#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 11, 2024; 7:52 GMT TreeBASE (cc) 1994-2008 Study reference: Landvik S., Kristiansen K., & Schumacher T. 1999. Pindara: A Miniature Helvella. Mycologia, 91(2): 278-285. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10318] [ The following blocks are input data for analysis step 5766 ] BEGIN TAXA; TITLE TaxaForAnalysisStep5766; DIMENSIONS NTAX=10; TAXLABELS Helvella_aestivalis Helvella_chinensis Helvella_corium Helvella_cupuliformis Helvella_dovrensis Helvella_macropus Helvella_rivularis Helvella_silvicola Helvella_solitaria Pindara_terrestris ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M4953] TITLE Pindara_ITS; LINK TAXA = TaxaForAnalysisStep5766; DIMENSIONS NCHAR=992; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 970 980 990 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Helvella_aestivalis GGATCATTATGGAGTCCCGACCCACCCAG-GAATAATGAAG-----TAAGACCCACCCAGTGCGAGGGGGGCGACATGAGCACATTAGCCGGCCGCCCTCGCGTGGGGGG--CAATCCTGCAAAA-CCCTCACTGCGT-------ACCA------------------A????CCC--GTTG-----------------------------CTTCCCCGGGGCGG-CAGTACA-------------------CCTGCCTGGGT?CCGGGCGCCACGGCG???CCCGGGAGTCACCC--GGGAAGG-TCCCCC------------------------CCCC-AAA------------ACAACCA-----TCCCT-------AGCC----TCCGTCTGAC--AGGCCTC-------------GTGCTCTGACACAAC-CAAGC-------AAAAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGTATT-CCGGGGGGCATGCCTGTTTGAGCGTCTCGTGCGCAA---ACTCT--CACA----CGTTGTTGTGGTGATGGCCGAGGTGG-GATGGCCGCCAATC??----C-ACCCT---GCCGGAAAG--CAAAGG--CGGACGCACCTGTGGCCGGTACGTAGTATGGACTCAG--AATTCCGTGCGGCCCGC-AGC-----------------------------------------TTGAG--CATCCAGCACGGCAAGCCGGAA??CCAAAC????CCCGCA-------------------------------------------------------------------------TTCCT-CAAAT-CAGGTAGGGATACC??????????????????????????????????? Helvella_chinensis -------------------------------------------------------------------------------------------------------------------CCCCCGGGTCCGGGGGT-CTACACTCTAGCGTCGGG------AGCTC-GC--GCG??CGGT?A?CTCGC?T?CGACG--ACTCCCGCCCCCCTACTGCCAAACGGC----------GA-------TTTCCAAA---CCCAACCC----TCTGCGTACAC---ATCCCTGTT?CTTCCC-GGGGAC????CCCCGAGGCTCC-------GAGC---A-ACG----?G------------CCCAACCAACC--------AGAGGCC--CC--CCTCCGTCTGA---AGGCC--AGCGTGATCCACGGAAGAA-GTAAC-GAGCGAGC--AAATAAGAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGCATT-CCGGGGGGCATGCCTGTTCGAGCGTCTCCTGGACGA---ATCCT-GCGCCA-GTGAAGGGCGCGGTCGTGGCGGCGGTGGCGTG-CCCGATAGCGGCGGCC--ACCG???-GCTGGAA----TCCATGG-CGGACG--CCTGCCGCGT-GGCCGAGCGTGATATG------TTTCACTGGACGCTGCTGCGCGGC-------------------GAAGGCTGCCAGCCCAG?C--------------CGTTTGTCGGGCGGGGCAGAGCGAGACATTTGGAACTCCTCGA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Helvella_corium GGATCATTA---CCATCAAATTCACAAAGTGTAACTTGAAAGGCTGTGG------------------GGTAGCTGCCC-ACTGTGGACAGCTCCCAGGTCTGGGGATGGGATGTGGTGGGTTGGTTGCGCAAAGCTTGG-GC-AGTGTCTTCCTGCCTCTCTGTGGGGCGTTCCACTGCCCCCCCACCCCCCCCCCCTCCATCCCCCTCTTCCTCCGTTAAGTCGGCACAATG-------TTTTCCA----AAACACATAGACTCTGCGTACAT---ACCCCTGTTGCTTCCCT---GGGGA-CATCCCTGGGGGAGGTAACTGAGC--------ACAACACACTG--------CCCAACCAAC-----------AGGT-GCC-TCCTCTGTCTGT---AGGCC--AGTGTG--CCAA-GAAACAAGGAAC-AAGCAAG--GAAATAAAAAAAACTTTCAACAACGGATCTCTTGGTTCCCACATTGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCCTGGCATT-CTGGGGGGCATGCCTGTTTGAGCGTCTCCTGGACAACT-ACTCA--CGTGAGTGGAT--GCGTGGTCATGGTGGTGGAGGCGAGCCCC-TAGAGGG-TGGCC-ACCAC---GCTGGAA----TCCATGGGTGGACG--CCTGCCGCAT--GCCGAGCGTGAT--------ATTACACATCATGTCGCTGT------------GGTTG----AGCATGGTGAGGCTGCCAGCCCT---------------------------------------------------------GGTCCCTGTGTTGGGTGGGGAGAGC---------------------AAGACATTAGAAC-TCCT-CAAAT-CAGGTAGGGATACC-??????????????????????????????????? Helvella_cupuliformis ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-AGG------ACATAACA--------------------------TTTGAACACTGTCTGAGTTGCAGTCTGAGTTTTTATTAAC------------AATAATTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAATTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCATTAGCTGCCCTCAA----GCACGGCTTGTGTGTTGGGCTTCC------------GTCCCTGGTAACGGGGAGGCCC------------AAAAG--GCAGTGG-CGGCA---CCATGTCTGGTCCTCGAGCGT-AT----------------------------------------GGGGCTTTGTCACCCGCTCCCGTAGGTCCAG-CT--GGCAGCTAGCCTCG-CAACCAAT-CTTTTTAACCAGGTTGACCTCG???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Helvella_dovrensis GGATCATTA-------CAAATCCAC---------------------------------GCCGTGGC---TAGC------------------CCCTCGGCGGATGGGGGGCGTGCCGGCCCATTGGCCAATCGCGCGCCCGACCCCC-CCAAACTC-----TCTGCGT-----ACACATCCCCGTTGCTTCCCC--GGGCAGGCGT-CACGCT--CCCGGGGGAGGACACACCGACAGCACACGATGCCGGCAAACA---GG--CCC--GTCCA----ACCC------------------------TCCCC------------------------------------------ACTCAAT-CCACC--TGTCC-GAAGCCAGC--ACGGCCGTGGGA---AGGAGG-AGCGAG--CTAGGGACGGAGAGAATGAAAGAAGAAGAACGTAAAGAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGCATT-CCGGGGGGCATGCCTGTTCGAGCGTCTCTGGAAAGTAG-ACTCACGCGACG--AAACGCGTGGTGGTGACGGCGGCGGCGG-TCCCTGTTGCAGGGGAGGCC-ACCCCG--GC-GGAA----ACCATGGGCGGACG--ACTGCCGCGT-CGCAGAGCGTGAT--------AATTCGCTATCGCCTCGAGC--GCGGA---CCGGTTG----------CCAGCCCTCGCAAGGCGCCCGCCAAGCTGCAGAGTGTGACGGTCT-CGCCCTCGCCT-CGAGC?CGGCAAGGCTGCCGACCCTGGCCCACCGCCAG-CTCCGG---CCGGGTGCCAGGAG-AAGACATTGGAACT-CCT-CGAAT-CAGGTAGGGATACC??????????????????????????????????? Helvella_macropus ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCGCTGGCTTCGGCATGT--GA---GCGCCGT-------CAGAG---------------CCATCAATTCTGCCTATCC---------------------------------------------------AGTATTA-TCAG-AAACAA-AAAACATA-------ATAGTAAA--CAACTTTCAACAACGGATCTCTTGGTTCCAGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATT-CCGGGGGGCATGCCTGTTCGAGCGTCATTA-CACCCCTCAA----GCGTA----GCTTGG--TATTGGGTT----------CTGCCCCCC--GCGGCGTGCC------------GAAAAG---CAGTGG-CGGTCCGGTGTGACTTTA-AGCGCAG-----TA-------AATCTTCCCCGCTTT--------------------------------------------------GAAAGTTCGCC-CC-GT--GGCTTG-CCAGACAACCCCATTTATTTCAATGATTGACCT?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Helvella_rivularis ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TTTTT------AACAGGAGAGAACAT?TGCACG------CCTCGCAATCCATTT---GAAAACCACACTG-CACTTCAGAGGGGGA--GCCTCTCTTGG--CCTCTCCTTCTTTC-ATCACTACAAACAC---------------------TTTGAA---------AGTTTT--TGTATTTGTTGGTTAACTAT-------AATGTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATT-CCGAGGAGCATGCCTGTTTGAGTGTC--GTGTAATTCTCAATCT-CAACTTTTTTTGTTGTGGATTGGATTTGGGAGCTTGTCGTGTCTCTTTGCTATAAG------------TGAAAGA----------------GGGTTAGACTCTCCTTG----------------AATGCATTAGCTCGGTCACGTAGGTTTGCCCGACGGTTCACGTGTG????