#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; 8:07 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 19274 ] BEGIN TAXA; TITLE TaxaForAnalysisStep19274; DIMENSIONS NTAX=17; TAXLABELS 'Calonectria_ilicicola_CBS.190.50_*_AY725726.1|' 'Calonectria_naviculata_CBS.101121_*_GQ267317.1|' 'Curvicladiella_cignea_CBS.101411_*_KM231866.1|' 'Curvicladiella_cignea_CBS.109168_*_KM231868.1|' 'Gliocephalotrichum_bulbilium_CPC.23333_*_KF513434.1|' 'Gliocephalotrichum_cylindrosporum_CBS.902.70_*_KF513435.1|' 'Gliocephalotrichum_longibrachium_CBS.126571_*_KF513449.1|' 'Gliocladiopsis_irregularis_CBS.755.97_*_JQ666099.1|' 'Gliocladiopsis_pseudotenuis_CBS.116074_*_JQ666106.1|' 'Gliocladiopsis_sagariensis_CBS.199.55_*_JQ666107.1|' PS0221| PS0427| PS0768| PS0772| PS1001.EF1f| 'Xenocylindrocladium_guianense_CBS.112179_*_KM231895.1|' 'Xenocylindrocladium_serpens_CBS.128439_*_KM231894.1|' ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M38332] TITLE 'Gliocladiopsis / Hypocreales TEF'; LINK TAXA = TaxaForAnalysisStep19274; DIMENSIONS NCHAR=534; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] 'Calonectria_ilicicola_CBS.190.50_*_AY725726.1|' -GACCGTCGA---------TTCGCGCGTCGCCGTGTCTGCTCCACCCGAAACACCTCCC-----------CTCGCCACCCCTCTTTG--------TCGATCTAAAAATTTTCTGCACACATC--CTCTGGGTTT-GTGGTGGGGGCAT-TTACCCCGCCGCCCACAGGACGTCGT---CAAACCC---GCCCCGCCCCACTTTGAC-TTTCGCACCAAA---TCACATTTG--GCATCTC-GCCACACATATTGAT-TGACACTGT--GCTGACTCTCAC---AAACAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTCTGGAAGTTCGAGACTCCCAAGTACGATGTCACCGTCATTGGTAAGTCTTAATACTACTCAGCTTCTGTCCT---------------------TCAGCCTCTAAC-CGACTCTCAACAGACGCTCCCGGTCACCGTGACTTTCATC- 'Calonectria_naviculata_CBS.101121_*_GQ267317.1|' CGACGGCCGA--------TTTCCGAGTCCGCCGTGGCTGCCACACCCGAAACATCCTCTGGGCCCCGGGCCCCGCTCCTCCCCTCCCCTC-----GACATCGAAAAATTTTTTGCGCACATC--CTTTGTTTT--GTGGT-GGGGCAA-TTACCCCGCCGCCCACAGGACGTCGC----AAACTT---GCACTGCCCCACTT-----TACTTCCGCACCCGATCGCCTCT--TGCATCTA-GTCATGT---------TGACACTGT--GCTGACTCCCAC---CAACAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACGATGTCACCGTCATTGGTAAGCTT-------------TCACTCCCTCAA-----CCCGAGGTGTTCACACATGGTCTAAC-AGTCAACCAATAGACGCTCCCGGTCACCGTGACTTTCATC- 'Curvicladiella_cignea_CBS.101411_*_KM231866.1|' CGACCGTCGA--------TTTCT--AGTCGCCGCGTCTTCA--ATCCGAAACGC-CACT----------GCTCGCTTCCCCCCTCCTTG------ACGAACGAAAAAAAATTCACCCACAAC--TTTGTGCTTCGGGAGT-GGGGCTT-CTACCCCGCCGCCCACACGACGTCGC----AAATTT----CCCTACCCCAC-------CAGAGCAACACC---ACCATCCCACCGTGTCTTAGTCACATGTTTTC---TGAAGCGCT--GCTGACTCTCAT---CAATAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACGATGTCACCGTCATTGGTAAGCTT-------------TATCTACCTCGCAAAATCTCGCAATTTCA--------TCTAAC-CATCAATGAATAGATGCCCCCGGTCACCGTGACTTTCATC- 