#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 19, 2024; 23:41 GMT TreeBASE (cc) 1994-2008 Study reference: Adetutu E.M., Thorpe K., Bourne S., Cao X., Shahsavari E., Kirby G., & Ball A.S. 2011. Phylogenetic Diversity of Fungal Communities in Tourist Accessible and Inaccessible Areas in Naracoorte Caves. Mycologia, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11262] [ The following blocks are input data for analysis step 6995 ] BEGIN TAXA; TITLE TaxaForAnalysisStep6995; DIMENSIONS NTAX=23; TAXLABELS Cladosporium_sp_AJ279487 Cladosporium_sp_FJ755823 Cladosporium_sp_FJ790249 Cladosporium_sp._KD6 Davidiella_FJ471623 Doratomyces_sp_AJ608085 Doratomyces_sp._KD1 Doratomyces_sp._KD8 Doratomyces_stemonitis_AJ608983 Fusarium_oxysporium_EU839400 Fusarium_proliferatum_FJ798594 Fusarium_sp_EU750679 Fusarium_sp_EU750695 Fusarium_sp._KD7 Gibberella_moniliformis_FJ439583 Hypocreales_sp._EF060613 Neonectria_macrodidyma_AM419076 Neonectria_macrodidyma_GQ_169024 Neonectria_radicola_FJ861416 Neonectria_sp_FJ798594 Neonectria_sp._KD3 Wardomyces_Inflatus_AM774155 Wardomyces_Inflatus_AM774157 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M8059] TITLE '11_02_22 DGGE bands 4 paper'; LINK TAXA = TaxaForAnalysisStep6995; DIMENSIONS NCHAR=259; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . ] Cladosporium_sp_AJ279487 -TGCGGAGGG-ATCATT-ACAAGTGACCCCGGTCTAACCACCGGGATGTTCATAACCCTTT----GTTGTC-CGACTCTGTTGCCTCCGGG----GCG--------ACCCTGCC-TTCGGGCGGGGGCTCCGGGTGGACACTTC---AAACTCTTGCGTA-ACTTTGCA-------GTCTGA--GTAAACTTAATT-AATAAATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Cladosporium_sp_FJ755823 -TGCGGAGGG-ATCATT-ACAAGTGACCCCGGTCTAACCACCGGGATGTTCATAACCCTTT----GTTGTC-CGACTCTGTTGCCTCCGGG----GCG--------ACCCTGCC-TTCGGGCGGGGGCTCCGGGTGGACACTTC---AAACTCTTGCGTA-ACTTTGCA-------GTCTGA--GTAAACTTAATT-AATAAATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Cladosporium_sp_FJ790249 -TGCGGAGGG-ATCATT-ACAAGTGACCCCGGTCTAACCACCGGGATGTTCATAACCCTTT----GTTGTC-CGACTCTGTTGCCTCCGGG----GCG--------ACCCTGCC-TTCGGGCGGGGGCTCCGGGTGGACACTTC---AAACTCTTGCGTA-ACTTTGCA-------GTCTGA--GTAAACTTAATT-AATAAATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Cladosporium_sp._KD6 --GCGGAGGG-ATCATT-ACAAGTGACCCCGGTCTAACCACCGGGATGTTCATAACCCTTT----GTTGTC-CGACTCTGTTGCCTCCGGG----GCG--------ACCCTGCC-TTCGGGCGGGGGCTCCGGGCGGACACTTGCGTAAACTCTTGCGTA-ACTT-GCA-------GTCTGA--GTAAACTTAATT-AATAA-TTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGA--- Davidiella_FJ471623 -------------CATT-ACAAGAACGCCCGGGCTT-CGGCCTGGTTATTCATAACCCTTT----GTTGTC-CGACTCTGTTGCCTCCGGG----GCG--------ACCCTGCC-TTCGGGCGGGGGCTCCGGGTGGACACTTC---AAACTCTTGCGTA-ACTTTGCA-------GTCTGA--GTA--CTTAATT-AATAA-TTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Doratomyces_sp_AJ608085 -TGCGGAGGG-ATCATTACCGAAGTT---CCTTCAAA-CCCACTGTGAACCTTACCTCTTGCCGCGTTGTCTCGGCG--GGAGGCGGTGTGCGTCGCGCGCCCT--AGCGGGCCGTGCCGCTCCC-GTCCCCGCCGGCAGCGCC---AAACTCTAAA-TGCACAGCGGACTGTACGTTCTGA--TTTA-CAAAAAA-AACAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Doratomyces_sp._KD1 --GCGGAGGG-ATCATTACCGAAGTTAC-CCTTCAAAACCCATTGTGAACCATACCTCTTGCCGCGTTGTCTCGGCG--GGAGGCGCTG--------------------GGGC--TTCGGCTCCGCGTCCCCGCCGGCAGCGCC---AAACTCTAAACTGCAAAGCGTACTGCATGTTCTGA--TTTA-CAAAAAA-AACAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCC-- Doratomyces_sp._KD8 ----GGAGGG-ATCATTACCGAAGTTA--CCTTCAAAACCCACTGTGAACCTTACCTCTTGCCGCGTTGTCTCGGCG--GGAGGCGGTGTGCGTCGCGCGCCCT--AGCGGGCCGTGCCGCTCCC-GTCCCCGCCGGCAGCGCC---AAACTCTAAA-TGCACAGCGGACTGTACGTTCTGA--TTTA-CAAAAAA-AACAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGA-GAACG------- Doratomyces_stemonitis_AJ608983 -TGCGGAGGG-ATCATTACCGAAGTT---CCTTCAAA-CCCACTGTGAACCTTACCTCTTGCCGCGTTGTCTCGGCG--GGAGGCGGTGTGCGTCGCGCGCCCT--AGCGGGCCGCGCCGCTCCC-GTCCCCGCCGGCAGCGCC---AAACTCTAAA-TGCACAGCGGACTGTACGTTCTGA--TTTA-CAAAAAA-AACAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Fusarium_oxysporium_EU839400 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCACTT-----GTTGCCTCGGCGGATCAGCCCGCTC------------------CCGGTAAAACGGGACGG----CCCGCCAGAGGACCCC-TAAACTCTGTT-TCTATATGTAA------CTTCTGA--GTAAAACCAT-A-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAA- Fusarium_proliferatum_FJ798594 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCACTT-----GTTGCCTCGGCGGATCAGCCCGCTC------------------CCGGTAAAACGGGACGG----CCCGCCAGAGGACCCC-TAAACTCTGTT-TCTATATGTAA------CTTCTGA--GTAAAACCAT-A-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAA- Fusarium_sp_EU750679 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCTATAC----GTTGCCTCGGCGGATCAGCCCGCGC------------------CCCGTAAAAAGGGACGG----CCCGCCCGAGGACCCC-TAAACTCTGTT-TTTAG-TGGAA------CTTCTGA--GTAAAACAAACA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAA- Fusarium_sp_EU750695 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCTATAC----GTTGCCTCGGCGGATCAGCCCGCGC------------------CCCGTAAAAAGGGACGG----CCCGCCCGAGGACCCC-TAAACTCTGTT-TTTAG-TGGAA------CTTCTGA--GTAAAACAAACA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAA- Fusarium_sp._KD7 -----GAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTGGTGAAC-ATACCACTT-----GTTGCCTCGGCGGATCAGCCCGCTC------------------CCGGTAAAACGGGACGG----CCCGCCAGAGGACCCC-TAAACTCTGTT-TCTATATGTAA------CTTCTGA--GTAAAACCAT-A-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGATTAACGCAGA--- Gibberella_moniliformis_FJ439583 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCACTT-----GTTGCCTCGGCGGATCAGCCCGCTC------------------CCGGTAAAACGGGACGG----CCCGCCAGAGGACCCC-TAAACTCTGTT-TCTATATGTAA------CTTCTGA--GTAAAACCAT-A-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAA- Hypocreales_sp._EF060613 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCTATAC----GTTGCCTCGGCGGATCAGCCCGCGC------------------CCTGTAAAACGGGACGG----CCCGCCCGAGGACCC--TAAACTCTGTT-TTTAG-TGGAA------CTTCTGA--GTAAAACAAACA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAA- Neonectria_macrodidyma_AM419076 