#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; 8:01 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 19276 ] BEGIN TAXA; TITLE TaxaForAnalysisStep19276; DIMENSIONS NTAX=14; TAXLABELS '9742_Xylaria_*_C._insignis_BCI_{2-14}_*_GU300074.1' 'B355_Xylaria_*_C._insignis_BCI_{9-9}_*_JQ760996.1' 'Endolichenic_Sordariomycetes_sp._*_JQ760996.1' 'Endolichenic_Sordariomycetes_sp._FL1030_*_Cladonia_evansii_*_JQ760654.1' 'Endolichenic_Sordariomycetes_sp._FL1283_*_JQ760898.1' 'Endophytic_Xylaria_sp._*_Hevea_*_HQ022442.1' 'Endophytic_Xylariaceae_sp._*_Lasianthus_cyanocarpus_*_AB741611.1' 'F0051_Xylaria_*_LS_*_EF026149.1' 'P0394_Xylaria_*_Xylopia_macrantha_BCI_*_AB741611.1' 'Xylaria_grammica_*_GU300097.1' 'Xylaria_liquidambaris_*_GU300094.1' 'Xylaria_tuberoides_*_GU300074.1' 'Xylaria_venosula_*_EF026149.1' 'Xylaria_venustula_*_GU300091.1' ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M38342] TITLE 'Xylaria "HY" / Xylariales'; LINK TAXA = TaxaForAnalysisStep19276; DIMENSIONS NCHAR=548; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] '9742_Xylaria_*_C._insignis_BCI_{2-14}_*_GU300074.1' GAGTTGACCCTAACTCCA-TACCCTTTGTGAAAATACCTTTTATGTTGCTTCGGCAGGCC-----------TGGAAAGG------------------------------------------TCTGCCGGAGATCTATGAACTTCTGTTT----TATGATAAGTTA-CTCTG-AAATTATGTGGGAAAATAAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAGGTAATGTGAATTGCAGAACTCAGTGAATCATCGAATTTTTGAACGCACATTGCGCCCACTAGTATTCTGGTGGGCATGCCTGTTCGAGCGTCATTTCAAACCCTTATGCCTCTGTTGCATAGTGTTGGGGGATTAT-----CCTACCTTGGTAGAATAACCTCTGAAAGTGAGTGGCGGAGTTGT-CTTATTCTCTGGATGTAGTAGTTAAATCTTTTAATCTCACCAATAGAATAAGCCGACG-TCTAGCCAGAAAACCCATTGTTTTAT----ACTGGTTGACCTCG- 'B355_Xylaria_*_C._insignis_BCI_{9-9}_*_JQ760996.1' GAGTTTAATAAAACTCCT-AAACCCCTGTGAACTTACTGGTG--TTTGGCTCGGCAAATCGACTGCCTGCCCTGTGAGGTTTCTGCTTCGCGGATCGCCTACCCGTGAGTCACAGGCAGCTTCTGCCGCGGGTCCGTAAAACTATATTCTTAGTATAGTTTGTTA-TTCTG--AAT-AAAAACTTAAACTAG-TTAAAACTTTCAACAACGGATCTCTTGGTT{CT}TGGCAT{CT}GATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTG{CG}{CG}CCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCCCTGTTGCTTAGCGTTGGGAGCCTACAG---CCTGC--------TGTAGCTCCTTAAAGGTAGTGG{AC}GGAGTCGG-TTCACACTCTAGACGTAGTAAA-----------ATC-------------------------------------------------------------------- 'Endolichenic_Sordariomycetes_sp._*_JQ760996.1' GAGTTTAATAAAACTCCT-AAACCCCTGTGAACTTACTGGTG--TTTGGCTCGGCAAATCGACTGCCTGCCCTGTGAGGTTTCTGCTTCGCGGATCGCCTACCCGTGAGTCACAGGCAGCTTCTGCCGCGGGTCCGTAAAACTATATTCTTAGTATAGTTTGTTA-TTCTG--AAT-AAAAACTTAAACTAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCCCTGTTGCTTAGCGTTGGGAGCCTACAG---CCTGC--------TGTAGCTCCTTAAAGGTAGTGGCGGAGTCGG-TTCACACTCTAGACGTAGTAAA-----ATCTTTATCTCGCCTATGG-ATGAGCCGGCG-CCTTGCCGTAAAA-CCCCTAATCTTTCA--CAAGGTTGACCTCG- 'Endolichenic_Sordariomycetes_sp._FL1030_*_Cladonia_evansii_*_JQ760654.1' GAG--TTAAACAACTCCT-AAACCCATGTGAACCTACCTTT---GTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGG-ACCTACCCTGTAGGGACCTTACCCGGTAGTTGCGGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT-----TACTA--TGTTA-TTCTG--AATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATACCTGTTCGAGCGTCATTTCAA-CCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGCCTACAGATACCCTC--------TGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTT-ATCTCGCCTATAG-ATGAGCCGGTC-CCTTGCCGTAAAACCCCCTAATTTCT----AAAGGTTGACCTCG- 