#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 December 09, 2025; 20:11 GMT TreeBASE (cc) 1994-2008 Study reference: Vaghefi N., Kikkert J.R., Hay F.S., Carver G.D., Koenick L.B., Bolton M.D., Hanson L., Secor G., & Pethybridge S.J. 2017. Cryptic diversity, pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris. IMA Fungus, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S21453] [ The following blocks are input data for analysis step 21474 ] BEGIN TAXA; TITLE TaxaForAnalysisStep21474; DIMENSIONS NTAX=27; TAXLABELS Cercospora_apii_CBS_116455_CPC_11556 Cercospora_apii_Haplotype_4 Cercospora_beticola_CBS_116456_CPC_11557 Cercospora_beticola_Haplotype_1_1 Cercospora_beticola_Haplotype_1_2 Cercospora_beticola_Haplotype_2_1 Cercospora_beticola_Haplotype_2_2 Cercospora_beticola_Haplotype_3 Cercospora_beticola_Haplotype_5 Cercospora_beticola_Haplotype_7 Cercospora_beticola_Haplotype_8 Cercospora_cf_flagellaris_Haplotype_10 Cercospora_cf_flagellaris_Haplotype_11 Cercospora_cf_flagellaris_Haplotype_12_1 Cercospora_cf_flagellaris_Haplotype_12_2 Cercospora_cf_flagellaris_Haplotype_13 Cercospora_cf_flagellaris_Haplotype_14 Cercospora_cf_flagellaris_Haplotype_15 Cercospora_cf_flagellaris_Haplotype_16 Cercospora_cf_flagellaris_Haplotype_17 Cercospora_cf_flagellaris_Haplotype_18 Cercospora_cf_flagellaris_Haplotype_19 Cercospora_cf_flagellaris_Haplotype_20 Cercospora_sp_G_Haplotype_6 Cercospora_zeae_maydis_CZM Cercospora_zebrina_Haplotype_21 Cercospora_zebrina_Haplotype_9 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M42347] TITLE Cercospora_Cmd_phylogeny; LINK TAXA = TaxaForAnalysisStep21474; DIMENSIONS NCHAR=280; 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . .] Cercospora_apii_CBS_116455_CPC_11556 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGAGAGCACCACAGGACAAGGACGGCGATGGTATGAAGTGCGACCACCCTCTGCAACTGCGCTGAACTAATCTCAACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAATGAGGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_apii_Haplotype_4 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGAGAGCACCACAGGACAAGGACGGCGATGGTATGAAGTGCGACCACCCTCTGCAACTGCGCTGAACTAATCTCAACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAATGAGGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_CBS_116456_CPC_11557 CCTTCTCTCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_1_1 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_1_2 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_2_1 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_2_2 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_3 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_5 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_7 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_beticola_Haplotype_8 CCTTCTCCCTCTTCGTACGTACAGTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCAACACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAACTAACCTCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_10 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGATAGCACCGCAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_11 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_12_1 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_12_2 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_13 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_14 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_15 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_16 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_17 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_18 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_19 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_cf_flagellaris_Haplotype_20 