#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 September 18, 2025; 7:34 GMT TreeBASE (cc) 1994-2008 Study reference: Santos J., Correia V., & Phillips A. 2010. Primers for mating-type diagnosis in Diaporthe and Phomopsis: their use in teleomorph induction in vitro and biological species definition. Fungal Biology, 114(2-3): 255-270. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10264] [ The following blocks are input data for analysis step 5631 ] BEGIN TAXA; TITLE TaxaForAnalysisStep5631; DIMENSIONS NTAX=39; TAXLABELS Diaporthe_G_type_AB199327 Diaporthe_W_type_AB199325 Diaporthe_alleghaniensis_CBS_495_72 Diaporthe_ambigua_CBS_114015 Diaporthe_ambigua_CBS_123210 Diaporthe_ambigua_CBS_123211 Diaporthe_angelicae_Ph_C032_1 Diaporthe_angelicae_Ph_C068_2 Diaporthe_aspalathi_CBS_117169 Diaporthe_hickoriae_CBS_145_26 Diaporthe_lusitanicae_CBS_123212 Diaporthe_lusitanicae_Ph_C170_1 Diaporthe_melonis_CBS_507_78 Diaporthe_neotheicola_CBS_123209 Diaporthe_neotheicola_Di_C004_6 Diaporthe_neotheicola_Ph_C182_1 Diaporthe_neotheicola_Ph_C195_1 Diaporthe_sp_Di_C005_1 Diaporthe_sp_Di_C005_2 Diaporthe_sp_Di_C005_8 Diaporthe_sp_Di_C007 Diaporthe_stewartii_CBS_193_36 Diaporthe_viticola_111 Diaporthe_viticola_CBS_113201 Diaporthe_viticola_Di_C006_2 Phomopsis_amygdali_11A Phomopsis_amygdali_16A Phomopsis_cotoneastri_CBS_439_82 Phomopsis_cotoneastri_Di_C005_5 Phomopsis_cotoneastri_Di_C005_6 Phomopsis_dauci_CBS_315_49 Phomopsis_phoenicicola_CBS_161_64 Phomopsis_sp_Ph_AC002 Phomopsis_sp_Ph_AC003 Phomopsis_sp_Ph_C169_1 Phomopsis_sp_Ph_C174_1 Phomopsis_sp_Ph_C189_1 Phomopsis_sp_Ph_C194_1 Phomopsis_viticola_114 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M4835] TITLE 'MAT 1-2-1'; LINK TAXA = TaxaForAnalysisStep5631; DIMENSIONS NCHAR=187; 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 ] [ . . . . . . . . . . . . . . . . . . ] Diaporthe_G_type_AB199327 ATTTACCGCAGCGAGAGACACCAGAGCGTGAAGGAGGCACACCCAGAGGCCAAGAACAACGACATCTCCAAGATCCTCGGCCGACAGTGGCAACAGGAGCCTGAGGAAGTTCGAGATGCGTACAAGAAGAAGTCTGAGGACATCAAGCAGGAGTTCATGCGCGTCTATCCCGACTACAAGTACAAAC Diaporthe_W_type_AB199325 ATCTACCGCACCGAGCGACACCAAACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_alleghaniensis_CBS_495_72 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_ambigua_CBS_114015 GTCTACCGCACCGAGCGACACCCGACTGTCAAGGAGGCAAACCCAAATGCCAAGAACAACGAAATCTCCAAGATCCTGGGCCGACAGTGGCAGATGGAGCCGGTGGAAGTTCGCAACGAGTACAAGAAGAAGTCTGAGGACATCAAGGAGGAATTCATGCGCCTCTACCCCAACTACAAGTACCAGC Diaporthe_ambigua_CBS_123210 GTCTACCGCACCGAGCGACACCCGACTGTCAAGGAGGCAAACCCAAATGCCAAGAACAACGAAATCTCCAAGATCCTGGGCCGACAGTGGCAGATGGAGCCGGTGGAAGTTCGCAACGAGTACAAGAAGAAGTCTGAGGACATCAAGGAGGAATTCATGCGCCTCTACCCCAACTACAAGTACCAGC Diaporthe_ambigua_CBS_123211 