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Helvella_silvicola GGATCATTAC--CAATCAGTATCACAAAGTGTAACTTGAAGG----------------GCCGTGGAAGGTAGC---CGCCTACTTTGCCAGGCCCCCGGAGTTGGGGGTGGG--------------TTGCGC--AG-GCTCAA-GCGGGTGTTCCTGCCTCCTCAGCA--CCACGTTCTGTCCCCCGTCACCCC-TCCC-------------TTAGGTCGCGAGGCCAC----------TTCCT-A-----AAACACAAGGACTCTGAGTACAT---ACCCCTGTTGCTTCCCC--GGGAAA--TCCC-AGGGAGGT-CTGAGC-CGATT------ACACCGCGCG---------CCAAACTACC-----------GGC-GCC-ATCTCCGTCTGA---AGGCC--AGCGCG--CCAATGAAAGAAGGAAC-GAGC--GAGGAAAT-AAAAAAACTTTCAACAACGGATCTCTTGTTTCCTGCATCGATGAAGAACTCAGTGAAATGCCATAAGTAATCTGAATTACAGAATTCAGTGAATCATCAAATCTTTGAAGGCACTTTGCGCCCGCTGGCATT-CCGGGGGGCATGCCTGTTTGAGCGTCTCCTGGACGACT-ACTCA--CACCA--GCAGATGCGTGGTCATGGTGGCAGAGGCG--GGCC-CAGAGAGGCAGCC-GCCAT---GCTAGAA----CACATGG-CAGACG--CCTGCCGCATG-ACCGAGTGTGAT--------ATCACACATCATGTCGCCGG---------------------AGTA-----------------------------------------------------GAGTGCGGCAAG-CTGCCAGCCCTGGCCCCTGTGTTGGGCAGGAAGAGC---------------------GAGACATTGGAAC-TCCT-CGAAT-CAGGTAGGGATACCCGCTGAACTT-AAGCATATC-AAT-AAGCGGAGGA Helvella_solitaria -------------------------------------------------------------------------------------------GCT-CCCTCGCCGGC?GGG---AAGC---CACTTGCCCTCCCGGCGT-TAACCGAAACCACCCTC-ACCCTGCGTACC-TTCCCACGTT------------------------------CTTCCCCGGGGC----ACGT------GCCTGCCCC?GC?GCCCTCCCCCTCCCCCCCGGAGAGGGCGGTC?CGG-GAGACTCCC--GGGAAGG-TCCCGAGCG---------------------------------------------AAACAC---GGCGG---------------------------AGACCCCAGTATGACGGCAGGTGCCGACCAACAAAGCAAGC-GAAATGAAAGAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGCATT-CCGGGGGGCATGCCTGTTCG?ACGTCTCATCGACGC---ACTCA----CA-GTG----GCTGTGGTCATGGCGGCGGTGGCGGG--CCGCAAGGTGCTGCC--ACCCC---GCTGGAA----TTCATAG-CGGACG--CCTGCAGCGT-GGCCGAGCGTGATAGGACACAAATTCG-----CCCGC-------------TC-------------GCCAGGACGCCAGTCCGGC??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Pindara_terrestris GGATCATTA--------CAGAGTTCAT--------------------------------------------GCCCTTCGGGTAGACCTCCACCCTTGCATACCTTACCTTTGTCGCTTTGGCGGCCCGCTCACCTTGTGTGAGCCACTGGTCTTGGCCGGTGCGTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCGTC----GA-AGG------TTATCAAC----------------TCTATA-------------------ATTTATG-TC-GTCTG-AAG-TAACTATAAA----ATAG---TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGGATCTTTGAACGCACATTGCGCCCCCTGGCATT-CCGGGGGGCATGCCTGTTCGAGCGTCATTAACACCACTCAA----GCTCAGCTTGGTATTGGGTCACGCCAGAAATGGTGA--ACCTCAAACTCAGTGGCGGCACC-------GT-----------TGGGC-------------------CCCGAG-CGTAGTA----AATATCT--CGCT-----GAGG--GTTCC--TCCGGTT--------------------------------------------------------------GGCGACCA-ACAACCCAATTTTCTAAGGTTGA-----------------------------------------------------CCT-CGGAA-CAGGTAGGAATACCCGCTGAACTT-AAGCATATC-AAT-AAGCGGAGGA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Pindara_ITS) = N: 1-992; CODONPOSSET CodonPositions (CHARACTERS = Pindara_ITS) = N: 1-992; END; [ The following blocks are output data for analysis step 5766 ] BEGIN TREES; TITLE Pindara_ITS; LINK TAXA = TaxaForAnalysisStep5766; TREE Unpublished_ITS_tree = [&R] (((((Pindara_terrestris,Helvella_cupuliformis),Helvella_rivularis),Helvella_macropus),(Helvella_aestivalis,Helvella_solitaria)),((Helvella_silvicola,(Helvella_corium,Helvella_chinensis)),Helvella_dovrensis)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6983] END;