#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; 8:03 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 19287 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep19287;
        DIMENSIONS NTAX=15;
        TAXLABELS
            'Calonectria_acicola_*_GQ280546.1'
            'Calonectria_acicola_*_GQ280547.1'
            'Calonectria_madagascariensis_*_GQ280592.1'
            'Calonectria_madagascariensis_*_GQ280593.1'
            'Calonectria_multiseptata_*_GQ280598.1'
            'Calonectria_pentaseptata_*_JX855953.1'
            'Calonectria_pseudoreteaudii_*_GQ280613.1'
            'Calonectria_pseudoreteaudii_*_GQ280614.1'
            'Calonectria_queenslandica_*_GQ280619.1'
            'Calonectria_reteaudii_*_GQ280620.1'
            'Calonectria_reteaudii_*_GQ280621.1'
            'Endophyte_177_*_Ichnanthus_pallens_Panama_*_EU686953.1'
            'Endophyte_212_*_Ichnanthus_pallens_Panama_*_EU687024.1'
            'P3139_Fusarium_*_Hirtella_triandra_BCI_*_JX855953.1'
            'P3343_Fusarium_*_Cupania_rufescens_BCI_*_AF348258.2'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M38329]

	TITLE 'Calonectria / Hypocreales';
	LINK TAXA = TaxaForAnalysisStep19287;
	DIMENSIONS NCHAR=436;
	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      ]
[                                                                   .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .      ]
'Calonectria_acicola_*_GQ280546.1'                         AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATAAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGGCCACGCCGTAAAACCCCCAAC--TTTTCTGG-TGACCTCGAATCA-GTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_acicola_*_GQ280547.1'                         AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATAAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGGCCACGCCGTAAAACCCCCAAC--TTTTCTGG-TGACCTCGAATCA-GTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_madagascariensis_*_GQ280592.1'                AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAGGGCGTCCTTCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC--TTTTCTGG-TGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_madagascariensis_*_GQ280593.1'                AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAGGGCGTCCTTCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC--TTTTCTGG-TGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_multiseptata_*_GQ280598.1'                    AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTGAAAAAAAAACAATAAATAAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGGCCACGCCGTAAAAACCCCAAC--TTTTCTGG-TGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_pentaseptata_*_JX855953.1'                    AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC-TTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_pseudoreteaudii_*_GQ280613.1'                 AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTGAAAAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC-TTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_pseudoreteaudii_*_GQ280614.1'                 AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTGAAAAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC-TTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_queenslandica_*_GQ280619.1'                   AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC-TTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_reteaudii_*_GQ280620.1'                       AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC--TTTTCTGG-TGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Calonectria_reteaudii_*_GQ280621.1'                       AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC--TTTTCTGG-TGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Endophyte_177_*_Ichnanthus_pallens_Panama_*_EU686953.1'   AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTA--AAAAATACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTTAGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATTTAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAAC-TTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'Endophyte_212_*_Ichnanthus_pallens_Panama_*_EU687024.1'   AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTA--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCTGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATATAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGACCACGCCGTAAAACCCCCAACTTTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'P3139_Fusarium_*_Hirtella_triandra_BCI_*_JX855953.1'      AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTA--AAACAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCTGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCCCAAATATAGTGGCGGTCTCGCTGTAGCTTCCTCTGCGTAGTAATACACCTCGCTCTGGAGTCTCGGTGCGGCCACGCCGTAAAACCCCCAACTTTTTTCTGGTTGACCTCGAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAG-
'P3343_Fusarium_*_Cupania_rufescens_BCI_*_AF348258.2'      AACAAACTCTTTTGAATTTTTCAGTATCTTCTGAGTG--AAAAAAACAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTCTGCTTGGTGTTGGGGATCGGCAAGGCGTCCTCCGGGTCGCGCCGTCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------
;
END;

[ The following blocks are output data for analysis step 19287 ]
BEGIN TREES;
      TITLE 'Calonectria - ITS MLT';
      LINK TAXA = TaxaForAnalysisStep19287;
      TREE 'Calonectria - ITS ML Tree' = [&R] ('Calonectria_acicola_*_GQ280547.1':0.0,('Calonectria_multiseptata_*_GQ280598.1':0.039655,(('P3343_Fusarium_*_Cupania_rufescens_BCI_*_AF348258.2':0.0,('Endophyte_212_*_Ichnanthus_pallens_Panama_*_EU687024.1':0.0,'P3139_Fusarium_*_Hirtella_triandra_BCI_*_JX855953.1':0.083335):0.062694):0.062418,(('Calonectria_pseudoreteaudii_*_GQ280614.1':0.0,'Calonectria_pseudoreteaudii_*_GQ280613.1':0.0):0.0,(('Calonectria_queenslandica_*_GQ280619.1':0.0,'Calonectria_pentaseptata_*_JX855953.1':0.0):0.0,((('Calonectria_madagascariensis_*_GQ280592.1':0.0,'Calonectria_madagascariensis_*_GQ280593.1':0.0):0.082791,'Endophyte_177_*_Ichnanthus_pallens_Panama_*_EU686953.1':0.128912):0.0,('Calonectria_reteaudii_*_GQ280621.1':0.0,'Calonectria_reteaudii_*_GQ280620.1':0.0):0.0):0.0):0.0):0.0):0.082471):0.0,'Calonectria_acicola_*_GQ280546.1':0.0);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr98683]


END;