#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 20, 2025; 9:22 GMT TreeBASE (cc) 1994-2008 Study reference: Steele K., & Vilgalys R. 1994. Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany, 19: 126-142. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S120] [ The following blocks are input data for analysis step 61 ] BEGIN TAXA; TITLE TaxaForAnalysisStep61; DIMENSIONS NTAX=28; TAXLABELS Acanthogilla_gloriosa Allophyllum_giliodes Bonplandia_geminiflora Cantua_buxifolia Cantua_cuzcoensis Cobaea_scandens Collomia_rawsoniana Eriastrum_wilcoxii Gilia_achilleifolia Gilia_capitata Gilia_diegensis Gilia_leptantha Hordeum Ipomopsis_aggregata Lactuca_sativa Leptodacylon_pungens Linanthus_grandiflorus Loeseliastrum_matthewsii Madia_bolanderi Navarretia_divaricata Nicotiana_tabacum Oryza Phlox_diffusa Phlox_gracilis Pisum Polemonium_occidentale Sinapsis Solanum_tuberosum ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2676] TITLE Appendix_1; LINK TAXA = TaxaForAnalysisStep61; DIMENSIONS NCHAR=270; FORMAT DATATYPE=Standard SYMBOLS= "A T C G 0 1" 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . .] Acanthogilla_gloriosa TTAGGGTCCTTTTATTCGGACCGTTACAGGTCACAGGGCCTCCTCTCAGCCCTCCCACTCTGGCCCCGCAAGCTGCAAGTAGGTAGCTATTGGCGGTCCATAGTAATTCCGGCGTCGGAAGACGTTAATGAGCTGCGTCCTCACGTATATCCCTCAGCAAGGTGATTCAGGGGTACACATGTGTACTTACTGAGATTCGGAGACTTGTCCCAAAAGTTTCCGCCGGGGTCAAAAAGGCATATTGTTTGTTATCTATCATGACGATCGGG0 Allophyllum_giliodes TTAGGGTCCGTTTATCCAGACCGTTACAGGTCACAGGGCCTTCTATAAGCCCTCCCACTCTGACCTGGCAAGTTGTAAGTAGGGAGCTGTTAGCGGTCCATCCTGAGTCCGGTGTCGGATCACGTTAATAGGCTGCGTCCTCACGTATATCCTTCAGCAAGGCGATTCAGAGGTACACCTGTGTAACTACCGCGATTCCGAAACTTGTCCCAAAGGTTTGCGCCGGGG---CAAAGACATATT?TTTGTTGTCGATAATGACGATCGGG1 Bonplandia_geminiflora TTAGGATCCTTTTATCCGGACCGTTACAGGTCACAGGGCCTCCTCTCAGCTCTCCCACTCTGGCCTCGCAAGCTGCAAGTAGGTAGCTATTGGCGATCCAGAGTAATTCAGTCGTCGGAAGACGTTAATGAGCTGCGTTCTTACTTATATCCCTCACGAAGGTGATTCAGGGGTACACATGTGTAATTACTGAGATTCGGAGACTTGTCCCAAAAGTTTCCGCCGGGGTTAAAAAGGTATATTGTTTGTTATCTATTACAATGATCGGG0 Cantua_buxifolia TTAGGGCCCTTTTATCCGGACCGTTACAGGTCACAGGGCCATCTCTCAGCCCTCTCACTCTGGCCCCGCAAGCTGCAAGGAGGTAGCTATTGGCGATCCATAGTAATTCCGGCGTCGTAAGACGTTAATGAGCTGTGTTCTCACGTATATCCCTCAGCACGGTGATTCCGGGATACACATGTGTAATTACTGAGATTTGGAGACTTATCCCAAAAATTTCCGCCGGGGTTAAAAA?ACATATTGTTTTTTATCTATCATAACGATCGGG0 