#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 21476 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep21476;
        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:M42351]

	TITLE Cercospora_Tef_Phylogeny;
	LINK TAXA = TaxaForAnalysisStep21476;
	DIMENSIONS NCHAR=294;
	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    ]
[                                                     .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .    ]
Cercospora_apii_CBS_116455_CPC_11556         GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCGTTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_apii_Haplotype_4                  GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_CBS_116456_CPC_11557     GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_1_1            GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_1_2            GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_2_1            GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_2_2            GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_3              GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_5              GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_7              GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_beticola_Haplotype_8              GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCATTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTTGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATCTGCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_10       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_11       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATGAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_12_1     GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_12_2     GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_13       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_14       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_15       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_16       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_17       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_18       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_19       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTCGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_cf_flagellaris_Haplotype_20       GAGAAGTTCGAGAAGGTGAGCAACTACCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACATATCTCCACGACCACACTTCGCATCAAGAATAGACTGCTGACAATGGCTCCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_sp_G_Haplotype_6                  GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACGAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAT-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACATTTGCACAACCACACTTCACATCAAGAATAGACTGCTGACGATGGCTTCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_zeae_maydis_CZM                   GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACGCGAACGCACTTCGTCGCGCAAATTTTCGCCGCTTGTCGCTTTTGCGCTGCTGCCCCTCCAAAAACTGGCTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTTTGCGGCTCGCGATGACTTCATCCGCTATGACTCCGCGCCCACGGCCCAACGTATTGGGCATACCGCCAGCACACAACACATGCACCCACACGCCCTTCATGTCGAGGACGGACTGCTGACCATGCACTCTCACAGGAAGCTGCTGAACTCGGCAAGG
Cercospora_zebrina_Haplotype_21              GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCACTTTGTCGCACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACACTTGCACGACCACACTTCACATCGAGAATAGACTGCTGACGATGGCTTCTCACAGGAAGCAGCTGAACTCGGTAAGG
Cercospora_zebrina_Haplotype_9               GAGAAGTTCGAGAAGGTGAGCAACTGCCAGCACACAAATGCACTTTGTCACACAAATTTTCGCCGCTTGTCGCCTCTGCGCTGGTGCCCCTCCAAAA-----CTGGTGGGGTGCGAGAATTTCGGCGCTTTGGGCTCTGCCGCTCGCGATGACTTCATCCGCTATGACTCCTCGCCCACCGCTCAACGCATTGGGCATACCGCCAGCACACCACACACTTGCACGACCACACTTCACATCGAGAATAGACTGCTGACGATGGCTTCTCACAGGAAGCAGCTGAACTCGGTAAGG
;
END;

[ The following blocks are output data for analysis step 21476 ]
BEGIN TREES;
      TITLE 'Cercospora Fig4E_TEF_allhaps';
      LINK TAXA = TaxaForAnalysisStep21476;
      TREE Fig._4E = [&R] ((((Cercospora_apii_CBS_116455_CPC_11556:0.012886677306495868,((Cercospora_beticola_CBS_116456_CPC_11557:0.008799278695784705,Cercospora_beticola_Haplotype_1_2:0.008799278695784705):0.0038181845649183175,((((Cercospora_beticola_Haplotype_1_1:0.00890230922511004,Cercospora_beticola_Haplotype_2_2:0.008902309225110039):0.002654391848876298,(Cercospora_beticola_Haplotype_2_1:0.009029660196297501,Cercospora_apii_Haplotype_4:0.009029660196297501):0.0025270408776888378):6.400177883841337E-4,(Cercospora_beticola_Haplotype_3:0.008808890377527353,Cercospora_beticola_Haplotype_7:0.008808890377527353):0.0033878284848431195):2.724998672874023E-4,(Cercospora_beticola_Haplotype_5:0.00889385003139181,Cercospora_beticola_Haplotype_8:0.00889385003139181):0.0035753686982660654):1.482445310451476E-4):2.6921404579284547E-4):0.016674009155439304,(((((Cercospora_cf_flagellaris_Haplotype_10:0.008901083737935795,Cercospora_cf_flagellaris_Haplotype_17:0.008901083737935795):0.0019244375365862643,Cercospora_cf_flagellaris_Haplotype_15:0.010825521274522059):0.0014349687979891106,((Cercospora_cf_flagellaris_Haplotype_12_1:0.00914681945666085,Cercospora_cf_flagellaris_Haplotype_20:0.00914681945666085):0.002434381946758964,(Cercospora_cf_flagellaris_Haplotype_12_2:0.009112331801066527,Cercospora_cf_flagellaris_Haplotype_18:0.009112331801066527):0.0024688696023532873):6.792886690913554E-4):4.7847048080876427E-4,((Cercospora_cf_flagellaris_Haplotype_13:0.010175250944558054,Cercospora_cf_flagellaris_Haplotype_19:0.010175250944558054):0.0017667738143817419,(Cercospora_cf_flagellaris_Haplotype_14:0.00904144751959802,Cercospora_cf_flagellaris_Haplotype_16:0.00904144751959802):0.0029005772393417752):7.969357943801384E-4):1.7118148277954492E-4,Cercospora_cf_flagellaris_Haplotype_11:0.012910142036099479):0.016650544425835693):0.016915015110123378,((Cercospora_zebrina_Haplotype_21:0.006546672262554894,Cercospora_zebrina_Haplotype_9:0.006546672262554894):0.02064164449518785,Cercospora_sp_G_Haplotype_6:0.027188316757742744):0.019287384814315807):0.09881598356404381,Cercospora_zeae_maydis_CZM:0.14529168513610236):0.0;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr106455]


END;