GTCTACCGCACCGAGCGACACCCGACTGTCAAGGAGGCAAACCCAAATGCCAAGAACAACGAAATCTCCAAGATCCTGGGCCGACAGTGGCAGATGGAGCCGGTGGAAGTTCGCAACGAGTACAAGAAGAAGTCTGAGGACATCAAGGAGGAATTCATGCGCCTCTACCCCAACTACAAGTACCAGC Diaporthe_angelicae_Ph_C032_1 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGAACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCAGCAGTGGCAGCTTGAGTCAGTGGAGGTTCGCGACGAGTACAAGAAGAAGTCTGACGCCATCAAGGAGGAGTTCATGCGCATCTACCCCGACTACAAGTACCAGC Diaporthe_angelicae_Ph_C068_2 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGAACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCAGCAGTGGCAGCTTGAGTCAGTGGAGGTTCGCGACGAGTACAAGAAGAAGTCTGACGCCATCAAGGAGGAGTTCATGCGCATCTACCCCGACTACAAGTACCAGC Diaporthe_aspalathi_CBS_117169 ATCTACCGCACCGAGAGACACCAGACCGTCAAGGACGCAAACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCAAACAGTGGCAGATGGAGCCAGATGAGGTTCGTGATGCCTACAAGAAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCGTCTACCCCGAGTACAAGTACCAGC Diaporthe_hickoriae_CBS_145_26 ATCTACCGCACCGAGAGGCACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCGACAGTGGCAGATGGAGCCAGACGAGGTTCGCGACGAGTACAAGAAGAAGTCCGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_lusitanicae_CBS_123212 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGGACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCAGCAGTGGCAGCTTGAGCCAGTGGAGGTTCGCGACGAGTACAAGAAGAAGTCTGACGCCATCAAGGAGGAATTCATGCGCCTCTACCCCGACTACAAGTACCAGC Diaporthe_lusitanicae_Ph_C170_1 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGGACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCAGCAGTGGCAGCTTGAGCCAGTGGAGGTTCGCGACGAGTACAAGAAGAAGTCTGACGCCATCAAGGAGGAATTCATGCGCCTCTACCCCGACTACAAGTACCAGC Diaporthe_melonis_CBS_507_78 ATCTACCGTACCGAGCGCCATCAGAGCGTCAAGGACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCGCCAGTGGCAGCTGGAGCCAGATGTCGTTCGCGACGAGTACAAGAAGAAGTCTGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_neotheicola_CBS_123209 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAATGACATCTCCAAGATCCTTGGCCGACAGTGGCAGATGGAGCCAGACGAGGTTCGCGACGAGTACAAGAAGAAATCCGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_neotheicola_Di_C004_6 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAATGACATCTCCAAGATCCTTGGCCGACAGTGGCAGATGGAGCCAGACGAGGTTCGCGACGAGTACAAGAAGAAATCCGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_neotheicola_Ph_C182_1 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAATGACATCTCCAAGATCCTTGGCCGACAGTGGCAGATGGAGCCAGACGAGGTTCGCGACGAGTACAAGAAGAAATCCGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_neotheicola_Ph_C195_1 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAATGACATCTCCAAGATCCTTGGCCGACAGTGGCAGATGGAGCCAGACGAGGTTCGCGACGAGTACAAGAAGAAATCCGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_sp_Di_C005_1 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_sp_Di_C005_2 