'Curvicladiella_cignea_CBS.109168_*_KM231868.1|' CGACCGTCGA--------TTTCT--AGTCGCCGCGTCTTC--AATCCGAAACGC-CACT----------GCTCGCTTCCCCCCTCCTTG------ACGAACGAAAAAAAATTCACCCACAAC--TTTGTGCTTCGGGAGT-GGGGCTT-CTACCCCGCCGCCCACACGACGTCGC----AAATTT----CCCTACCCCACCAGAGC-AACACCACCA---------TCCCACCGTGTCTTAGTCACATGTTTTC---TGAAGCGCT--GCTGACTCTCAT---CAATAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACGATGTCACCGTCATTGGTAAGCTT-------------TATCTACCTCGCAAAATCTCGCAATTTCA--------TCTAAC-CATCAATGAATAGATGCCCCCGGTCACCGTGACTTTCATC- 'Gliocephalotrichum_bulbilium_CPC.23333_*_KF513434.1|' CGATCGTCACACAAGACTTTTCCCACGATGCTGCGCCTTC---ATCCGAAACGCTCATC----------TTCCGTTACCCCTCCTTC-GA-----TC--GAAAAAAAATTTCTG-CCACATC--CTGTGGGAA--TTAGT-GGGGCAC-TTACCCCGCCTCCCACAGGTCGTTGG--AAAAATTTCACACT-TGCCCCACCATCACCCAGTACAGCAAA---TCACTGTCA-CGGGTTCT-ATCATCTGATCTT---TGACACGAT--GCTAACTGGATTGTCAAATAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTGAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACTCCCCGCTACTATGTCACCGTCATTGGTAAGCTT-------------CACCTGCTGCAACCATATCATCAAAGATGACACATCCGCTAAC-TCTCCATCTCCAGACGCCCCCGGTCACCGTGACTTTCATC- 'Gliocephalotrichum_cylindrosporum_CBS.902.70_*_KF513435.1|' CGACAGTCGAA-------TCTCCTGCGACGCCGCGCATC----ACCCGAAACGCTTATC-----------CCCGCTACCCCTCCTTCGCTTTCGATCGAGAAAAAAAATTTCTGCCCACATC--TTGTG------GGAGT-GGGGCAT-CTACCCCGCCACCCACAGGACGTTGG--AAATTTTTCACACTCTGCCCCAC-------CTCCACAAC------TCACTGTCA-CGGGTTTC-GTCACCTGCTCCTCAATGACACTTT--GCTAACTGGACTGTCAAATAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTCTGGAAGTTCGAGACTCCCCGCTACTATGTCACCGTCATTGGTAAGCTC-------------CACCCGCCTTGTCT---CACTTGAGAGATGCACAGTTGCTAACATGTTCCCCCACAGACGCTCCCGGTCACCGTGACTTTCATC- 'Gliocephalotrichum_longibrachium_CBS.126571_*_KF513449.1|' CGACTGTCGA--------TTTCCTGCGACGCCGCATCCAC---ACACGAAACGCTTATC-----------CCCGCTACCCCTCCTTC-GCTTCGATCGAGAAAAAAAAATTTCGCCCACGTT--CTGTG------GGAGT-GGGGCAC-TTACCCCGCCACCCACAGGACGCTGGAAAAAAAATTCACACTCTGCCCCAC-------CACAACACCAC----TCTTCATCC-CGGGCTTT-ATCACCTGCTGCTTATTGACACAAT--GCTAACTGGGTTGTCAAATAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTCTGGAAGTTCGAGACTCCCCGCTACTATGTCACCGTCATTGGTAAGCTT-------------CACCT--CTCACTTCATCTCACCATGAGATCATCGTTACTAAC-ATCTCCTCCCCAGACGCTCCCGGTCACCGTGACTTTCATC- 'Gliocladiopsis_irregularis_CBS.755.97_*_JQ666099.1|' CGGCCGTCGA--------TTTCCCACGTCGCCGCGTCCGC---TTCCGAAACGCACACC----------CCTCGCTCCCCCTCCTTC--------CACGAACAAA-TTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGC-AAAAAATC---ACCCTGCCCCAC-------TACAGCAACACTGAATGGCTATCA-CGCCCCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCCTCAGTAGACCCGAGTACTAAC-CTATCACCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- 