Cantua_cuzcoensis TTAGGGCCCTTTTATCCGGACCGTTACAGGTCACAGGGCCATCTCTCAGCCCTCTCACTCTGGCCCCGCAAGCTGCAAGGAGGTAGCTATTGGCGATCCATAGTAATTCCGGCGTCGTAAGACGTTAATGAGCTGTGTTCTCACGTATATCCCTCAGCACGGTGATTCCGGGATACACATGTGTAATTACTGAGATTTGGAGACTTATCCCAAAAATTTCCGCCGGGGTTAAAAAGACATATTGAATTTTATCTATCATAACGATCGGG0 Cobaea_scandens TTAGGGTCCTTTTATCCGGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCCCACTCTGGCCCCGCAAGCTGCAAGTAGGTAGCTATTGGCGATCCATGTTAATTCCGGCGTCGGAAGACCTTAACGAGCTGCGTTCTCATGTATATCCCTCAGCAAGGTGATTCAGGGGTACACCTGTGTAATTACTAAGATTCCGAGACTTGTCTCAAAAGTTTCCGTCGGGGTTAAAAAGGCATATTGTTTGTTGTTTATCATAACGATCGGG0 Collomia_rawsoniana ???????????TTATCCCTACCGTTACAGGTCACAGGGCCTTCTATAAGCCCTCCCACTCTGACCCGGCAAGCTGTAAAGAGGGAGTTGTTAAAAGTCCATCCTGAGTCCGGCGACGGCAGACGTTAACGAGCTGTGTCCTCACGTATATCATTCACGAAGGCGATTCAGAGGTACACCTGTGTAACTACCGCGATTCTGAAACTTGTCTCAAAGGTTTCCGCCGGGG---CAAAGGCATATTGTTTGTTATCGATCATGATGATCGGG1 Eriastrum_wilcoxii TTAGGGTCCTTTTATCTAAAACGTTACGGGTCACAGGACCTCCTCTAAGCCCTCCCACTCTGACCCCGCAAGCTGTAAGTAGGTACCTATTGGCGGTCCATAGTAATTACGGCGTCGGAAGACGTTAATAAGCTGCGTCCGTACGTATATCCCTCGGCAAGATGATTCAGATATACACATATGTAATTACTGAGGTTCAGAGACTTGTCCAAAAAGTTTACGCGGGGGCCAAAAAGGCATATTGTTTGTTATCTATCATGATGATCGGG0 Gilia_achilleifolia ????????????T?TCCAGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCCCACTCTGACCCGACAAGCTGTAAGTAGGTAGCTGCTGGTGGTCCATAGTTATTCCGGCGTCGGAAGACGTTAGTAGGCTGCATCCTCACGTATATCCTTCGGCAAGGCGATTCAGAGGTACACCTGTGTAACTACCGCGATTCCGAGACTTGTCCCAAGGGTTTCCCCTGGTT---CAAAGGCATATTGTTTGTTATTTATCATGACGATCGGG1 Gilia_capitata ????????????TATCCAGACCGTTACAGGTCACAGGGCCTCATCTAAGCCCTCCCACTCTGACCTGGCAAGTTGTAAGTAGGTAGCTGCTGGTGGTCCATAGTTATTCCGGCGTCGGATGACGTTAATAGGCTGCATCCTCACGTATAT?CTTCGGC??GGCGATTCAGAGGTACACCTGTGTAACTACCGCGATTCCGAGACTTGTCCCAAGGGTTTCCCCTGGTT---CAAAGGCATATTGTTTGTTATTTATCATGACGATCGGG1 Gilia_diegensis ????????????TATCCAGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCCCACTCTCACCCGACAAGCTGTAAGTAGGTAGCTGCTGGCGGTCCATGGTTATTCCGGCGTCGGAAGACGTTAATAGGCTTCATCCTCACGTATATCCTTCGGCAAGGCGATTCAGAGGTACACCTGTGTAACTGTCGCGATTCCGAGACTTGTCCCAAGGGTTTCCCCCGGTT---CAAAGGCATATTGTTTGTTATTTATCATGACGATCGGG1 Gilia_leptantha TTAGGATCCGTATATCCAGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCCCACTCTGACCCGACAAGCTGTAAGTAGGTAGCTGCTGGCGGTCCATAGTTATTCCGGCGTCGGATGACGTTAACAGGCTGCATCCTCACGTATATCCTTCGGCAAGGCGATTCAGAGGTACACATGTGTAACTATCGCGATTCCGAGACTTGTCCCAAGGGTTTCCCCCGGTT---CAAGGCATTATTGTTTGTTATTTATCATGACGATCGGG1 Hordeum ACAGCTTTTTAGTGCCCACACCATCTTTTGACGCGGGACCTCCGACTCTGCTTCTAGACCTACATCCTTGTTAGACGGTCAGATCCGAATGAACGATCCATAGCCGCTCCCGCATAGTCAACTGGCGGTACATTAGGTAGGTATGTGGGTCTCTTACTGACGTGCACCAGAGTTACATACGAAACATTGTTGTAATTCGGAAGATTGTGCCCAAAACAAC--------CTTTCTTTCAGTGGACCCATGGTATGGTATTGGTTTATTCG0 Ipomopsis_aggregata ????????????TATCCAGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCTTACTTTGACCCCGCAAGCTGTAAGTAGGTAGCTATAGGCGGTCCATAGTAATTCTGGCGTCGGAAGACGTTAATAAGCTGCGTCCGCGCGTATATCCCTCGGCAAGGTGATTCAGAGATACACATGTGTAATTATTGAGATTCGGAAACTTGTCCCAAAA-----CGCGGGGGCTAAAAAGGCATATTGTTTGTTGTCTATCATGATGATCGGA0 Lactuca_sativa TCAGGGTTCTTTTATCTGCACACTTACCGGTCACAGGGTTTCCTCTCATCCCTTCCGTTCGGGCGCCTCAATCCGCAAGCTGA?AGCTATTGGTGAGCTATTGTAATGCTGGAGGTTTAAAAA???????????????????????????????????????????????AGTTGCATACTTGTAATTCCTGAAACTCGGAAAATCGCCTCAAGGGTTTCTCCGAAGGTACAGAAGGCGGATTGTTTGTTATGTATCATGATGGCCCGG0 Leptodacylon_pungens TTAGGGTCCTTTTATCCCGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCCCACTCTGACCCGGCAAGCTGTAAGTAGGTAGAGATTGGCGGTCCATAGTAA?TCCGGCGTCGGAAGACGTTAAAAAGCTG?GTCCTCACGTATATCCCTCGGCAAGGTAATTCAGAGGTACACCTGCGTAATTACTGTGATTCGGAGACTTGTCCAAAAAGTTTCCGCCGGGGCCAAAAAGGCATATTGTTTGTTATCTATCATGACGATCGGG0 Linanthus_grandiflorus TTAGGGTCCTTTTATCTAGACGCGTACAGGTCACAGGGCCTTATCTAAGCCCTACTACTCTGACCCGGCAAGCTGTAAGTAGGTAGATATTGGTGGTCCATAGTAATTCCGCCGTCGGAAGACCTTAAAAAGCTGCGTCCTCACGTATATACCTCGGCAAGGTAATTCAGAGGTACACCTG?GTAATTATTGTGATTCGGAGACTTGTCCAAAAAGTTTACGCCGGGATCAAAAAGGCATATTGTTTGTTACCTATCATGACGATCGGG0 Loeseliastrum_matthewsii ????????????TATCCAGACCGTTACAGGTCACAGGACCTCCTCTAAGCCCTCTCAATCTGACCCCGCAAGCTGTAAG?AGGTACCTATAGG????CCATAGTAATTACGGCGTCGGAAAACGTTAATAAGCTGCGTCCTAACGTATATCCCTCGGCAAGATGAGTCAGATATACACATGTGTAATTACTGAGATTCCGAGACTAGTCCCAAAAGGTTACGCGGGGGCCAAAAAGGCATATTGTTTGTTATCTATCATGATGATCGGG0 Madia_bolanderi TTAGGGTTCTTTTATCTGCACACTTACCGGTCACAGGGTTTCCTCTCATCCCTTCTGTTCGGGCGCCTCAATCCGCAAACCGATAGCTATTTGTGATGTATTGTAATGCCGGAGTTTGAAAAA???????????????????????????????????????????????AGTTGCATATTTGTAATTCTTGAGGCTCAGAAAATCGCCTCAAGAGTTTCTCCGAAGGTCCAGAAGGCGGATTGTTTGTTGTGTATCACGATGGCCCTG0 Navarretia_divaricata