#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 18, 2024; 8:34 GMT TreeBASE (cc) 1994-2008 Study reference: Ogawa Y., Suda A., Kusama-eguchi K., Watanabe K., & Tokumasu S. 2005. Intraspecific groups of Umbelopsis ramanniana inferred from nucleotide sequences of nuclear rDNA internal transcribed spacer regions and sporangiospore morphology. Mycoscience, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1427] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=15; TAXLABELS Mucor_hiemalis_f_luteus_AY243951 Umbelopsis_isabellina_YODK039 Umbelopsis_isabellina_YODK041 Umbelopsis_ramanniana_YODK004 Umbelopsis_ramanniana_YODK028 Umbelopsis_ramanniana_YODK036 Umbelopsis_ramanniana_YODK101 Umbelopsis_ramanniana_YODK106 Umbelopsis_ramanniana_YODK119 Umbelopsis_ramanniana_YODK120 Umbelopsis_ramanniana_YODK122 Umbelopsis_ramanniana_YODK126 Umbelopsis_ramanniana_YODK129 Umbelopsis_ramanniana_YODK130 Umbelopsis_ramanniana_YODK170 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1565] TITLE nrDNA_ITS_regions; LINK TAXA = Taxa1; DIMENSIONS NCHAR=602; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Mucor_hiemalis_f_luteus_AY243951 AAGGCTTGGCTTCCGGGTCACGCTCTTCTATAATTTACTGTGAACCTGTATTATTTTCTGGCGTTTGAGAAATGTCCTGCTGGCTATAAGGATAGGCCTGGTAGGAATGTTAATCGAGTCAGAGTCAGGCTTAGGCCTGGTATCCTATTATTATTTACCAAAAGAATTCAGTATTATAATTGTAACATAAGCGTAAAAAACTTA-TAAAAACAACTTTTAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGTAGC-AAAGTGCGATAACTAGTGTGAATTGCATA-TTCAGTGAATCATCGAGTCTTTGAACGC-ATCTTGCGCCTGATGGTATTCCATCAGGCACGCCTGTTTCAGTATCAAAAACACCCCACATTCCAAAC---CTTGCGT--TTGAA-A-TGGACTTGAGAAGTTCCACCTTGG-------TGGATTTCTTTAAATACATTAGGCCTGAACTTTGGTTTTTCTGCCTGA-ACATTTTTTTAATATAAAGGAATGCTCTAGTAAAAA----AGACTTTCTTGGG------------GGCCTCCCAAATAAATCATTCT------------------------TA Umbelopsis_isabellina_YODK039 CCAAAAGAT-AATC---TTTCA--TTCGAAAGA--TCTTT-CC--TTGTGCTGGCTTTGACCGTAT--GTAATTTTG-----GGACTTAAACATGATCCGCCTTACGGT--------GTATCGGTCCCAAAAACAATATATCATCCTT-ATTAAAAACTTACTGAAC----T-AAACAATT---GATTTAA------TAATCTGTTTAAAACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGTACGC-ACATTGCACTCCTTGGTATTCCGAGGAGTATGCCTGTTTCAGTATCATGAGCACTCTCACACC-TAAC---CTTTGGGTTATGTT--GTGGAATTGGGATGCGCCGATTTTACACTAGTCGGCACCCCTAAAATGTAGCTCTTG-GCTGTTT-CCTACTACAGCAGT----TTGGCCTAATA-GTTTTGAC--TTTTGTC-AAATCTTTGGCTACATTTGCTTCTGGAA-ATCAGTCTTGATAATACAGAAAACT-------------------CATT-CA Umbelopsis_isabellina_YODK041 CCAAAAGAT-AATC---TTTCAA-CTCGAAAGA--TCTTTTCCT-TTGTGCTGGCTTTGACCGTAT--GTAATTTTG-----GGACTTAAACATGGTAAGCCTTACGGT--------TTACCGGTCCCAAAAACAATATATCATCCTT-ATGAAAAACTTACTGAACA-ACT-AAACAATG---ATTTTAA------TAATCTGTTTAAAACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCCACATTGCACTCCTTGGTATTCCGAGGAGTATGCCTGTTTCAGTATCATGAGCACTCTCACACC-TAAC---CTTTGGGTTATGTC--GTGGAATTGGGATGCGCCGATTTTT-ACTAGTCGGCACTCC?AAAATGTAGCTCTTG-GCTGTTT-CCTATTACAGCAGT----TTGGCCTAATA-GTTTTGAC--TTTTGTC-AAATCTTTGGCTACATTTGCTTCTGGAA-ATCAGTCTTGATAATACAGAAAACT-------------------CATTTCA Umbelopsis_ramanniana_YODK004 CTGAAGTG--AGTC----TTCA-TCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTTATGTTG-----GGGATTAAACATGGTT----A-GAATTTAT----TTTAGCCGTCCCCAACAATT-ATCTCATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAA---TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAAC---TTTATTGTTGTAAT-AGTGGACTTGGAATGCGCTGGTGTCA-A----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGCGATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTT--GAGGT-GACTTGT-CTCCTCTTCA Umbelopsis_ramanniana_YODK028 