#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 July 01, 2025; 13:37 GMT TreeBASE (cc) 1994-2008 Study reference: Donadío S., Giussani L., Kellogg E., Zuloaga F., & Morrone O. 2008. A preliminary molecular phylogeny of Pennisetum and Cenchrus (Poaceae-Paniceae) based on the trnL-F, rpl16 chloroplast markers. Taxon, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2136] [ The following blocks are input data for analysis step 4458 ] BEGIN TAXA; TITLE TaxaForAnalysisStep4458; DIMENSIONS NTAX=41; TAXLABELS Cenchrus_brownii Cenchrus_ciliaris Cenchrus_echinatus Cenchrus_incertus Cenchrus_myosuroides Cenchrus_pilosus Cenchrus_setigerus Chasmanthium_latifolium Ixophorus_unisetus Panicum_repens Paspalidium_geminatum Pennisetum_alopecuroides Pennisetum_chilense Pennisetum_clandestinum Pennisetum_flaccidum Pennisetum_frutescens Pennisetum_glaucum Pennisetum_lanatum Pennisetum_latifolium Pennisetum_macrourum Pennisetum_montanum_Morrone_4931 Pennisetum_montanum_Morrone_sn Pennisetum_nervosum Pennisetum_polystachion Pennisetum_purpureum_Morrone_4220 Pennisetum_purpureum_Morrone_4473 Pennisetum_ramosum Pennisetum_setaceum Pennisetum_sieberianum Pennisetum_squamulatum Pennisetum_tristachyon Pennisetum_unisetum Pennisetum_villosum_Doust_1500 Pennisetum_villosum_PI_304750 Pseudoraphis_paradoxa Sacciolepis_vilvoides Setaria_lachnea Setaria_sulcata Stenotaphrum_secundatum Urochloa_panicoides Zea_mays ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3798] TITLE 'PI trnL-F + PI rpl16 + PI coded indels'; LINK TAXA = TaxaForAnalysisStep4458; DIMENSIONS NCHAR=138; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 ] [ . . . . . . . . . . . . . ] Cenchrus_brownii AGAAGCGGGCACTATCACTCATTACGTGA?AGTCGACGACATGCCAGGATGATAATTTAT?AATTTCGAGTTACCCAGCTGTGAAAGGGCGATCCTATCCCGCACTCTC???ACGAGCGACAATAAATTTAA???TT? Cenchrus_ciliaris AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGACATGCCAGGATGATTATTTAT?AATTTCGAGTTACCCAGCTGTGAAATGGCGATCCTATCCCGCACTCTC???ACGAGCGACAATAAATTTAAAAATT? Cenchrus_echinatus AGAAGCGGGCACTATCACTCATTACGTGA?AGTCGACGACATGCCAGGATGATAATTTAT?AATTTCGAGTTACCCAGCTGTGAAAGGGCGATCCTATCCCGCACTCTC???ACGAGCGACAATAAATTTAATA?TT? Cenchrus_incertus AGAAACGGGCACTATCGCTCATTACGTGA?GGTCGACGACATGCCAGGATGATAATTTAT?AATTTCGAGTTACCCAGCTGTGAAATGGCGATCCTAACCCGCACTCTC???ACGAGCGCCAATAAATT?TATA?TT? Cenchrus_myosuroides AGAAACGGGCACTATCGCTCATTACGTGA?GGTCGACGACATGCCAGGATGATAATTTAT?AATTTCGAGTTACCCAGCTGTGAAATGGCGATCCTAACCCGCACTCTC???ACGAGCGACAATAAATT?TATA?TT? Cenchrus_pilosus