'Gliocladiopsis_pseudotenuis_CBS.116074_*_JQ666106.1|' CGGCCGTCGA--------TTTCCCACGTCGCCGCGTCCGC---TTCCGAAACGCACACC----------CCTCGCTCCCCCTCCTTC--------CACGAACAAA-TTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGCAAAAAAATC---ACCCTGCCCCAC-------TACAGCAACACTGAATGGCTATCA-CGCCTCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCTTCAGTAGACCCGAGTACTAAC-CTATCATCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- 'Gliocladiopsis_sagariensis_CBS.199.55_*_JQ666107.1|' CGGCCGTCGA--------TTTCCCACGTCGCCGCGCCCGC---TTCCGAAACGCACACC----------CCTCGCTTCCCCTCC-----------CACGAACAAATTTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGC-AAAAATTC---ACCCTGCCCCAC-------TATAGCAACACTGAATGGCTATCA-CGCCTCAC-GTCACATGTC------TGCGACAGT--ACTAACCGTCATGTTCTATAGGAAGCCGCTGAGCTCGGCAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCTGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACTCCCCGCTACTTCGTCACCGTCATTGGTAAGCCT-------------CTTTCCTCTCATGCAAGCCTC----ATTGAATCAAGTTCTAAC--TCGTACCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- PS0221| -GGCCGTCGA--------TTTCCCACGTCGCCGCGTCCGC---TTCCGAAACGCACACC----------CCTCGCTCCCCCTCCTTC--------CACGAACAAATTTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGCAAAAAAATC---ACCCTGCCCCAC-------TACAGCAACACTGAATGGCTATCA-CGCCTCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCTTCAGTCGACCCGAGTACTAAC-CTATCATCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- PS0427| -GGCCGTCGA--------TTTCCCACGTCGCCGCGTCCGC---TTCCGAAACGCACACT----------CCTCGCTCCCCCTCCTTC--------CACGAACAAATTTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGCAAAAAAATC---ACCCTGCCCCAC-------TACAGCAACACTGAATGGCTATCA-CGCCTCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCTTCAGTCGACCCGAGTACTAAC-CTATCATCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- PS0768| -GGCCGTCGA--------TTTCCCACGTCGCCGCGTCCGC---TTCCGAAACGCACACC----------CCTCGCTCCCCCTCCTTC--------CACGAACAAATTTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGCAAAAAAATC---ACCCTGCCCCAC-------TACAGCAACACTGAATGGCTATCA-CGCCTCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCTTCAGTCGACCCGAGTACTAAC-CTATCATCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- PS0772| -GGCCGTCGA--------TTTCCCACGTCGCCGCGTCCGC---TTCCGAAACGCACACC----------CCTCGCTCCCCCTCCTTC--------CACGAACAAATTTTTTTTACCCACATT--CTCTGGTTT--GTGGT-GGGGCACTTTACCCCGCCACCCACAGGACGTTGGCAAAAAAATC---ACCCTGCCCCAC-------TACAGCAACACTGAATGGCTATCA-CGCCTCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCTTCAGTCGACCCGAGTACTAAC-CTATCATCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- PS1001.EF1f| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATC---ACCCTGCCCCACG------TACAGCAACACTGAATGGCTATCA-CGCCTCTC-GTCACATGTCTG----CGACACAGT--ACTAACTGTCATGTTCTATAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCCGCTACTTCGTCACCGTCATTGGTAAGCTT-------------CTTCCCTCTCATGCAAGCCTCTTCAGTCGACCCGAGTACTAAC-CTATCATCTCCAGACGCTCCCGGTCACCGTGA-TTTCATC- 