TTAGGGTCCGTTTATCCATACCGTTACAGGTCACAGGGCCTTCTATAAGCCCTCCCACTCTGACCCGGCAAGCTGTGAATAGGGAGTGGTTAACAGTCCATCCTGAGTCCGGCGTCGAAAGACGTTAATAGGCTGCGTCCTTACGTATATCATTCAGCAAGGCGATTCAGAGGTACACCTGTGTAACTACCGCGATTCCGAAACTTGTCCAAAAGGTTTCCGCCGGGG???CAAAGGCATATTGTTTGTTTCTCAATATTTACAATGGG1 Nicotiana_tabacum TCAGGGTTCTTTTTTCCGCATCGCTCTCGCTTCAAGGGCCTCCTCTCATCCCGTCAGCTCTGGCTCCTCAATCTGTAATCCAATAGCAATTGGCGATCCCTTGTAATTCTGGAAGTGAACACCGTTAGCAGGTTTCGTACTCATGGGTGCCTTTCACTCACATGATTCAGAGTGACACATTCATAATCGCTGAGACACGTCGAACTGCCCCACGAGCTTCGTTGGGGAGAAAGAAGTCGGATTGTTTGTTTTGTATCATGACGGCGTCG0 Oryza ACAGATCTCTAGTGTCCGCCGCATCCTTTGACACGCAGCCTCCGACTCTGCTTCTCGGCTTACATTCTTGTTAGACGGTCAGATCCAAATGAACGATCCAAAGCTGCTCCCGTAGAGCCAACTGGCGGTAAATTACGTGGGTGTGTGGGTCTCCTACTAACGTGCACCAGAGTTACATACGAGACGTTGTTGTAATTCGGAAGATTGTGCCCAAAACAAC--------TCTTCTTTCCGTGGACCCATGGTATGGATTTCTCTATCGCG0 Phlox_diffusa ????????????TATCTAGACGCTTACAGGTCACAGGGCCTCCTCCAAGCCCTCCCACTCTGACCCGGCAAGCTGTAAAAAGGTAGATATTGGCGGTCCATAGTAATTCCGCCGTCGGAAGACTCTAAAAAGCTGCGTCCTCACGTATATCCCTTGGCAAGGTAATTCAGAGGTAACACTGCGTAATTACTGTGATTCGGAGACTTGTCCAAAAAGTTTCCGCCGGGGTCAAAAAGGCATATTGTTTGTTACCTATCATGACGATCGGG0 Phlox_gracilis ????????CTTTTATCTAGACGCTTA?AGGTCACAGGGCCACCTCCAAGCCCTCCCACTCTGACCCCGCAAGCTGTAAATAGGTAGATATTGGCGGTCCATAGTAATTCCACCGTCGGAAGACTCTAAAAGGCTGCGTCCTCACGTATATCCCTTGGCAAGGTAATTCAGAGGTAACACTGTGTAATTACTGTGATTCGGAGACTTGTCCAAAAAGTTTACGCCGGGGTCAAAAAGGCATATTGTTTGTTACTTATCATGACGATCGGG0 Pisum TCGATGCCTTTTCACTTACCACGTTATGTGTCACAAGGCATCCTCACATCATTTGTACTTTGGCTCGTCAGTCGGCGAACCGAATGTTATCAAGGATTAATAGTAATTCCAACGGTGGAAAATGTTAGCGGGTCGCGCCTTTATTGGAGCCCTTTACCAAGGTGATTTAAGGTTACACATTCGTAATCATTAAGACTCAGAGAAATGTTTCAAGAGATTCCTCAGAGGTAAAGAAATCGTATTGTTTGTTCTTCAGTACGACGGTCGGG0 Polemonium_occidentale TTAGGGTCCTTTTATCTAGACCGTTACAGGTCACAGGGCCTCCTCTAAGCCCTCCCACTCTGACCCCGCAAGCTGTAAGTAGGTAGCTATTGGCGGTCCATAGTAAGTCCGGCGTCGGAAGACGTTAATAAGCTGCGTCCTCATGTATATCCCTCGGCAAGGTGATTCAGAGGTACACCTGTGTAATTACTGAGATTCAGAGACTTGTCCCAAAAGTTTCCGCCGGGGCCAAAAAGGCCTATTGTTTGTTATCTATCATGACGATCGGG0 Sinapsis ACGATGCCCTTTCATTTGTAACGTTCCGAGTTATGCAGTATTCTTAGATATTTTACGTTTTGGCTTCTTAGTCTGCAATCAGATAGTTAGCAACGATGCAACATAACTTATGGGGTGTAAAATGTTAGCAGACCAGGCACTCATTGGTGCACTCCACTAAAGTGATTTAAGGTTACACATTCGTAGTTGCTGAAACTCGGGGCACTATCCCAAGAAGTGACCAAAAGATAACGAGTGCGGGTTGTTTGTTCTATCTTATGATGGTCCGA0 Solanum_tuberosum