'Endolichenic_Sordariomycetes_sp._FL1283_*_JQ760898.1' GAG-TTAAAACAACTCCT-AAACCCATGTGAACCTACCATT---GTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGT-CCCTACCCTGTAGGGACCTTACCCGGTAGTTGCGGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT-----TACTA--TGTTA-TTCTG--AATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGCCTACAGATACCCTC--------TGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTT-ATCTCGCCTATAG-ATGAGCCGGTC-CCTTGCCGTAAAAACCCCTAATTTCT----AAAGGTTGACCTCG- 'Endophytic_Xylaria_sp._*_Hevea_*_HQ022442.1' GAG--TGTAATAACTCCC-AAACCCATGTGAACTTACCTTCT--GTTGCCTCGGCAGGTC-GCG-CCTACCCTGTGAGA-CCCTACCCTGTAGAG-TCTTACCCGGTAAACGCGAGCAACCCCTGCCGGCGGCCCATTCAACTCTGTT-----TACTGA-TGTTATTTCTG--AAT-TAACAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCTCTGTTGCTTAGTGTTGGGAGCCTACAG---TCCTC--------TGTAGCTCCCTAAAGTTAGTGGCGGAGTCGG-TTCACACTCTAGACGTAGTAAT------TTTTTATCTCGCCTATAG-ATGGACCGGCG-CCTTGCCGTAAAACCCCCTACTTTTTT---AAAGGTTGACCTCG- 'Endophytic_Xylariaceae_sp._*_Lasianthus_cyanocarpus_*_AB741611.1' GAG--TGTAACAACTCCCTAAACCCATGTGAACTTACCTTCT--GTTGCCTCGGCAGGTC-GCG-CCTACCCTGTAAGA-CCCTACCCTGTAGAG-TCCTACCCGGGAGACGCGGGT-AACCCTGCCGGCGGCCTACAAAACTCTGTT-----TACTCA-TGTTATTTCTG--AAC-CTATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCTCTGTTGCTTAGTGTTGGGAGCCTACAG---TCCCC--------TGTAGCTCCCTAAAGTTAGTGGCGGAGTCGG-TTCACACTCTAGACGTAGTAAA------TTTTTATCTCGCCTACAG-ATGGACCGGCG-CCCTGCCGTAAAACCCCCCTAATTTTTT--AATGGTTGACCTCG- 'F0051_Xylaria_*_LS_*_EF026149.1' GAG-TTAAAACAACTCCT-AAACCCATGTGAACCTACCATT---GTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGG-ACCTACCCTGTAGGGAACTTACCCGGTAGTTGCGGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT-----TACTA--TGTTA-TTCTG--AATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGTCTACAGATACCCTC--------TGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTT-ATCTCGCCTATAG-ATGAGCCGGTC-CCTTGCCGTAAAAACCCCTAATTTCT----AAAGGTTGACCTCG- 'P0394_Xylaria_*_Xylopia_macrantha_BCI_*_AB741611.1' GAG--TGTAATAACTCCC-AAACCCATGTGAACTTACCTTCT--GTTGCCTCGGCAGGTC-GCG-CCTACCCTGTGAGA-CCCTACCCTGTAGAG-TCTTACCCGGTAAACGCGAAT-ACCCCTGCCGGCGGCCCATTAAACTCTGTT-----TACTGA-TGTTATTTCTG--AAT-TTATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCTCTGTTGCTTAGTGTTGGGAGCCTACAG---TCCTC--------TGTAGCTCCCTAAAGTTAGTGGCGGAGTCGG-TTCACACTCTAGACGTAGTAAA------TTTTTATCTCGCCTATAG-ATGGACCGGTG-TCTTGCCGTAAAACCCCCTACTTTTTT---AAAGGTTGACCTCG- 'Xylaria_grammica_*_GU300097.1' GAG-TTATTACAACTCCC-AAACCCATGTGAACTTACCTTCT--GTTGCCTCGGCAGGTC-GCGACCTACCCTGTGAGG-CCCTACCCTGTAGGG-CCCTACCTGGTAGTCGCGGGT-ACGCCTGCCGGTGGCCCATGAAACTCTGTT-----TATTCT-TGTTA-TTCTG--AAT-CTATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCTCTGTTGCTTAGCGTTGGGAGCCTACAG---CCTTC--------TGTAGCTCCCCAAAGTTAGTGGCGGAGTCGG-TTTACACTCTAGACGTAGTAAA------TTTT-ATCTCGTCTGCAG-TTAGGCCGGTC-CCTCGCCGTAAAACCCCCCAATTTTT----AAAGGTTGACCTCG- 