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_sp_Di_C005_8 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_sp_Di_C007 ATCTACCGCACCGAGCGTCACCAGACTGTCAAGGACGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATACTTGGCCGCCAGTGGCAGCTGGAGTCAGACGACGTTCGCGACGAGTACAAGAAGAAGTCTGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Diaporthe_stewartii_CBS_193_36 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGAACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCAGCAGTGGCAGCTTGAGTCAGTGGAGGTTCGCGACGAGTACAAGAAGAAGTCTGACGCCATCAAGGAGGAGTTCATGCGCATCTACCCCGACTACAAGTACCAGC Diaporthe_viticola_111 ATCTATCGCAGTGAGCGACACCAGAGTGTGAAGGAGGCGTACCCAGATGCCAAGAACAACGACATCTCCAAGATTCTCGGCAAACAGTGGCAGGGTGAGCCCGACGACGTCCGCATTAGGTACAAGCAGAAGTCTGAGGAGATCAAGGAGGAGTTCATGCGCCTCTACCCCGACTACAAGTACAAGC Diaporthe_viticola_CBS_113201 ATCTATCGCAGTGAGCGACACCAGAGTGTGAAGGAGGCGTACCCAGATGCCAAGAACAACGACATCTCCAAGATTCTCGGCAAACAGTGGCAGGGTGAGCCCGACGACGTCCGCATTAGGTACAAGCAGAAGTCTGAGGAGATCAAGGAGGAGTTCATGCGCCTCTACCCCGACTACAAGTACAAGC Diaporthe_viticola_Di_C006_2 ATCTATCGCAGTGAGCGACACCAGAGTGTGAAGGAGGCGTACCCAGATGCCAAGAACAACGACATCTCCAAGATTCTCGGCAAACAGTGGCAGGGTGAGCCCGACGACGTCCGCATTAGGTACAAGCAGAAGTCTGAGGAGATCAAGGAGGAGTTCATGCGCCTCTACCCCGACTACAAGTACAAGC Phomopsis_amygdali_11A ATTTACCGCAGCGAGAGACACCAGAGCGTGAAGGAGGCACACCCAGAGGCCAAGAACAACGACATCTCCAAGATCCTCGGCCGACAGTGGCAACAGGAGCCTGAGGAAGTTCGAGATGCGTACAAGAAGAAGTCTGAGGACATCAAGCAGGAGTTCATGCGCGTCTATCCCGACTACAAGTACAAAC Phomopsis_amygdali_16A ATTTACCGCAGCGAGAGACACCAGAGCGTGAAGGAGGCACACCCAGAGGCCAAGAACAACGACATCTCCAAGATCCTCGGCCGACAGTGGCAACAGGAGCCTGAGGAAGTTCGAGATGCGTACAAGAAGAAGTCTGAGGACATCAAGCAGGAGTTCATGCGCGTCTATCCCGACTACAAGTACAAAC Phomopsis_cotoneastri_CBS_439_82 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_cotoneastri_Di_C005_5 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_cotoneastri_Di_C005_6 ATCTACCGCACCGAGCGACACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATTCTTGGCCGACAGTGGCAGGCGGAGCCGGATGAAGTTCGCGACGTGTACAAGCAGAAGTCTGAGGCCATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_dauci_CBS_315_49 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGAACGCACACCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCCAGCAGTGGCAGCTTGAGTCAGTGGAGGTTCGCGACGAGTACAAGAAGAAGTCTGACGCCATCAAGGAGGAGTTCATGCGCATCTACCCCGACTACAAGTACCAGC Phomopsis_phoenicicola_CBS_161_64 ATCTACCGCACCGAGAGACACCAGACTGTCAAGGAGGCGAATCCAGATGCCAAGAACAACGACATCTCCAAGATCCTTGGCAAACAGTGGCAGGCGGAGCCGGAGGAGGTTCGCGACATTTACAAGCAGAAGTCCGAGGACATCAAGAAGGAATTCATGCGCATCTACCCTGACTACAAGTACCAGC Phomopsis_sp_Ph_AC002 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAATGACATCTCCAAGATCCTTGGCCGCCAGTGGCAGATGGAGTCAGATGAAGTTCGCGACGAGTACAAGAAGAAGTCTGACGACATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_sp_Ph_AC003 