AGAAGCGGGCACTATCACTCATTACGTGA?AGTCGACGACATGCCAGGATGATAATTTAT?AATTTCGAGTTACCCAGCTGTGAAAGGGCGATCCTATCCCGCACTCTC???ACGAGCGACAATAAATTTAATA?TT? Cenchrus_setigerus AGAAGCGGGCACTGTCACTCATTACGTGA?GATCGACGACATGCCAGGATGATTATTTAT?AATTT???????????????????????????????????????????????????????????????????????? Chasmanthium_latifolium GACAGCGTACTAGACCAATCAGATTGATGTGG???ACTGATTCCCAGGCTGAAAATAA?A?ATAAATCGACA?CACCACGGCGGAG?GGCGTCTAGCTTGTG???TTAACCGACGCGCGCAGA?AATTTTA????AAA Ixophorus_unisetus AACAGCGTGCACTATCGCTCATTATGTGG?AACCAACTGCCGCCCAGGCTAAAAATTTAT?AATTT??AGGTACCCAACTGTGGAA?AGCGATCCTATCCTGCGCTCTA???ACGAGCGCCAATAATTTTAATA?TT? Panicum_repens GGCAGCGTGCTATACCAATCATATTTTGGAGA???????????????????AAAAATA????????TCGGGAAAACAACTGTGGAATGGCGACCATATCCTGCGC?CT?TCAACGAGCGCCAATAAATTTAA???TAT Paspalidium_geminatum AGCAGCGTGCACTGTCACTCATAATGTGG?GATCAGCTGCCGCCCAGGCTGAAAATTTAT?AATTT?????????CAACAGTGGAATGGCGATCATATCCTGCGCTCTC???ACGAGCGCCA??AAATTTAA???TT? Pennisetum_alopecuroides AGAAGCGGGCACTATCACTCATAACGTGG?GATCGACGGCATCCCAGTCTGAAAATTTAT?AATTTTGAGTTACCCAACTGTGAAATGGCGATCCTATCCTGCGCTCTT???ACGAGCGCCAATAAATTTAATA?TT? Pennisetum_chilense AGAAGCGGGCACTATCGCTCGTAACGTGG?GATCGAC???ATCCCAG????AAAATTTAT?T?TTTTAAGTTACCCAACTGTGATATGGCAATCCTATCCTGCGCTCTA???ACGAACGCCAATAAATTTAATA?TT? Pennisetum_clandestinum AGCAGCGGGCACTATCACTCGTCACGTGG?GATCAACGGCATGCCAGGCTGTAAATTTAT?AATTT??????ACCCAACTGTGAAATGGCGATCCTATCCTACGCTCTC???ACAAGCGCTATTAAATTTAATA?TT? Pennisetum_flaccidum AGAGGCGGGCACTATCACTCATTACTTGG?GATCGACGGCATGCCAGGATGATAATTTAT?AATTT???????????????????AAGGCGATCCTATCCCGCGC?CTA???ACGAGCGCTA???AATTTAA???TT? Pennisetum_frutescens AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGGCATGCCAGGATGATAATTTAT?AATTTTGAGTTACCCAGCTGTGAAATGGAGATCCTATCCCGCACTCTC???ACGAGCGACAATAAATTTAATA?TT? Pennisetum_glaucum AGAGGCGGGCACTATTACTCATAACGTGG?GATCGACGGTATGCTAGGCGGAAAATTTAT?AATTTTGAGTTACCCAATTGTAAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCAATAAATTTATAAATT? Pennisetum_lanatum AGCAGCGTGCACTATCACTCATAATGTGG?GA??AACTGCCGCCCAAGCTGAAAATTTAA?AATTTTCAGTTACCCAGCAGTGGAATGGCGATCCTATCCTGCGCTCTT???ACGAGCGCCAATAAATTTAATA?TT? Pennisetum_latifolium AGAAGCGGGCACTATCACTCGTAACGTGG?GATCGAC???ATGCCAGGCTGAAAATTTAT?T?TTTTAAGTTACCCAACTGTGATATGGCAATCCTATCCTGCGCTCTC???ACGAACGCCAATAAAATTAATA?TT? Pennisetum_macrourum ?GCAGCGGGGACTATCGCTCGTAACGTGG?GATCAATGGCATGCCAGGCTGTAAATTTAT?AATTT???????CCTAACTGTGAAATGGAGATCCTATCCTACGCTCTC???ACAAGCGCTATTAAATTTAATA?TT? Pennisetum_montanum_Morrone_4931 