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCTATTT----GTTGCCTCGGCGG---TGCCTGTTC------------------C-----------GACAG----CCCGCCAGAGGACCCC--AAACCCTGAT-TACATTTAAGAAG---TCTTCTGA--GTAAACCGATTA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAA Neonectria_macrodidyma_GQ_169024 ------------------------------CTCCCAAACCCCTG-TGAAC-ATACCTATTT----GTTGCCTCGGCGG---TGCCTGTTC------------------C-----------GACAG----CCCGCCAGAGGACCCC--AAACCCTGAT-TACATTTAAGAAG---TCTTCTGA--GTAAACCGATTA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAA Neonectria_radicola_FJ861416 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACC-ATTT----GTTGCCTCGGCGG---TGCCTGCTT------------------C-----------GGCAG----CCCGCCAGAGGACCCA--AACCCTTGAT-TTTATACAGTA-----TCTTCTGA--GTAAAT-GATTA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Neonectria_sp_FJ798594 ----------------------------------------------------------------------------------GCCCGCTC------------------C-----------GGCGG----CCCGCCAGAGGACCCC-CAAACTCTTGT-TTTATACAGTA-----TCTTCTGA--GTAACACGATTA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Neonectria_sp._KD3 -AGCGGAGGG-ATCATTACCGAGTTTACAACTCCCAAACCCCTG-TGAAC-ATACCTATTT----GTTGCCTCGGCGG---TGCCTGTTC------------------C-----------GACAG----CCCGCCAGAGGACCCC--AAACCCTGAT-TACATTTAAGAAG---TCTTCTGA--GTAAACCGATTA-AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC--- Wardomyces_Inflatus_AM774155 ---ACGA-GG-ATCATT-CCGAAGTTA--CCTTCAAAACCCACTGTGAACCTTACCTCTTGCCGCGTTGTCTCGGCG--GGAGGCGGGGGACGTCACGCGCCCCGCAACGGGCCGTGCCGCTCCCCGTCCCCGCCGGCGGCGCC---AAACTCTAAA-TGCACAGCGGACTGTATGTTCTGA--TTTA-CAAAAAA-AACAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- Wardomyces_Inflatus_AM774157 -AGCGGAAGG-ATCATA-CCGAAGTTA--CCTTCAAAACCCACTGTGAACCTTACCTCTTGCCGCGTTGTCTCGGCG--GGAGGCGGGGTGCGTCAAG-GCCCT----CGGGCCGCGCCGCTCCCCGTCCCCGCCGGCGGCGCC---AAACTCTAAA-TGCACAGCGGACTGTACGTTCTGA--TTTA-CAAAAAA-AACAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGA- ; END; [ The following blocks are output data for analysis step 6995 ] BEGIN TREES; TITLE '11_02_22 DGGE bands 4 paper'; LINK TAXA = TaxaForAnalysisStep6995; TREE DGGE_band = [&R] ((Doratomyces_sp._KD1:0.0049,((Wardomyces_Inflatus_AM774155:0.0,Wardomyces_Inflatus_AM774157:0.0)0.91:0.01944,(Doratomyces_stemonitis_AJ608983:0.0,(Doratomyces_sp_AJ608085:0.0,Doratomyces_sp._KD8:0.0)0:0.0)0:0.0)0.28:0.03578)0.93:0.3143,((Cladosporium_sp._KD6:0.00983,(Cladosporium_sp_FJ790249:0.0,(Cladosporium_sp_FJ755823:0.0,(Cladosporium_sp_AJ279487:0.0,Davidiella_FJ471623:0.0)0:0.0)0:0.0)0.68:0.00933)0.96:0.349,((((Fusarium_oxysporium_EU839400:0.0,(Gibberella_moniliformis_FJ439583:0.0,Fusarium_sp._KD7:0.00955)0:0.0)0:0.0,Fusarium_proliferatum_FJ798594:0.0)0.8:0.0255,(Neonectria_sp_FJ798594:0.01465,(Neonectria_radicola_FJ861416:0.02792,(Neonectria_sp._KD3:0.0,(Neonectria_macrodidyma_GQ_169024:0.0,Neonectria_macrodidyma_AM419076:0.0)0:0.0)0.95:0.07353)0.69:0.04963)0.88:0.04854)0.9:0.0518,(Hypocreales_sp._EF060613:0.0,(Fusarium_sp_EU750679:0.0,Fusarium_sp_EU750695:0.0)0:0.0)0:0.0)0.65:0.09521)0.93:0.01063); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr31160] END;