CTGAAGTG--AGTC----TTCAATCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTA-----GGGATTAAACATGGTTGGAAAA---TTTTT----TTCAGCCGTCCCTAACAATTTATCTTATCCTTTATAAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAA---TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTACACC---TTTTTTGTTGTAAG-AGTGGACTTGGAATGCGCTGGTGTCA-A----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTT--GAGGTTGAC--G---CCTCTTTCA Umbelopsis_ramanniana_YODK036 CTGAAGTG--AGTC----TTCAATCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTG-----GGGATTAAACATGGTTGAGA--GAAAT-------CTTGGCCGTCCCCAACAAATTATCTTATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAAAA-TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAACATTTTTTTTGTTGTAATTAGTGGACTTGGGATGCGCTGGTGTCAAA----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTTTTGAGGT------TTTACCTCTTTCA Umbelopsis_ramanniana_YODK101 CTGAAGTG--AGTC----TTCAATCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTG-----GGGATTAAACATGGTTGAGA--GAAAT-------CTTGGCCGTCCCCAACAAATTATCTTATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAAAA-TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAACATTTTTTTTGTTGTAAT-AGTGGACTTGGGATGCGCTGGTGTCAAA----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTTTTGAGGT-------TTACCTCTT-CA Umbelopsis_ramanniana_YODK106 CTGAAGTG--AGTC----TTCAATCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTG-----GGGATTAAACATGGTTGAGA--GAAAT-------CTTGGCCGTCCCCAACAAATTATCTTATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAAAA-TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAACATTTTTTTTGTTGTAATTAGTGGACTTGGGATGCGCTGGTGTCAAA----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTTTTGAGGT------TTTACCTCTTTCA Umbelopsis_ramanniana_YODK119 CTGAAGTG--AGTC----TTCAATCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTG-----GGGATTAAACATGGTTGAGA--GAAAT-------CTTGGCCGTCCCCAACAAATTATCTTATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAAAAATAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAACATTTTTTTTGTTGTAATTAGTGGACTTGGGATGCGCTGGTGTCAAA----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTTTTGAGGT------TTTACCTCTTTCA Umbelopsis_ramanniana_YODK120 CTGAAGTG--AGTC----TTCA-TCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTG-----GGGATTAAACATGGTTGAAT-----TTT------TTTAGCCGTCCCCAACAATTTATCTTATCCTTTATAAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAA---TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAAC---TTTTTTGTTGTAAG-AGTGGACTTGGAATGCGCTGGTGTCA-A----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGTATCTGACAGTCTTGATA-TACAGAATTTTT-GAGGTTAAC--G---CCTCTTTCA Umbelopsis_ramanniana_YODK122 CTGAAGTG--AGTC----TTCA-TCATTTGAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTATT-GTAATGTTG-----GGGATTAAACATGGTTGA-------TTTAT----TTCGGCCGTCCCCAACAATTTATCTTATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAAA--TAATCT-TTTAATACAACTTTCAACAACGGATCCCTTGGTTCTCGCATCGATGAAGAACGCAGCCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAAC---TTTTTTGTTGTAAG-AGTGGACTTGGAATGCGCTGGTGTCA-A----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTTT-GAGGTTAAC--G---CTTCTTTCA Umbelopsis_ramanniana_YODK126 CTGAAGTG--AGTC----TTCA-TCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTTATGTTG-----GGGATTAAACATGGTTGAAA-----TTTAT----TTCAGCCGTCTCCAACAATT-ATCTCATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAA---TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAAC---TTTATTGTTGTAAT-AGTGGACTTGGGATGCGCTGGTGTCA-A----TCAGCCCTCCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGTAATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATCACTGGCTTTTTTTACTTAGAATCTGACAGTCTTGATA-TACAGAATTTT--GAGGT-GACTTGT-CTCCTCTTCA