'Xenocylindrocladium_guianense_CBS.112179_*_KM231895.1|' CGGCCGTCGAT-------TATCACACGTCGCCGCGTCTGC---ACCCGAAACGCCTACC----------CCTCG-------------------------ATTGAAAATTTTTTACCCACTTC--CTCTTGGTTTTGTGGTGGTGGGGCATTACCCCGCCGCCCACACGACGTTCG--CAAAATTT---ACCCTGCCCCAC-------CACAACACCAAAACTTCCCTACC--CGCACCTG-GTCACATGTTCT----TGATGCAGT-TACTGACTCGCAA---CAATAGGAAGCCGCCGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCAAGTACCAGGTCACCGTCATTGGTAAGCTG-------------CCACCGCACCGT-----CTGCTCACGTTGACACTTGTTCTAAC-TATCCCATCACAGATGCTCCCGGTCACCGTGACTTTCATC- 'Xenocylindrocladium_serpens_CBS.128439_*_KM231894.1|' GGGCCGTCGAT-------TTTTACACATCGCCGCGCCTGC---ACCCGAAACGTTTACC----------CCTC----------------------CACGATCGAAAATTTTTTACCCACACTTGTTTTGGTTTTTGTGGT-GGGGCA--TTACCCCGCCGCCCACAGGACGTCGC--AAAATTTT---GCCCTGCCCCAC-------CACAACACCAAA---TTCTCCTCGCCGCATCTG-GTCACATGTTTCT---TGAAGCAGTACACTGACTTGCATCAACAACAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTCTGGAAGTTCGAGACCCCCAAGTACCAGGTCACCGTCATTGGTAAGCTC-------------CTGCTGCACC----------------------------------------------GATGCTCCCGGTCACCGTGACTTTCATC- ; END; [ The following blocks are output data for analysis step 19274 ] BEGIN TREES; TITLE 'Gliocladiopsis - TEF MLT'; LINK TAXA = TaxaForAnalysisStep19274; TREE 'Gliocladiopsis - TEF ML Tree' = [&R] (('Gliocephalotrichum_longibrachium_CBS.126571_*_KF513449.1|':0.113154,'Gliocephalotrichum_cylindrosporum_CBS.902.70_*_KF513435.1|':0.098828):0.019763,((((((PS0768|:1.0E-6,(PS1001.EF1f|:1.0E-6,PS0427|:1.0E-6):0.00224):1.0E-6,PS0221|:1.0E-6):1.0E-6,PS0772|:1.0E-6):1.0E-6,('Gliocladiopsis_irregularis_CBS.755.97_*_JQ666099.1|':0.006739,'Gliocladiopsis_pseudotenuis_CBS.116074_*_JQ666106.1|':1.0E-6):0.002233):0.014581,'Gliocladiopsis_sagariensis_CBS.199.55_*_JQ666107.1|':0.047901):0.135044,(('Xenocylindrocladium_guianense_CBS.112179_*_KM231895.1|':0.102283,'Xenocylindrocladium_serpens_CBS.128439_*_KM231894.1|':0.079747):0.084712,('Calonectria_ilicicola_CBS.190.50_*_AY725726.1|':0.208284,('Calonectria_naviculata_CBS.101121_*_GQ267317.1|':0.195812,('Curvicladiella_cignea_CBS.101411_*_KM231866.1|':0.005362,'Curvicladiella_cignea_CBS.109168_*_KM231868.1|':0.004953):0.224461):0.081285):0.045961):0.076324):0.168728,'Gliocephalotrichum_bulbilium_CPC.23333_*_KF513434.1|':0.13255); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr98662] END;