#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 July 01, 2025; 8:15 GMT

TreeBASE (cc) 1994-2008

Study reference:
Shaffer J.P., Sarmiento C., Zalamea P., Gallery R.E., Davis A.S., Baltrus D.A., &
Arnold A. 2016. Diversity, specificity, and phylogenetic relationships of endohyphal
bacteria in fungi that inhabit tropical seeds and leaves. Frontiers in Ecology
and Evolution, 4(116).

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S19714]

[ The following blocks are input data for analysis step 19285 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep19285;
        DIMENSIONS NTAX=9;
        TAXLABELS
            Allantonectria_miltina_Agave_americana_Spain_KM231835
            Allantonectria_miltina_Yucca_elata_USA_KM23183
            Fusarium_F0259_Cyclopeltis_semicordata_LS_JN997425
            Nectria_miltina_Agave_americana_Italy_HM484547
            Nectria_sp._Populus_China_JN997424
            'Nectria_sp._*_Populus_China_*_JN997425.1'
            'Nectria_sp._*_Populus_China_*_JN997426.1'
            Thyronectria_caudata_KM225679
            Thyronectria_caudata_KM225680
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M38327]

	TITLE 'Allantonectria / Hypocreales';
	LINK TAXA = TaxaForAnalysisStep19285;
	DIMENSIONS NCHAR=485;
	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     ]
[                                                                  .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .     ]
Allantonectria_miltina_Agave_americana_Spain_KM231835     ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTCTTGTTGCTTCGGCGGGACCGCCCCGG-GCCCC-GTGCCCGGAACCAGGCGCCCGCCGGAGGCCCCTAACTCTTGTTTTC-TTATGGAATCTTCTGAGTCAAACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CCCCCGGGCTTGGTGTTGGGGACCGGCCGCCGCTC--ACCCGGTGGCCGCCCCCGAATTCCATTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGCAGTGGAACGCGGCGCGGCCACGCCGTAAAACCCCCAACTTCTGAATGT-
Allantonectria_miltina_Yucca_elata_USA_KM23183            ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTCTTGTTGCTTCGGCGGGACCGCCCCGG-GCCACCGTGCCCGGAACCAGGCGCCCGCCGGAGACCCTTAACTCTTGTTTTCATCATGGAATCTTCTGAGTCACACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CTCCCGGGCTTGG-GTTGGGGACCGGCCGCCGCTTCACCCCGGCGGCCGCCCCCGAATTCTAGTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGCAGTGGAACGCGGCGCGGCCACGCCATAAAACCCCCCACTTCTGAAAGT-
Fusarium_F0259_Cyclopeltis_semicordata_LS_JN997425        ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTC-TGTTGCTTCGGCGGGACCGCCCCGG-GCCACCGTGCCCGGAACCAGGCGCCCGCCGGAGACCCTTAACTCTTGTTTTCATCATGGAATCTTCTGAGTCAAACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CCCCCGGGCTTGGTGTTGGGGACCGGCCGCCGCTTCACCCCGGCGGCCGCCCCCGAATTCTAGTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGCAGTGGAACGCGGCGCGGCCACGCCGTAAAACCCCCCACTTCTGAAAGT-
Nectria_miltina_Agave_americana_Italy_HM484547            ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTCTTGTTGCTTCGGCGGGACCGCCCCGG-GCCCC-GTGCCCGGAACCAGGCGCCCGCCGGAGGCCCCTAACTCTTGTTTTC-TTATGGAATCTTCTGAGTCAAACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CCCCCGGGCTTGGTGTTGGGGACCGGCCGCCGCTC--ACCCGGTGGCCGCCCCCGAATTCCATTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGCAGTGGAACGCGGCGCGGCCACGCCGTAAAACCCCCAACTTCTGAATGT-
