#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 April 19, 2024; 1:41 GMT TreeBASE (cc) 1994-2008 Study reference: Deckert R., Hsiang T., & Peterson R. 2002. Genetic relationships of endophytic Lophodermium nitens isolates from needles of Pinus strobus L. Molecular Ecology, 106 (3): 305-313. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S835] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=13; TAXLABELS AF203470 Elytroderma_deformans Lophodermium_australe 'Lophodermium nitens BRMC1-7' 'Lophodermium nitens BRMC3-3' 'Lophodermium nitens NS4-2' 'Lophodermium nitens NS5-3' 'Lophodermium nitens NSWL4-3' Lophodermium_piceae Lophodermium_pinastri Lophodermium_seditiosum Meloderma_desmazieresii epistomatal_fungus ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M274] TITLE '5.8S, ITS 1 and 2 of rDNA'; LINK TAXA = Taxa1; DIMENSIONS NCHAR=435; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] AF203470 -TTTACCAAAACTCTTGTTGCC-TTGGCGCATTCGTGC--GCCAAAGGAAT---CAAACCCTT---GAATCTCTGCTGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCTGGTATTCCGGGAGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTATTGGGCTCGCCT--C-------CTCTGGCCTGCCTCAAAATCAGT-GGCGGC-ACAGTCCGATCCTCAAGCGCAGTAA--TACA-CGACGCTTGCCGGTGAAGGTTGCT---GCTCCAG--AAACCCCCCACAAACTAAAGGTTGAC Elytroderma_deformans -TTTACCA-CAC-TTTGTTGCC-TTGGCGCCT---AGC--GCCAGCGGATC---AAAACCCTT---GAATCATTGCTGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCAGCTTGGTGTTGGGCTCGCCC--CG-CTTACCCGGGGCTTGCCTCAAAATCAGT-AGCGGCCGCCGTCCGA-CCTTCAGCGCAGTAA--TACT-CGTCGCTCGGAGGGAAAGACGGTA----TCGTTAACCCGAACCCC-CACACA--AGGTTGAC Lophodermium_australe -TTTACCA-CACTGTAGTTGCC-TTGGCGCTC---CGC--GCCAGTGGATC---GAAACTCCT---GAATCATTGCCGTCTGAGT---ACTATTCAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGTATTCCGGGGGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTGTTGAGCCCGCCC--CGGC?TGCCCGGGGCTCGCTTCAAAGTCAGT-GGCGGCCGCCGTCCGA-CCTT{AC}AGCGCAGTAA--TGCTTCGCCGCTGTTAGGGAAGGGTAGCAAGGGCCGTCA-TACAACCCCCACACACA--AGGTTGAC 'Lophodermium nitens BRMC1-7' -CCTACCAACCCTCTTGTTGCC-TTGGCGCATTCGTGC--GCCAAAGGAAT---TTTTTCCTT---GAATCTCTGCTGGCTGAGT---ACTATATAAGAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCTGGTATTCCGGGAGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTATTGGGCTCGCCT--C-------CTTTGGCCTGCCTCAAAATCAGT-GGCGGC-ACAGTCCGATCCTCAAGCGCAGTAA--TACA-CGACGCTTGCTGGCGAAGGTTGCT---GCTCCAG--AAACCCCCCACAAACTAAAGGTTGAC 'Lophodermium nitens BRMC3-3' -CCTACCAAAACTCTTGTTGCC-TTGGCGCATTCGTGC--GCCAAAGGAAT---CAAACCCTT---GAATCTCTGCTGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCTGGTATTCCGGGAGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTATTGGGCTCGCCT--T-------CTTTGGCCTGCCTCAAAATCAGT-GGCGGC-ACAGTCCGATCCTCAAGCGCAGTAA--TACA-CGACGCTTGCTGGTGAAGGTTGCT---GCTCCAG--AAACCCCCCACAAACTAAAGGTTGAC 'Lophodermium nitens NS4-2' -TTTACCAAAACTCTTGTTGCC-TTGGCGCATTCGTGC--GCCAAAGGAAT---CAAACCCTT---GAATCTCTGCTGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCTGGTATTCCGGGAGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTATTGGGCTCGCCT--C-------CTTTGGCCTGCCTCAAAATCAGT-GGCGGC-ACAGTCCGATCCTCAAGCGCAGTAA--TACA-CGACGCTTGCCGGTGAAGGTTGCT---GCTCCAG--AAACCCCCCACAAACTAAAGGTTGAC 'Lophodermium nitens