AGAAGCGGGAACTATCACCCGTAACGTGG?GATCGAC???ATGCCAGGCTGAAAATTTAT?T?TTT??AGTTGC???????????ATGGCAATACTATCCT????TCTA???ACGAACGCCAAT?TAAT??????TT? Pennisetum_montanum_Morrone_sn AGAAGCGGGAACTATCACCCGTAACGTGG?GATCGAC???ATGCCAGGCTGAAAATTTAT?T?TTTTAAGTTGCCCAACATTGATATGGCAATACTATCCTGCGCTCTC???ACGAACGCCAATATAATTAATA?TT? Pennisetum_nervosum AGAAGCGGGCACTATTACTCATAACGTGG?GATCGACGGTAT?????????AAAATTTAT?AATT?TGAGTTACCCAACTGTGAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCAATAAATTTATAATTT? Pennisetum_polystachion AGAAGCGGGCACTATCTCTCGTTACGTGA?GATCGACGGC??????GGATGATAATTTAT?AA???TGAGTTAACCAACTGTGAAATGGCAATCCTAACCCGCACTCTA???ACGAGTGACAATTAATTTAA???TT? Pennisetum_purpureum_Morrone_4220 AGAAGCGGGCACTATTACTCATAACGTGG?GATCGACGGTATGCTAGGCGGAAAATTTAT?AATTTTGAGTTACCCAACTGTGAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCAATAAATTTATAATTT? Pennisetum_purpureum_Morrone_4473 AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGACATGCCAGGATGATTATTTAT?AATTT????????CCAGCTGTGAAATGGCGATCCTATCCCGCAC???????ACGAGCGACA??AAATTTAA????T? Pennisetum_ramosum AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGGCATGCCAGGATGATAATTTAT?AATTTTGAGTTACCCAGCTGTGAAATGGCGATCCTATTCCGCACTTTA???ACGAGCGACAATAAAATTAATA?TT? Pennisetum_setaceum AGAAGCGGGCACTATCACTCATGACGTGA?GGTCGACGACATGCCAGGATGATAATTTAT?AATTTCGAGTTACC??GCTTTGAAATGGCGATACTATCCCGCACTCTC???ACGAGCGACAATAAATTTAATA?TT? Pennisetum_sieberianum AGAGGCGGGCACTATTACTCATAACGTGG?GATCGACGGTATGCTAGGCGGAAAATTTAT?AATTTTGAGTTACCCAATTGTAAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCAATAAATTTATAAATT? Pennisetum_squamulatum AGAAGCGGGCACTATTACTCATAACGTGG?GA??GACGGTATGCTAGGCGGAAAATTT?T?AATTTTGAGTTACCCAACTGTGAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCAATAAATTTAT???TT? Pennisetum_tristachyon AGAAGCGGGCACTATCACTCGTCACGTGG?GATCGAC???ATGCCAG????AAAATTTAT?T?TTTTAAGTTACCCAACTGTGATATGGCAATCCTATCCTGCGCTCTC???ACGAACGCCAATAAATTTAATA?TT? Pennisetum_unisetum AGAAGCGGGCACTATCACTTATAACGTGG?GA????TAGCATGCCAAGCT?AAAATTT???AATTTTAAGTTACCCAACAGTGAAAT???????????CCTGCGCTCTA???ACGAGTGCCAATAAAT?TAATA?TT? Pennisetum_villosum_Doust_1500 AGCAGAAGTCACTGTCGC??ATAACGTGG?GATCAACGGCATGCCAGGCTGTTATTTTAATAATTTTAAGTTACCCAACTGTGAAA?GACGATCCTATCCTGCGTGCTC???ATGAGCGCCAATAATTTTAATA?TT? Pennisetum_villosum_PI_304750 AGCAGAAGTCACTGTCGC??ATAACGTGG?GATCAACGGCATGCCAGGCTGTTATTTTAATAATTT??????????AACTGTGAAA?GACGATCCTATCCTGCGTGCTC???ATGAGCGCCA??AATTTTAA???TT? Pseudoraphis_paradoxa