#NEXUS [MacClade 4.08 registered to Evolutionary Phytopathology, CBS-KNAW] BEGIN DATA; DIMENSIONS NTAX=25 NCHAR=716; FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=. ; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Pilidiella_sp._GU062317 -----------t---agaggaagtaaaagtcgtaacaaggtctccgttggtgaaccagcggagggatcattgctggaactgtgt-ccgcaaggacacaa-ccccag-a-taccctttgtgaacttattc---ttatatcgttgcctcggcgctgagctgggggcttctttcc------------------------------------aaggagctctcccatagtctctcg-ggacgatggagcaagcccgccggcggcccttctaaac-tctt-gtttttattacgtatctcttctgagttatt--ca-aaacaaaatgaatcaaaactttcaacaacggatctcttggttctggcatcg-atgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcacattgcgcccgctggaattccagcgggcatgcctgttcgagcgtcatttcacccctcaagccttgcttggtgttggagcactaccgtttgtataaagcggtaggctctgaaattcagtggcgggctcgctaagactctgagcg-tagtagtttatcacctcgctttgg-aaggattagcggtgc--tcttgccgtaaaacccc-ccaa------------------------------------------------------------------------ [575] Pilidiella_diplodiella_EU301051 --------------------------------------------------......t...........................-..............-......-.-....................---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccg------------------------------ [578] Pilidiella_diplodiella_AY339324 -------------------------------------------------------------.......................-..............-......-.-....................---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [584] Pilidiella_diplodiella_AY339323 -------------------------------------------------------------.......................-..............-......-.-....................---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [584] Pilidiella_diplodiopsis_AY339333 ---------------------------------------------------------------.....................-..............-......-.-....................---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [582] Pilidiella_diplodiopsis_AY339334 -------------------------------------------------------------.-.....................-..............-......-.-....................---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [583] Pilidiella_diplodiopsis_AY339332 -------------------------------------------------------------.-.....................-..............-......-.-....................---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [583] Schizoparme_straminea_AY339348 -------------------------------------------------------------.-.....................-..............-......-.-....................---........................................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...a...........--.................-....-ttt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [582] Pilidiella_sp._AY339346 ---------------------------------------------------------------.....................-..............-......-.-......a.............---...................t....................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................................................................................................-........................-...............--.................-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [582] Pilidiella_quercicola_AY339344 -------------------------------------------------------------------.................-..............-......-.-....................---........................................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................c...............................................................................-........................-...............--.................-....-ttt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [577] Pilidiella_quercicola_DQ914688 ---------------------------------------------------------------.....................-..............-......-.-....................---........................................------------------------------------...............g........-.....................................-....-..............................--..-...................................................-........................................................................................................................................c...............................................................................-........................-...............--.................-....-ttt---ctgaattttgacctc-------------------------------------------------- [544] Pilidiella_granati_HQ166057 cttggtctcat.tag.....................................................................-..............-......-.-....................---........................................------------------------------------...a...........g........-.....................................-....-......c.......................--..-...................................................-.................................................................................................a...................................................................c..................................................-........................-...............--.................a....-ttt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatcaataagcggagga [658] Pilidiella_granati_AY339342 -------------------------------------------------------------------.................-..............-......t.-....................---........................................------------------------------------...a...........g........-.....................................-....-......c.......................--..-...................................................-..............................................t.....................................g............a...................................................................c..................................................t........................-............a..--................-a....-ttt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [579] Pilidiella_tibouchinae_BECM2 ---------------------------------...........................................-.......-.t....a.......-......-.-....................---........................................------------------------------------...............ct..---------g.................................-....-..............................--..-...................................................-........................................................................................................................................a......................c..t.-cg...t.............................................-........................-...............--.................-....-ctt---ctgaa-tttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [600] Pilidiella_tibouchinae_BECM1 ---------------------------------...........................................-.......-.t....a.......-......-.-....................---........................................------------------------------------...............ct..---------g.................................-....-..............................--..-...................................................-........................................................................................................................................a......................c..t.-cg...t.............................................-........................-...............--.................-....-ctt---ctgaa-tttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [600] Pilidiella_crousii_HQ264189 -------------------------------------------------------------------------------------------------------------.-..................---...................t............c....ct.cgg---------------------------------...ac..........t..tc....t.....................................-....-......c.......................--..-...................................................c.........................................a......t.........c.............................................................................c......................c.....c....t.............................................-.......................ac...............--............-....-....attt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatcaataagcggagga [557] Pilidiella_macrospora_AY339343 -------------------------------------------------------------.-.....................-..............a......-.t..........a.......a.ctt..t.................................gcttc-----------------------------------t..a...........tt.......ta..............................t-....c...--....a........................caa..a....-..............................................