAGTCAACGG-CAAC-------CTACCAACCCCCCC-CCCGTTA-----TC-TTGACCCTAAA-TTTTAGTTGGGGCGACTTCGGAACCAAACCAAACTTCCGAGC-AAACGACCTTAAATCTCAA-AAAGACCCACAAGTCTAAACCAAATGACCCAGTAAGACTGATAAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAATA?????
Tropidurus_etheridgei_LG1096           AAGTATTAAAGGTAACGCCTGCCCAGTGAAACTTTTAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGAAATCATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGAGGGCTAACCTGTCTCCTTTAACCCATCAGTGAAACTGATCTACCAGTACAAAAGCTGGTATACCCACATAAGACGAGAAGACCCTGTGGAGCTTTAAATTAAAAGTCAACGG-AAAC-------CCACCAG----ACC-CCCGTTA-----TT-TTGACCCTAAATTTTTAGTTGGGGCGACTTCGGAACTAAACTAAACTTCCGAGC-AAATGACCTTAAATCTCAA-AAAGACCAACAAGTCTAAACCAAATGACCCAGTAAAACTGATAAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAATAGTCCT
Tropidurus_etheridgei_SMF101595        AAGTATTAAAGGTAACGCCTGCCCAGTGAAACTTTTAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGAAATCATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGAGGGCTAACCTGTCTCCTTTAACCCATCAGTGAAACTGATCTACCAGTACAAAAGCTGGTATACCCACATAAGACGAGAAGACCCTGTGGAGCTTTAAATTAAAAGTCAACGG-AAAC-------CCACCAG----ACC-CCCGTTA-----TT-TTGACCCTAAATTTTTAGTTGGGGCGACTTCGGAACTAAACTAAACTTCCGAGC-AAATGACCTTAAATCTCAA-AAAGACCAACAAGTCTAAACCAAATGACCCAGTAAAACTGATAAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAATAGTCCT
Tropidurus_etheridgei_SMF101596        AAGTATTAAAGGTAACGCCTGCCCAGTGAAACTTTTAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGAAATCATTTGTCCTCTAAATAAGGACCAGTATGAATGGCTAAATGAGGGCTAACCTGTCTCCTTTAACCCATCAGTGAAACTGATCTACCAGTACAAAAGCTGGTATACCCACATAAGACGAGAAGACCCTGTGGAGCTTTAAATTAAAAGTCAACGG-AAAC-------CCACCAG----ACC-CCCGTTA-----TT-TTGACCCTAAATTTTTAGTTGGGGCGACTTCGGAACTAAACTAAACTTCCGAGC-AAATGACCTTAAATCTCAA-AAAGACCAACAAGTCTAAACCAAATGACCCAGTAAAACTGATAAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTC-ATATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAATAGTCCT
Tropidurus_guarani_SMF100095           TAGTATTAAAGGTAACGCCTGCCCAGTGAAAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGGCCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTTCCAGTACAAAAGCTGGAATGACCCTATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAA-TAATCATC--ACCACCAG----ACC----------------CTGGCCCATTAATTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AGATAGACCTTGATCTTAT-CTAGACCCACAAGTCTAAACTCACTGACCCAGTAACACTGACCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_guarani_SMF100096           TAGTATTAAAGGTAACGCCTGCCCAGTGAAAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGGCCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTTCCAGTACAAAAGCTGGAATGACCCTATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAA-TAATCATC--ACCACCAG----ACC----------------CTGGCCCATTAATTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AGATAGACCTTGATCTTAT-CTAGACCCACAAGTCTAAACTCACTGACCCAGTAACACTGACCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_lagunablanca_SMF103320      TAGTATTAAAGGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAGGGACTAGTATGAACGGCTAAATGAGGGGCCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTCCCAGTACAAAAGCTGGGATAACCATATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAA-CAACCA--CCT-CCACC--------------AC-----GCCCTGGCCTATTAATTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AAGTAGACCTTAATCTTGC-CTAGACCCACAAGTCTAAATTCACTGACCCAGTAGCACTGATCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTAT{AT}AAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_spinulosus_AMCC204478       TAGTATTAAAGGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGACCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTTCCAGTACAAAAGCTGGAATGACCCTATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAATAATC----ATCACCACC--------------AGACC---C-TGGCCCATTAA-TTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AGATAGACCTTGATCTTAT-CTAGACCCACAAGTCTAAACTCACTGACCCAGTAACACTGACCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_spinulosus_IIBPH3463        TAGTATTAAAGGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGGCCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTTCCAGTACAAAAGCTGGAATGACCCCATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAATTATC----ATCACCACC--------------AGACC---C-TGGCCCATTAA-TTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AGATAGACCTTGATCTTAT-CTAGACCCACAAGTCTAAATCTACTGACCCAGTAACACTGATCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTAGTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_spinulosus_SMF100094        TAGTATTAAAGGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGACCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTTCCAGTACAAAAGCTGGAATGACCCTATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAATAATC----ATCACCACC--------------AGACC---C-TGGCCCATTAA-TTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AGATAGACCTTGATCTTAT-CTAGACCCACAAGTCTAAACTCACTGACCCAGTAACACTGACCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCGATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_tarara_SMF103314            TAGTATTAAAGGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGATCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTCCCAGTACAAAAGCTGGGATAACCATATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAACAACT----ACCTCCACC--------------ACGCC---C-TGGCCTATTAA-TTTCAGTTGGGGCGACTTCGGAAAACAAACAAACTTCCGAGC-AAGTAGACCTTAATCTTGC-CTAGACCCACAAGTCTAAATTCACTGACCCAGTAGCACTGATCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_tarara_SMF103315            ?????????????????????????????????TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGATCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTCCCAGTACAAAAGCTGGGATAACCATATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAACAACT----ACCTCCACC--------------ACGCC---C-TGGCCTATTAA-TTTCAGTTGGGGCGACTTCGGAAAACAAACAAACTTCCGAGC-AAGTAGACCTTAATCTTGC-CTAGACCCACAAGTCTAAATTCACTGACCCAGTAGCACTGATCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCT???????????????????????????????????
Tropidurus_tarara_SMF103316            TAGTATTAAAGGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAAGGACTAGTATGAACGGCTAAATGAGGGATCCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTCCCAGTACAAAAGCTGGGATAACCATATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACAACAACT----ACCTCCACC--------------ACGCC---C-TGGCCT-TTAA-TTTCAGTTGGGGCGACTTCGGAAAACAAACAAACTTCCGAGC-AAGTAGACCTTAATCTTGC-CTAGACCCACAAGTCTAAATTCACTGACCCAGTAGCACTGATCAACGAACCAAGTTACCCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAACAGTCCT
Tropidurus_teyumirim_AMNHFS20281       ?????????AAGTAACGCCTGCCCAGTGAGAC-TTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTCCCCTAAATAGGGACTAGTATGAACGGCTAAATGAGGGA-CCCCTGTCTCCTTTAACCAATCAGTGAAACTGATCTCCCAGTACAAAAGCTGGGATAACTATATAAGACGAGAAGACCCTGTGGAGCTTCAAATT-ATGGCCAACGACAACC----ATCTCCCCC--------------AGGCC---C-TGGCCTATTAA-TTTCAGTTGGGGCGACTTCGGAAAACAGACAAACTTCCGAGC-AAATAGACCTTAATCTTGC-CTAGACCCACAAGTCTAAATTCACTGACCCAGTAGCACTGATCAACGAACCAAGTTA-CCCAGGGATAACAGCGCAATCTTCTTCAAGAGTCCCTATCGACAAGAAGGTTTACGACCTCGATGTTGGATCAGGACACCCAATTGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCA-CGATTAACAGTCCT
;
END;

[ The following blocks are output data for analysis step 22361 ]
BEGIN TREES;
      TITLE Tropidurus_16S_ML;
      LINK TAXA = TaxaForAnalysisStep22361;
      TREE tree_1 = [&R] (Plica_plica_AMCC106953:0.036694,(((Tropidurus_catalanensis_SMF100093:3.0E-6,Tropidurus_catalanensis_SMF100090:0.002146):0.001782,Tropidurus_catalanensis_UFRGST2890:0.004427):0.015874,((Tropidurus_etheridgei_SMF101595:3.0E-6,Tropidurus_etheridgei_LG1096:3.0E-6):2.0E-6,Tropidurus_etheridgei_SMF101596:3.0E-6):0.013551):0.06056,((((Tropidurus_guarani_SMF100095:2.0E-6,Tropidurus_guarani_SMF100096:2.0E-6):0.002013,(Tropidurus_spinulosus_AMCC204478:2.0E-6,Tropidurus_spinulosus_SMF100094:0.001986):0.001976):0.003236,Tropidurus_spinulosus_IIBPH3463:0.011397):0.018831,((Tropidurus_lagunablanca_SMF103320:3.0E-6,((Tropidurus_tarara_SMF103314:3.0E-6,Tropidurus_tarara_SMF103316:3.0E-6):2.0E-6,Tropidurus_tarara_SMF103315:3.0E-6):0.010103):0.00312,Tropidurus_teyumirim_AMNHFS20281:0.021272):0.015827):0.11164);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr109664]


END;