TCAGGGTTCTTTTTTCCGCATCGCTCTAGCTTCAAGGGCCTCCTCCCATCCCGTCAGCTCTGGCTCATCAATCTGTAATCCAATACCAATTGGCGAGCCCTTGTAATTCTGGAAGTGACCACCGTTAGCAAGTTTCGTACTCATGGGTGCCTTTCACTCACATGATTCAGAGTGACACATTAATAATCGCTGAGACACGTCGAACTGCCCCACGAGCTTCGTTGGGGAGAAAGAAGTCGGATTGTTTGTTTTGTATCATGACGGCGTCG0 ; END; [ The following blocks are output data for analysis step 61 ] BEGIN TREES; TITLE Tb4840; LINK TAXA = TaxaForAnalysisStep61; TREE Fig._4 = [&R] ((((((Gilia_leptantha,Gilia_diegensis,Gilia_achilleifolia,Gilia_capitata),((Collomia_rawsoniana,Navarretia_divaricata),Allophyllum_giliodes)),((Phlox_gracilis,Phlox_diffusa),Linanthus_grandiflorus),(Cantua_cuzcoensis,Cantua_buxifolia),Leptodacylon_pungens,Cobaea_scandens,Bonplandia_geminiflora,Polemonium_occidentale,Ipomopsis_aggregata,Eriastrum_wilcoxii,Acanthogilla_gloriosa,Loeseliastrum_matthewsii)Polemoniaceae,(Solanum_tuberosum,Nicotiana_tabacum)),Madia_bolanderi),Lactuca_sativa); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2022] END; BEGIN TREES; TITLE Tb4840; LINK TAXA = TaxaForAnalysisStep61; TREE Fig._3 = [&R] ((((((((((Gilia_leptantha,Gilia_diegensis),(Gilia_achilleifolia,Gilia_capitata)),((Collomia_rawsoniana,Navarretia_divaricata),Allophyllum_giliodes)),(((Phlox_gracilis,Phlox_diffusa),Linanthus_grandiflorus),Leptodacylon_pungens)),Polemonium_occidentale),((Eriastrum_wilcoxii,Loeseliastrum_matthewsii),Ipomopsis_aggregata)),(Cantua_cuzcoensis,Cantua_buxifolia),Cobaea_scandens,Bonplandia_geminiflora,Acanthogilla_gloriosa)Polemoniaceae,(Solanum_tuberosum,Nicotiana_tabacum)),Madia_bolanderi),Lactuca_sativa); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2021] END; BEGIN TREES; TITLE Tb4840; LINK TAXA = TaxaForAnalysisStep61; TREE Fig._2 = [&R] (((((((((((((Gilia_leptantha,Gilia_diegensis),(Gilia_achilleifolia,Gilia_capitata)),((Collomia_rawsoniana,Navarretia_divaricata),Allophyllum_giliodes)),(((Phlox_gracilis,Phlox_diffusa),Linanthus_grandiflorus),Leptodacylon_pungens)),Polemonium_occidentale),((Eriastrum_wilcoxii,Loeseliastrum_matthewsii),Ipomopsis_aggregata)),Acanthogilla_gloriosa),(Cantua_cuzcoensis,Cantua_buxifolia)),Bonplandia_geminiflora),Cobaea_scandens)Polemoniaceae,(Solanum_tuberosum,Nicotiana_tabacum)),Madia_bolanderi),Lactuca_sativa); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2020] END;