#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 21473 ] BEGIN TAXA; TITLE TaxaForAnalysisStep21473; 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:M42345] TITLE Cercospora_Act_phylogeny; LINK TAXA = TaxaForAnalysisStep21473; DIMENSIONS NCHAR=186; 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 ] [ . . . . . . . . . . . . . . . . . . ] Cercospora_apii_CBS_116455_CPC_11556 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_apii_Haplotype_4 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_CBS_116456_CPC_11557 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_1_1 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_1_2 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_2_1 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_2_2 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_3 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_5 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGTCACCATGGGTATGCGATCCGTA-ATCTCCGCCGCTGCAGAATCAACCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_beticola_Haplotype_7 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATCAGACGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAAATTCCTCCTAACAAGAGCACAGCATCATGATTGGTATG Cercospora_beticola_Haplotype_8 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGTCACCATGGGTATGCGATCCGTA-ATCTCCGCCGCTGCAGAATCAACCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_10 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCACTGCAGAATCGTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_11 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCATCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_12_1 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCATCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_12_2 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCATCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_13 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAAACAGATGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCAACCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_14 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCATCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_15 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAAACAGATGCAAAAGCTGGCAGGAAGGAGGAGCTGACATTGGGACAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCAACCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_16 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCACTGCAGAATCGTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_17 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCACTGCAGAATCGTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_18 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCATCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_19 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCACTGCAGAATCGTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_cf_flagellaris_Haplotype_20 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCACTGCAGAATCGTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_sp_G_Haplotype_6 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACATTGAGATGCAAAAGCTGGCAGGAAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGAATCGTCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_zeae_maydis_CZM GACGATGCGCCACGAGCTGTCTTCCGTAAGTGATGCCACAATCGGGTGC-ACAGCGGGCGGGAAGGAAGAGCTGACACGGGGACAGCGTCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCCAATCTCCGCCGCTGCAGAATGAATCTAACACGAGCGCAGTATCATGATTGGAATG Cercospora_zebrina_Haplotype_21 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATGAGATACAAAAGCTGGCAGGGAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGATTCATCCTAACAAGAGCACAGTATCATGATTGGTATG Cercospora_zebrina_Haplotype_9 GACGATGCGCCACGAGCTGTCTTCCGTAAGTGCTGCCACAATGAGATACAAAAGCTGGCAGGGAGCAGGAGCTGACATTGGGATAGCATCCATCGTCGGACGACCGCGCCACCATGGGTATGCGATCCGCC-ATCTCCGCCGCTGCAGATTCATCCTAACAAGAGCACAGTATCATGATTGGAATG ; END; [ The following blocks are output data for analysis step 21473 ] BEGIN TREES; TITLE 'Cercospora Fig4B_ACT_allhaps'; LINK TAXA = TaxaForAnalysisStep21473; TREE Fig._4B = [&R] ((((((((Cercospora_apii_CBS_116455_CPC_11556:0.010055132834064935,Cercospora_beticola_Haplotype_3:0.010055132834064935):0.003125774957985397,(Cercospora_beticola_CBS_116456_CPC_11557:0.010062339536339933,Cercospora_beticola_Haplotype_2_2:0.010062339536339933):0.0031185682557103994):8.144435816690061E-4,(Cercospora_beticola_Haplotype_1_1:0.010300034433242044,Cercospora_beticola_Haplotype_1_2:0.010300034433242044):0.003695316940477294):2.8914414419320585E-4,(Cercospora_beticola_Haplotype_2_1:0.010206164008332571,Cercospora_apii_Haplotype_4:0.010206164008332571):0.004078331509579973):4.990855719684828E-4,Cercospora_beticola_Haplotype_7:0.014783581089881027):0.03826637573972521,(Cercospora_cf_flagellaris_Haplotype_13:0.0059645638512575636,Cercospora_cf_flagellaris_Haplotype_15:0.0059645638512575636):0.04708539297834867):0.005611537028950515,((((((Cercospora_cf_flagellaris_Haplotype_10:0.004378093280435394,Cercospora_cf_flagellaris_Haplotype_17:0.004378093280435394):0.0016459352585278739,(Cercospora_cf_flagellaris_Haplotype_16:0.005438192049952159,(Cercospora_cf_flagellaris_Haplotype_19:0.004494689119334905,Cercospora_cf_flagellaris_Haplotype_20:0.004494689119334905):9.435029306172531E-4):5.858364890111096E-4):0.005698590865634118,Cercospora_sp_G_Haplotype_6:0.011722619404597387):0.009772071921626735,((Cercospora_cf_flagellaris_Haplotype_11:0.013713268702970766,(Cercospora_cf_flagellaris_Haplotype_12_1:0.01074252554229175,Cercospora_cf_flagellaris_Haplotype_18:0.01074252554229175):0.002970743160679015):0.0018349106774718498,(Cercospora_cf_flagellaris_Haplotype_12_2:0.010903418166327639,Cercospora_cf_flagellaris_Haplotype_14:0.010903418166327639):0.0046447612141149765):0.005946511945781507):0.004336968861757263,(Cercospora_zebrina_Haplotype_21:0.0051858438721308865,Cercospora_zebrina_Haplotype_9:0.0051858438721308865):0.020645816315850496):0.010785245113879603,(Cercospora_beticola_Haplotype_5:0.0036343977684458345,Cercospora_beticola_Haplotype_8:0.0036343977684458345):0.032982507533415154):0.022044588556695763):0.03755952907777371,Cercospora_zeae_maydis_CZM:0.09622102293633046):0.0; [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr106451] END;