'Xylaria_liquidambaris_*_GU300094.1' GAG-TTATTACAACTCCC-AAACCCATGTGAACTTACCTTCT--GTTGCCTCGGCAGGTC-GTGG-CTACCCTGTGAGG-TCCTACCCTGTAGGA-CCCTACCCGGTGGTCTCGGTT-AAGCCTGCCGGTGGCCCAAGAAACTCTGTT-----AATTATATGTTA-TTCTG--AAT-CTATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCCCTGTTGCTTAGCGTTGGGAGCCTACAG---TTCGC--------TGTAGCTCCCCAAAGTTAGTGGCGGAGTCAG-TTTATGCTCTAGACGTAGTAAT------TTTT-TTCTCGTCTGTAG-CCGGGCTGGTCTCCTCGCCGTAAAA-CCCCCAATTTTT----AAAGGTTGACCTCG- 'Xylaria_tuberoides_*_GU300074.1' GAGTTGACCCTAACTCCT-AACCCTTTGTGAAATTACCTTTTA-GTTGCTTCGGTAGGCC-----------TTCCTAGG------------------------------------------CTTGCCGGGGTTGTATAGAATTCTGTTT----TGCGATTTGGTA-CTCTGAAAATTACGTGGGAAAATGAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAGGTAATGTGAATTGCAGAACTCAGTGAATCATCGAATTTTTGAACGCACATTGCGCCCACCAGTATTCTGGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCCTTATGCCTCTGTTGCATAGCGTTGGGGGATTA------TTCTACGTGGTAGTATAACCCCTAAAAATGAGTGGCGGAGTTGT-TTTATTCTCTGGATGTAGTAATTAAATCTTTTAATCTCACCGACAGGATAAACCAACG-TCTAGCCAAGAAAATTCAGTATTTTTAT--ATTGGTTGACCC--- 'Xylaria_venosula_*_EF026149.1' GAG-TTAAAACAACTCCT-AAACCCATGTGAACCTACCATT---GTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGG-ACCTACCCTGTAGGGACCTTACCCGGTAGTTGCCGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT-----TACTA--TGTTA-TTCTG--AATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGCCTACAGATACCCTC--------TGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTT-ATCTCGCCTATAG-ATGAGCCGGTC-CCTTGCCGTAAAAACCCCTAATTTCT----AAAGGTTGACCTCG- 'Xylaria_venustula_*_GU300091.1' GAG-TTTTTACAACTCCCTAAACCCATGTGAACTTACCATTT--GTTGCCTCGGCAGGTC-GCGCTTAACCCCGTGAGACCCCTACCCTGTAGGG-CCTTACCCGGTGGACGCGGGC-TTCCCTGCCGGCGGCCCATCAAACTCTGTTTTTA-TATTATATTTTACATCTG--AAT-CTATAACGGAATACGTTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAA-CCCTTAAGCCTCTGTTGCTTAGTGTTAGGAGCCTACAG---CCCTC--------TGTAGCTCCCCAAAGTTAGTGGCGGAGTCGGTCTCACACTCTAGACGTAGTAAATCTTTTTTTT-ATCTCGCCTACAG-AGGAGCCGGCG-CCTTGCCGTAAAACCCCCTCATTTTTTTTACAAGGTTGACCTCG- ; END; [ The following blocks are output data for analysis step 19276 ] BEGIN TREES; TITLE 'Xylaria "HY" - ITS MLT'; LINK TAXA = TaxaForAnalysisStep19276; TREE 'Xylaria "HY" - ITS ML Tree' = [&R] (('Xylaria_venosula_*_EF026149.1':0.002089,'F0051_Xylaria_*_LS_*_EF026149.1':0.004158):1.0E-6,('Endolichenic_Sordariomycetes_sp._FL1030_*_Cladonia_evansii_*_JQ760654.1':0.004263,((('Endolichenic_Sordariomycetes_sp._*_JQ760996.1':1.0E-6,'B355_Xylaria_*_C._insignis_BCI_{9-9}_*_JQ760996.1':1.0E-6):0.185773,(('Xylaria_grammica_*_GU300097.1':0.009228,'Xylaria_liquidambaris_*_GU300094.1':0.054021):0.028817,('Xylaria_venustula_*_GU300091.1':0.062349,('Endophytic_Xylariaceae_sp._*_Lasianthus_cyanocarpus_*_AB741611.1':0.033803,('Endophytic_Xylaria_sp._*_Hevea_*_HQ022442.1':0.010568,'P0394_Xylaria_*_Xylopia_macrantha_BCI_*_AB741611.1':0.006354):0.016223):0.019681):0.013212):0.020962):1.0E-6,('9742_Xylaria_*_C._insignis_BCI_{2-14}_*_GU300074.1':0.061938,'Xylaria_tuberoides_*_GU300074.1':0.119378):0.308588):0.039973):0.004092,'Endolichenic_Sordariomycetes_sp._FL1283_*_JQ760898.1':0.004162); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr98668] END;