AGCAGCGTGCACTATCACTCATTATGAGG?GATCAACTGCCGCCCAGGCTGAAAATTTAAAAATTTTCAGTTACCCAACAGTGGAATGGCGATCCTATCCTGCGCTCTC???ACGAGCGCCAATAAATTAAATA?TT? Sacciolepis_vilvoides GGCAGCGTGCTAGACCAATCAGATTGAGGAGACTAGCTGCTGCCCTGGCTGAAAATTATT?ATAAATCGAGAAA?CAACTGCGGAA?GGCGACCAGATCCTGAGCTCT?TAAACGAGCTACGAAAATTAAAA???AAT Setaria_lachnea AGCAGCGTGCACTATCACTCATAATGTGG?GATCAACTGCCGCCCAGGCTGAAAATTTAT?AATTTTCAGGTACCCAACTGTGGAATGGCGATCCTATCCTGCGCTCTC???ACGAGCGCCAATAAATTTAATA?TT? Setaria_sulcata GGCAGCGTGCACTATCACTCATAATGTGG?GATTAACTGCCGCCCAGTCTGAAAATTTAT?AATTTTCGGTTACCCAACTTTGGAA?GGCGTTCCTATCCT????TCTA???ACGAGCGCCAATAATTATA??T?TT? Stenotaphrum_secundatum AGCAGCGTGCACTATCACTCATAATGTGG?GATCAACTGCCGCCCAGGC??AAAATTTAT?AATTTTCAGGTACCTAACTGTGGAATGGCCATCCTATCCTGCGCTCTC???ACGAGCGCCAATTAATTTAATA?TT? Urochloa_panicoides GGCAGCGTGCTATACCAATCATAATGTGGAGATCAACTGCTGCTCAGGCTGAAAATTATAAATTTA??????AAACAACAGTGGAATGGCAACCATATCCTGAGCTCTC???ACGAGCACCA?AAAATTTAA?T?TT? Zea_mays GGCAGC??????????AATTATATTGATGTGGTCAACTGCTGCTCTGGCTAATAAAAATT?ATAAATC?????AACCACTGCGGAGTGGCGACCATCTCGTGCACTCACCAGACGCGCACCGATAAATT??ATA?TAA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'PI trnL-F + PI rpl16 + PI coded indels') = N: 1-138; CODONPOSSET CodonPositions (CHARACTERS = 'PI trnL-F + PI rpl16 + PI coded indels') = N: 1-138; END; [ The following blocks are output data for analysis step 4458 ] BEGIN TREES; TITLE Tb9230; LINK TAXA = TaxaForAnalysisStep4458; TREE Fig._1 = [&R] (Chasmanthium_latifolium,(Zea_mays,(Sacciolepis_vilvoides,(Panicum_repens,(Urochloa_panicoides,(Ixophorus_unisetus,Paspalidium_geminatum,Setaria_sulcata,Setaria_lachnea,Stenotaphrum_secundatum,(Pseudoraphis_paradoxa,Pennisetum_lanatum),((Pennisetum_unisetum,((Pennisetum_alopecuroides,(Pennisetum_nervosum,Pennisetum_purpureum_Morrone_4220,Pennisetum_squamulatum,(Pennisetum_glaucum,Pennisetum_sieberianum))),(Pennisetum_flaccidum,(Pennisetum_polystachion,(Pennisetum_ramosum,(Pennisetum_frutescens,((Pennisetum_purpureum_Morrone_4473,Cenchrus_ciliaris,Cenchrus_setigerus),(Pennisetum_setaceum,(Cenchrus_brownii,Cenchrus_echinatus,Cenchrus_pilosus),(Cenchrus_incertus,Cenchrus_myosuroides)))))))),(Pennisetum_chilense,Pennisetum_tristachyon,(Pennisetum_latifolium,(Pennisetum_montanum_Morrone_sn,Pennisetum_montanum_Morrone_4931)))),((Pennisetum_clandestinum,Pennisetum_macrourum),(Pennisetum_villosum_PI_304750,Pennisetum_villosum_Doust_1500))))))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5274] END;