#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 April 26, 2024; 7:03 GMT TreeBASE (cc) 1994-2008 Study reference: Whitlock B., & Baum D. 1999. Phylogenetic relationships of Theobroma and Herrania based on sequences of the nuclear gene vicilin. Systematic Botany, 24(2): 128-138. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S412] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=30; TAXLABELS Abroma_augusta Guazuma_ulmifolia_1 Guazuma_ulmifolia_2 Herrania_cuatrecasana Herrania_kanukuensis Herrania_nitida Herrania_nycterodendron Herrania_purpurea_1 Herrania_purpurea_2 Herrania_umbratica Theobroma_angustifolium Theobroma_bicolor_A Theobroma_bicolor_B Theobroma_cacao_A Theobroma_cacao_B1 Theobroma_cacao_B2 Theobroma_cacao_C Theobroma_chocoense_1 Theobroma_chocoense_2 Theobroma_gileri_1 Theobroma_gileri_2 Theobroma_grandiflorum_1 Theobroma_grandiflorum_2 Theobroma_mammosum Theobroma_microcarpum_1 Theobroma_microcarpum_2 Theobroma_simiarum Theobroma_speciosum Theobroma_velutinum taxon_30 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2094] TITLE vicilin_gene; LINK TAXA = Taxa1; DIMENSIONS NCHAR=1220; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX Abroma_augusta Guazuma_ulmifolia_1 Guazuma_ulmifolia_2 Herrania_cuatrecasana Herrania_kanukuensis Herrania_nitida Herrania_nycterodendron Herrania_purpurea_1 Herrania_purpurea_2 Herrania_umbratica Theobroma_angustifolium Theobroma_bicolor_A Theobroma_bicolor_B Theobroma_cacao_A Theobroma_cacao_B1 Theobroma_cacao_B2 Theobroma_cacao_C Theobroma_chocoense_1 Theobroma_chocoense_2 Theobroma_gileri_1 Theobroma_gileri_2 Theobroma_grandiflorum_1 Theobroma_grandiflorum_2 Theobroma_mammosum Theobroma_microcarpum_1 Theobroma_microcarpum_2 Theobroma_simiarum Theobroma_speciosum Theobroma_velutinum taxon_30 ; END; BEGIN SETS; CHARSET exon2 (CHARACTERS = vicilin_gene) = 259-434; CHARSET INDELS (CHARACTERS = vicilin_gene) = ; CHARSET exon1 (CHARACTERS = vicilin_gene) = 1-158; CHARSET exon5 (CHARACTERS = vicilin_gene) = 1203-1220; CHARSET exon4 (CHARACTERS = vicilin_gene) = 787-1074; CHARSET exon (CHARACTERS = vicilin_gene) = 1-158 259-434 584-664 787-1074 1203-1220; CHARSET exon3 (CHARACTERS = vicilin_gene) = 584-664; CHARSET intron (CHARACTERS = vicilin_gene) = 159-258 435-583 665-786 1075-1202; END; BEGIN CODONS; CODONPOSSET * UNTITLED (CHARACTERS = vicilin_gene) = N: 159-258 435-583 665-786 1075-1202, 1: 2-160\3 261-434\3 584-664\3 787-1074\3 1203-1218\3, 2: 3-158\3 259-435\3 585-665\3 788-1075\3 1204-1219\3, 3: 1-159\3 260-436\3 586-666\3 789-1076\3 1205-1220\3; END; BEGIN TREES; TITLE Tb5286; LINK TAXA = Taxa1; TRANSLATE 1 Abroma_augusta, 2 Herrania_kanukuensis, 3 Theobroma_velutinum, 4 Theobroma_angustifolium, 5 Theobroma_mammosum, 6 Theobroma_microcarpum_2, 7 Theobroma_grandiflorum_2, 8 Theobroma_grandiflorum_1, 9 Theobroma_gileri_2, 10 Theobroma_gileri_1, 11 Theobroma_chocoense_1, 12 Theobroma_bicolor_B, 13 Theobroma_bicolor_A, 14 Theobroma_cacao_B2, 15 Theobroma_cacao_B1, 16 Theobroma_cacao_C, 17 Theobroma_cacao_A, 18 Herrania_purpurea_2, 19 Herrania_purpurea_1, 20 Herrania_nycterodendron, 21 Herrania_cuatrecasana, 22 Herrania_umbratica, 23 Herrania_nitida, 24 Theobroma_microcarpum_1, 25 Theobroma_speciosum, 26 Guazuma_ulmifolia_2, 27 Guazuma_ulmifolia_1, 28 Theobroma_chocoense_2, 29 Theobroma_simiarum, 30 taxon_30; TREE Fig._3 = [&R] (1,(Rulingia_madagascariensis,((((((((29,(28,11)Theobroma_chocoense),(5,4)),(8,7)Theobroma_grandiflorum),((24,6)Theobroma_microcarpum,(10,9)Theobroma_gileri)),(17,16,(15,14))Theobroma_cacao),((25,3),(13,12)Theobroma_bicolor)),((23,(21,20),2),(22,(19,18)Herrania_purpurea))),(27,26)Guazuma_ulmifolia))); END;