Nectria_sp._Populus_China_JN997424                        ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTC-TGTTGCTTCGGCGGGACCGCCCCGG-GCCTC-GCGCCCGGAACCAGGCGCCCGCCGGAGACCATTAACTCTTGTTTTC-TTATGGAATCTTCTGAGTCACACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CCCCCGGGCTTGGTGTTGGGGACCGGCCGCCGCTC--ACCCGGTGGCCGCCCCCGAATTCTAGTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGTAGTGGAACGCGGCGCGGCCACGCCGTAAAACCCCCAACTTCTGAATGT-
'Nectria_sp._*_Populus_China_*_JN997425.1'                ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTC-TGTTGCTTCGGCGGGACCGCCCCGG-GCCTC-GTGCCCGGAACCAGGCGCCCGCCGGAGACCATTAACTCTTGTTTTC-TTATGGAATCTTCTGAGTCACACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CCCCCGGGCTTGGTGTTGGGGACCGGCCGCCGCTC--ACCCGGTGGCCGCCCCCGAATTCTAGTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGCAGTGGAACGCGGCGCGGCCACGCCGTAAAACCCCCAACTTCTGAATGT-
'Nectria_sp._*_Populus_China_*_JN997426.1'                ATTACCGAGTTTACAACTCCCAAACCCCTGTGAACATACCTC-TGTTGCTTCGGCGGGACCGCCCCGG-GCCTC-GCGCCCGGAACCAGGCGCCCGCCGGAGACCATTAACTCTTGTTTTC-TTATGGAATCTTCTGAGTCACACAAACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAG-CCCCCGGGCTTGGTGTTGGGGACCGGCCGCCGCTC--ACCCGGTGGCCGCCCCCGAATTCTAGTGGCGGTCTCGCTGTAGCCTCCCCTGCGTAGTAGCACACCTCGCAGTGGAACGCGGCGCGGCCACGCCGTAAAACCCCCAACTTCTGAATGT-
Thyronectria_caudata_KM225679                             ATTACCGAGTTTACAACTCCCTAACCCCTGTGAACATACCTCTTGTTGCTTCGGCGGGATCGCCCCGGCGCCTCTGTGCCCGGAATCAGGCGCCCGCCGGAGGCCCTAAACTCTTGTTTTC-TAGTGATATCTTCTGAGTCTTACAAACAAATAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCCCCCGGGCTTGGTGTTGGGGATCGGCCGCCGCCTCAACCCGGCGGCCGTCCCCTAATTCTAGTGGCGGTCTCGCTGTAGCCTCCTCTGCGTAGTAGCACACCTCGCACTGGAACGCAGCGCGGCCACGCCGTAAAA-CCCCAACTTCTGAATGT-
Thyronectria_caudata_KM225680                             ATTACCGAGTTTACAACTCCCTAACCCCTGTGAACATACCTCTTGTTGCTTCGGCGGGATCGCCCCGGCGCCTCTGTGCCCGGAATCAGGCGCCCGCCGGAGGCCCTAAACTCTTGTTTTC-TAGTGATATCTTCTGAGTCTTACAAACAAATAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTACTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCCCCCGGGCTTGGTGTTGGGGATCGGCCGCCGCCTCAACCCGGCGGCCGTCCCCTAATTCTAGTGGCGGTCTCGCTGTAGCCTCCTCTGCGTAGTAGCACACCTCGCACTGGAACGCAGCGCGGCCACGCCGTAAAA-CCCCAACTTCTGAATGT-
;
END;

[ The following blocks are output data for analysis step 19285 ]
BEGIN TREES;
      TITLE 'Allantonectria - ITS MLT';
      LINK TAXA = TaxaForAnalysisStep19285;
      TREE 'Allantonectria - ITS ML Tree' = [&R] (Allantonectria_miltina_Agave_americana_Spain_KM231835:0.0,(((Thyronectria_caudata_KM225679:0.0,Thyronectria_caudata_KM225680:0.0):0.244371,(Allantonectria_miltina_Yucca_elata_USA_KM23183:0.027718,Fusarium_F0259_Cyclopeltis_semicordata_LS_JN997425:0.0):0.050788):0.01957,((Nectria_sp._Populus_China_JN997424:0.009055,'Nectria_sp._*_Populus_China_*_JN997426.1':0.0):0.009054,'Nectria_sp._*_Populus_China_*_JN997425.1':0.0):0.019403):0.047586,Nectria_miltina_Agave_americana_Italy_HM484547:0.0);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr98682]


END;