-.............................................................................................................................................................t.c.gt..c-....a..............a.............................-........................-............c..--............c...--....tttttttctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [592] Pilidiella_eucalyptorum_EU301037 --------------------------------------------------......t...........................-..............-......-.-......a...........a.c-t..ga...............t.a..............-----------------------------------------..a...c.....g..t...t...-a..ac.c.....................ta.t-....-...--..............................--..-...................................................-........................................................................................t..............?................................a......................cg.---c.c..t.............................................-........a...............-...a...........--................--....-ctt---ctgaattttgacctcggatcaggtaggaatacccg------------------------------ [568] Pilidiella_eucalyptorum_AY339338 -------------------------------------------------------------.-.....................-..............-......-.-......a...........a.c-t..ga...............t.a..............-----------------------------------------..a...c.....g..t...t...-a..ac.c.....................ta.t-....-...--..............................--..-...................................................-........................................................................................t...............................................a......................cg.---c.c..t.............................................-........a...............-...a...........--................--....-ctt---ctgaattttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [573] Coniella_australiensis_AY339313 -------------------------------------------------------------.......................-..............-......-.-......a...........a.c-ta...........................aa..act.-----------------------------------------c..t...t.....ct.-----a.caat.ag.......g.........t.....a.t-....-....-....--...t--.t.a..............--..-....-........t.....................................-.........................c............................................................................................................t..............g........ag-----....a........c..c..................................-..........c.............-...a...........--................--....-cttt--tgaaaaattgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [565] Coniella_fragariae_AY339320 -------------------------------------------------------------.......................-..............-......-.-..................a.c-ta...........................aa..act.-----------------------------------------c..t...t.....ct.-----a.caat.ag.......g.........t.....a.t-....-....-....--....t-.g...tc...........--..-....-..............................................-.........................c............................................................................................................t..............g........ag-----....a........c.....................................-..........c.............-...............--................--....-cttt--tgaaaatttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [566] Coniella_fragariae_AY339319 -------------------------------------------------------------.......................-..............-......-.-..................a.c-ta...........................aa..act.-----------------------------------------c..t...t.....ct.-----a.caat.ag.......g.........t.....a.t-....-....-....--....t-.g...tc...........--..-....-..............................................-.........................c............................................................................................................t..............g........ag-----....a........c.....................................-..........c.............-...............--................--....-cttt--tgaaaatttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [566] Coniella_fragariae_AY339317 -------------------------------------------------------------.-.....................-..............-......-.-..................a.c-ta...........................aa..act.-----------------------------------------c..t...t.....ct.-----a.caat.ag.......g.........t.....a.t-....-....-....--...tt-.....tc...........--..-....-..............................................-.........................c............................................................................................................t..............g........ag-----....a........c.....................................-..........c.............-...............--................--....-cttt--tgaaaatttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [565] Coniella_fragariae_AY339316 -------------------------------------------------------------.-.....................-..............-......-.-..................a.c-ta...........................aa..act.-----------------------------------------c..t...t.....ct.-----a.caat.ag.......g.........t.....a.t-....-....-....--...tt-.....tc...........--..-....-..............................................-.........................c............................................................................................................t..............g........ag-----....a........c.....................................-..........c.............-...............--................--....-cttt--tgaaaatttgacctcggatcaggtaggaatacccgctgaacttaagcatatc------------- [565] Harknessia_eucalypti_AY720745 -------------------------------------------------------------.......................-..t..c..g....c-a.....-.-..................a.c-ac........................cc....gggaacc.tcaacccgttccccctccctcgggaaagcccgcgcgcccccct.ggggtgtgt..ggtgtctctt.ct.......g...............ac.-....-....t.......ga..................t..-at.c....-..............................................-..............................................................................................g.............................a...........a............g........cg-----.c.ca........c.....................................-..........c.............-.t...c.........tt.................-....-cttc--tgaaaatttgacctcggatcaggtagga------------------------------------- [597] ; END; BEGIN CODONS; CODONPOSSET * CodonPositions = N: 1-716; CODESET * UNTITLED = Universal: all ; END; BEGIN SETS; CHARSET ITS = 112-176 209-644; TAXSET outgroups = 25; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ; END; BEGIN TREES; [! >Data file = /Users/e.groenewald/RobertPilidiellaITS.nexus >Heuristic search settings: > Optimality criterion = parsimony > Character-status summary: > 215 characters are excluded > Of the remaining 501 included characters: > All characters are of type 'unord' > All characters have equal weight > 366 characters are constant > 49 variable characters are parsimony-uninformative > Number of (included) parsimony-informative characters = 86 > Gaps are treated as "fifth base" > Starting tree(s) obtained via stepwise addition > Addition sequence: random > Number of replicates = 50 > Starting seed = 134376130 > Number of trees held at each step during stepwise addition = 1 > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 1000 (will not be increased) > Branches collapsed (creating polytomies) if maximum branch length is zero > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 359809 > Score of best tree(s) found = 229 > Number of trees retained = 24 > Time used = 1 sec (CPU time = 0.28 sec) ] TREE * Fig._1 = [&R] ((((((((Pilidiella_sp._GU062317,((Pilidiella_diplodiella_EU301051,Pilidiella_diplodiella_AY339324,Pilidiella_diplodiella_AY339323,Pilidiella_diplodiopsis_AY339333,Pilidiella_diplodiopsis_AY339334,Pilidiella_diplodiopsis_AY339332),Schizoparme_straminea_AY339348),Pilidiella_sp._AY339346,(Pilidiella_quercicola_AY339344,Pilidiella_quercicola_DQ914688)),(Pilidiella_granati_HQ166057,Pilidiella_granati_AY339342)),(Pilidiella_tibouchinae_BECM2,Pilidiella_tibouchinae_BECM1)),Pilidiella_crousii_HQ264189),Pilidiella_macrospora_AY339343),(Pilidiella_eucalyptorum_EU301037,Pilidiella_eucalyptorum_AY339338)),(Coniella_australiensis_AY339313,((Coniella_fragariae_AY339320,Coniella_fragariae_AY339319),(Coniella_fragariae_AY339317,Coniella_fragariae_AY339316)))),Harknessia_eucalypti_AY720745); END; BEGIN 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