NS5-3' -TTTACCAAAACTCTTGTTGCC-TTGGCGCATTTATGC--GCCAAAGGAAT---CAAACCCTT---GAATCTCTGCTGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCTGGTATTCCGGGAGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTATTGGGCTCGCCT--C-------CTTTGGCCTGCCTCAAAATCAGT-GGCGGC-ACAGTCCGATCCTCAAGCGCAGTAA--TACA-CGACGCTTGCCGGTGAAGGTTGCT---GCTCCAG--AAACCCCCCACAAACTAAAGGTTGAC 'Lophodermium nitens NSWL4-3' -CCTACCAAAACTCTTGTTGCC-TTGGCGCATTCGTGC--GCCAAAGGAAT---CAAACCCTT---GAATCTCTGCTGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCTGGTATTCCGGGAGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTATTGGGCTCGCCT--C-------CTTTGGCCTGCCTCAAAATCAGT-GGCGGC-ACAGTCCGATCCTCAAGCGCAGTAA--TACA-CGACGCTTGCTGGTGAAGGTTGCT---GCTCCAG--AAACCCCCCACAAACTAAAGGTTGAC Lophodermium_piceae -TTTGGCAGGCCTCCGGCTTCGGCTGGGTCGT--GTCT--GCCAGAGGCCT-----AACTCTT---GAATCACTGCGGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAATTAATGTGAATTGCAGAACTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGGGGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTGTTGGGCTCGCCC--TG-------TAGGGCCTGCCTCAAAGTCAGT-GGCGGC-ACCGTCTGA-CCCTAAGCGTAGTAA--TACT-CGCCGCTTGTGGACTCAGCGCGTGGC--CTGCCA-GCCAACCCCCACCATCA--AGGTTGAC Lophodermium_pinastri -CCTACCA-TAC-ATTGTTGCC-TTGGCGCTT---TGC--GCCAGTGGACA---GAAACCCTT---GAATCATTGCCGTCTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGGGGGCATGCCTGTTTCGAGCGTCATTACAACCC---TCAAGCTCCGCTTGGTGTTGGGCTCGCCC--T-------CTAGGGCTTGCCTCAAAATCAGTTGGCGGCCACAGCCCGA-CCTCTAGCGCAGTAC--TACT-CGTCGCTGGAAGGAGAGGCC--TAGGCGCTATAG--ACAACCCCCTTTTTTACAAGGTTGAC Lophodermium_seditiosum -TTTACCA-CAC-TCAGTTGCC-TTGGCGCAC---AGC--GCCAGCGGATT---GAAACTCCT---GAATCATTGCTGTCTGAGT---ACTATTCAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTGTTGGGCTCGCCT--T--CGTCACGAAGGCCTGCCTCAAAATCAGT-GGCGGCCGCCGTCCGA-CCTTCAGCGCAGTAA--TGCT-CGTCGCTGGTAGGGAAGGACAGCAGGTGCCGTCAGCACAACCCCCACATACA--AGGTTGAC Meloderma_desmazieresii -TTTACCA-CAC-GTAGTTGCC-TTGGCGCAC---CGC--GCCAGTGGATC---GAAACTCCT---GAATCATTGCCGTGTGAGT---ACTATATAATAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTCCCGGTATTCCGGGGGGCATGCCTGTT-CGAGCGTCATTACAACCC---TCAAGCTCTGCTTGGTGTTGAGCCCGCCC--CG-CTTACCCGGGGCTCGCTTCAAAATCAGT-GGCGGCCGCCGTCCGA-CCTTCAGCGCAGTAA--TGCT-CGTCGCTGGTAGGGAAGGGCAGCAAGGGCCGTCA-TCCAACCCCCACACACACAAGGTTGAC epistomatal_fungus -TCGACCG--CCTCTGGCTCCTAGGAGCTCTTGAGCGCCCGCCGACGGGACCACGAAACTCTTCTTGAAACGA-GTCTTCTGAGCTAAATTATAAATACTTCAAAACTTTCAACAACGGATCTCTTGGTTTTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTT-CGAGCGTCATGTAAAGATATATCAAGCACTGCTTGGCCTTGGGCCTCTCCGCCCCCGTCACAGGGGGCGGGCCCTAAATACGTCGGCGGCGGCCACTGG--CCTCGAGCGTAGTAGATTATTCCGTCTACGAGCGCCCTTGACCGCC--CGCTTCTAGACCCCAAAATATACCCATGACATTGAC ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = '5.8S, ITS 1 and 2 of rDNA') = N: 1-435; CODONPOSSET CodonPositions (CHARACTERS = '5.8S, ITS 1 and 2 of rDNA') = N: 1-435; END; BEGIN TREES; TITLE Tb6148; LINK TAXA = Taxa1; TRANSLATE 1 epistomatal_fungus, 2 Lophodermium_piceae, 3 'Lophodermium nitens BRMC1-7', 4 'Lophodermium nitens BRMC3-3', 5 'Lophodermium nitens NSWL4-3', 6 AF203470, 7 'Lophodermium nitens NS5-3', 8 'Lophodermium nitens NS4-2', 9 Lophodermium_pinastri, 10 Elytroderma_deformans, 11 Lophodermium_seditiosum, 12 Meloderma_desmazieresii, 13 Lophodermium_australe; TREE Fig._1 = [&R] (((((((13,12),11),10),9),((((8,6),7),(5,4)),3)),2),1); END;