ATCTACCGCACCGAGCGCCACCAGACTGTCAAGGAGGCAAACCCAGATGCCAAGAACAATGACATCTCCAAGATCCTTGGCCGCCAGTGGCAGATGGAGTCAGATGAAGTTCGCGACGAGTACAAGAAGAAGTCTGACGACATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_sp_Ph_C169_1 ATCTATCGCAGTGAGCGACACCAGAGTGTGAAGGAGGCGTACCCAGATGCCAAGAACAACGACATCTCCAAGATTCTCGGCAAACAGTGGCAGGGTGAGCCCGACGACGTCCGCATTAGGTACAAGCAGAAGTCTGAGGAGATCAAGGAGGAGTTCATGCGCCTCTACCCCGACTACAAGTACAAGC Phomopsis_sp_Ph_C174_1 ATCTACCGCACCGAGCGTCACCAGACTGTCAAGGACGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATACTTGGCCGCCAGTGGCAGCTGGAGTCAGACGACGTTCGCGACGAGTACAAGAAGAAGTCTGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_sp_Ph_C189_1 ATCTACCGCACCGAGCGTCACCAGACTGTCAAGGACGCAAACCCAGATGCCAAGAATAACGACATCTCCAAGATACTTGGCCGCCAGTGGCAGCTGGAGTCAGACGACGTTCGCGACGAGTACAAGAAGAAGTCTGACGACATCAAGGAGGAATTCATGCGCCTCTACCCTGACTACAAGTACCAGC Phomopsis_sp_Ph_C194_1 ATTTACCGCACCGAGCGCCACCAGACTGTCAAGGACGCCCACCCCGATGCCAAGAACAACGACATCTCCAAGATCCTTGGGCAGCAGTGGCAGCTTGAGCCAGTGGAGGTTCGCGACGAGTACAAGAAAAAGTCTGACGCGATCAAGGAAGAATTCATGCGCCTCTACCCCGACTACAAGTACCAGC Phomopsis_viticola_114 ATCTACCGCACCGAGAGACACCAGACTGTCAAAGAGGCAAACCCAGATGCCAAGAACAACGACATCTCCAAGATTCTTGGTCGACAGTGGCAGATGGAGCCGGAGGAAGTTCGCGACGCGTACAAGAAGAAGTCTGAGGACATCAAGGAGGAGTTCATGCGCCTCTACCCTGACTACAAGTATCAGC ; END; BEGIN CODONS; CODONPOSSET CodonPositions (CHARACTERS = 'MAT 1-2-1') = N: 1-187; CODONPOSSET * CodonPositions (CHARACTERS = 'MAT 1-2-1') = N: 1-187; END; [ The following blocks are output data for analysis step 5631 ] BEGIN TREES; TITLE Tb11290; LINK TAXA = TaxaForAnalysisStep5631; TREE Fig._4 = [&R] ((((((((Diaporthe_angelicae_Ph_C032_1,Diaporthe_stewartii_CBS_193_36,Phomopsis_dauci_CBS_315_49,Diaporthe_angelicae_Ph_C068_2),((Diaporthe_lusitanicae_Ph_C170_1,Diaporthe_lusitanicae_CBS_123212),Phomopsis_sp_Ph_C194_1)),Diaporthe_melonis_CBS_507_78),(Phomopsis_sp_Ph_C174_1,Diaporthe_sp_Di_C007,Phomopsis_sp_Ph_C189_1)),(Phomopsis_sp_Ph_AC002,Phomopsis_sp_Ph_AC003)),(Diaporthe_hickoriae_CBS_145_26,(Diaporthe_neotheicola_Di_C004_6,Diaporthe_neotheicola_CBS_123209,Diaporthe_neotheicola_Ph_C182_1,Diaporthe_neotheicola_Ph_C195_1))),(Diaporthe_ambigua_CBS_123211,Diaporthe_ambigua_CBS_123210,Diaporthe_ambigua_CBS_114015)),(Phomopsis_viticola_114,(Phomopsis_phoenicicola_CBS_161_64,(Diaporthe_W_type_AB199325,(Phomopsis_cotoneastri_Di_C005_5,Diaporthe_sp_Di_C005_1,Diaporthe_sp_Di_C005_2,Phomopsis_cotoneastri_Di_C005_6,Diaporthe_sp_Di_C005_8,Phomopsis_cotoneastri_CBS_439_82,Diaporthe_alleghaniensis_CBS_495_72)))),(Diaporthe_aspalathi_CBS_117169,((Phomopsis_amygdali_11A,Phomopsis_amygdali_16A,Diaporthe_G_type_AB199327),(Diaporthe_viticola_CBS_113201,Phomopsis_sp_Ph_C169_1,Diaporthe_viticola_111,Diaporthe_viticola_Di_C006_2)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6938] END;