Umbelopsis_ramanniana_YODK129 CTGAAGTG--AGTC----TTCA-TCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTTATGTTG-----GGGATTAAACATGGTTGGAA-----TTTAT----TTCAGCCGTCCCCAACAATT-ATCTCATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAA---TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAAC---TTTATTGTTGTAAT-AGTGGACTTGGGATGCGCTGGTGTCA-A----TCAGCCCTCCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGTAATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATCACTGGCTTTTTTTACTTAGAATCTGACAGTCTTGATA-TACAGAATTTT--GAGGT-GACTTGT-CTCCTCTTCA Umbelopsis_ramanniana_YODK130 CTGAAGTG--AGTC----TTCA-TCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTTATGTTG-----GGGATTAAACATGGTTGGAA-----TTTAT----TTCAGCCGTCTCCAACAATT-ATCTCATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAA---TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAAC---TTTATTGTTGTAAT-AGTGGACTTGGAATGCGCTGGTGTCA-A----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGTAATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATCACTGGCTTTTTTTACTTAGAATCTGACAGTCTTGATA-TACAGAATTTT--GAGGT-GACTTGTTCTCCTCTTCA Umbelopsis_ramanniana_YODK170 CTGAAGTG--AGTC----TTCATTCATT-GAAGCTTCTT-CCCA-TTGTGCTGGCTTTGACCGTAT--GTAATGTTG-----GGGATTAAACATGGTTGAGA--GAAAT-------CTTGGCCGTCCCCAACAAATTATCTTATCCTTTATTAAA-TTGAACTGAACTCATT-TTGAGATT---ACATAAAAAAAA-TAATCT-TTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC-GAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGC-ACATTGCACTCTATGGTATTCCGTAGAGTATGCCTGTTTCAGTATCATGAACACCTCACTACTATAACATTTTTTTTGTTGTAATTAGTGGACTTGGGATGCGCTGGTGTCAAA----TCAGCCCTTCTAAAATGGAGTTCTTGCACTGTTGATTTGTTTTAACAGC-ATGTTGGCCTAATAAGTTTCGGCAGTAATGTTGAAATC-CTGGCTTTTTTTGCTTAGAATCTGACAGTCTTGATA-TACAGAATTTTTTGAGGT------TGTACCTCCTTCA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = nrDNA_ITS_regions) = N: 1-602; CODONPOSSET CodonPositions (CHARACTERS = nrDNA_ITS_regions) = N: 1-602; END; BEGIN TREES; TITLE Tb7507; LINK TAXA = Taxa1; TRANSLATE 1 Mucor_hiemalis_f_luteus_AY243951, 2 Umbelopsis_isabellina_YODK039, 3 Umbelopsis_isabellina_YODK041, 4 Umbelopsis_ramanniana_YODK170, 5 Umbelopsis_ramanniana_YODK119, 6 Umbelopsis_ramanniana_YODK106, 7 Umbelopsis_ramanniana_YODK101, 8 Umbelopsis_ramanniana_YODK036, 9 Umbelopsis_ramanniana_YODK122, 10 Umbelopsis_ramanniana_YODK120, 11 Umbelopsis_ramanniana_YODK028, 12 Umbelopsis_ramanniana_YODK130, 13 Umbelopsis_ramanniana_YODK129, 14 Umbelopsis_ramanniana_YODK126, 15 Umbelopsis_ramanniana_YODK004; TREE Fig._1_right = [&R] ((((15,(14,13,12))Umbelopsis_ramanniana_Group_I,(11,10,9)Umbelopsis_ramanniana_Group_II,(8,7,6,5,4)Umbelopsis_ramanniana_Group_III),(3,2)Umbelopsis_isabellina),1); END; BEGIN TREES; TITLE Tb7506; LINK TAXA = Taxa1; TRANSLATE 1 Mucor_hiemalis_f_luteus_AY243951, 2 Umbelopsis_isabellina_YODK039, 3 Umbelopsis_isabellina_YODK041, 4 Umbelopsis_ramanniana_YODK170, 5 Umbelopsis_ramanniana_YODK119, 6 Umbelopsis_ramanniana_YODK106, 7 Umbelopsis_ramanniana_YODK101, 8 Umbelopsis_ramanniana_YODK036, 9 Umbelopsis_ramanniana_YODK122, 10 Umbelopsis_ramanniana_YODK120, 11 Umbelopsis_ramanniana_YODK028, 12 Umbelopsis_ramanniana_YODK130, 13 Umbelopsis_ramanniana_YODK129, 14 Umbelopsis_ramanniana_YODK126, 15 Umbelopsis_ramanniana_YODK004; TREE Fig._1_left = [&R] (15,(((14,13),12)Umbelopsis_ramanniana_Group_I,(((11,10),9)Umbelopsis_ramanniana_Group_II,((8,(7,(6,(5,4))))Umbelopsis_ramanniana_Group_III,((3,2)Umbelopsis_isabellina,1))))); END;