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCCTCTGCGAATGTACTGAATTAACCTCGACCGAAGGACAAATCACTACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTTCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACTATCGATTTCCCCGAATTCCTCAC Cercospora_sp_G_Haplotype_6 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCGTCACAGGACAAGGACGGCGATGGTATGATGTGCGCCCACCTTCTGCGACGGCACTGAACTGACCTCAACCAAAGGACAAATCACCACCAAGGAGCTCGGCACCGTCATGCGCTCACTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGATATGATCAACGAGGTCGATGCCGACAACAACGGCACAATCGATTTCCCCGAATTTCTCAC Cercospora_zeae_maydis_CZM CCTTCTCCCTCTTCGTACGTACACCTTTGCGGAACAACCAGGCAGCCGCAGCCCCGAGCTAACCGCGGCACCACAGGACAAGGACGGCGATGGTACGATGCGGGCGCGGTCTTTGCGACTCAACTGAGCTAACCTCATACCAAGGACAAATCACCACCAAGGAGCTCGGCACCGTCATGCGCTCCCTCGGTCAGAACCCCAGCGAGTCCGAGCTGCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACGATCGATTTCCCCGAATTCCTCAC Cercospora_zebrina_Haplotype_21 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGACGTTCGCCCGCCCTCTGCGACTGTACTGAACTAACATCGACCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTGCAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC Cercospora_zebrina_Haplotype_9 CCTTCTCCCTCTTCGTACGTACACTTTTCTGAAACAATCAGGCAGCCGCGAGGCAGAGCTAACGACAGCACCACAGGACAAGGACGGCGATGGTATGACGTTCGCCCGCCCTCTGCGACTGTACTGAACTAACATCGGCCGAAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCAGCGAGTCTGAGCTACAGGACATGATCAACGAGGTCGACGCCGACAACAACGGCACAATCGATTTCCCCGAATTCCTCAC ; END; [ The following blocks are output data for analysis step 21474 ] BEGIN TREES; TITLE 'Cercospora Fig4C_CAL_allhaps'; LINK TAXA = TaxaForAnalysisStep21474; TREE Fig._4C = [&R] ((((Cercospora_apii_CBS_116455_CPC_11556:0.00212512270191759,Cercospora_apii_Haplotype_4:0.00212512270191759):0.04141409127809109,(((Cercospora_beticola_CBS_116456_CPC_11557:0.008530218365656957,((((Cercospora_beticola_Haplotype_1_1:0.005668661757307594,Cercospora_beticola_Haplotype_1_2:0.005668661757307594):0.0014236744418279065,Cercospora_beticola_Haplotype_5:0.007092336199135501):9.857353298946946E-4,((Cercospora_beticola_Haplotype_2_2:0.005845724594275863,Cercospora_beticola_Haplotype_3:0.005845724594275863):0.001245174597625972,Cercospora_beticola_Haplotype_8:0.007090899191901835):9.871723371283605E-4):2.1112366091509405E-4,(Cercospora_beticola_Haplotype_2_1:0.005748548702627635,Cercospora_beticola_Haplotype_7:0.005748548702627635):0.0025406464873176547):2.4102317571166737E-4):0.016287287091546983,(Cercospora_cf_flagellaris_Haplotype_10:0.009454924326922897,((((((Cercospora_cf_flagellaris_Haplotype_11:0.006468299326918672,Cercospora_cf_flagellaris_Haplotype_18:0.006468299326918673):0.0012810640025733644,Cercospora_cf_flagellaris_Haplotype_20:0.0077493633294920365):7.893151745096789E-4,(Cercospora_cf_flagellaris_Haplotype_12_1:0.006469758522068412,Cercospora_cf_flagellaris_Haplotype_16:0.006469758522068412):0.0020689199819333044):2.8805599420692225E-4,(Cercospora_cf_flagellaris_Haplotype_15:0.006399850311852928,Cercospora_cf_flagellaris_Haplotype_17:0.006399850311852928):0.00242688418635571):2.1618298301765738E-4,(Cercospora_cf_flagellaris_Haplotype_12_2:0.0066614029920297226,Cercospora_cf_flagellaris_Haplotype_13:0.0066614029920297226):0.0023815144891965734):8.623494091715943E-5,(Cercospora_cf_flagellaris_Haplotype_14:0.006546545249886237,Cercospora_cf_flagellaris_Haplotype_19:0.006546545249886237):0.0025826071722572187):3.2577190477944135E-4):0.015362581130281043):0.006564226335542739,(Cercospora_zebrina_Haplotype_21:0.006910995509206982,Cercospora_zebrina_Haplotype_9:0.006910995509206982):0.0244707362835397):0.012157482187262002):0.004264901153002085,Cercospora_sp_G_Haplotype_6:0.04780411513301076):0.04691939836357868,Cercospora_zeae_maydis_CZM:0.09472351349658945):0.0; [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr106452] END;