#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; 13:39 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 4457 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep4457;
        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:M3799]

	TITLE 'PI trnL-F + PI rpl16';
	LINK TAXA = TaxaForAnalysisStep4457;
	DIMENSIONS NCHAR=107;
	FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -;

MATRIX
[                                             10        20        30        40        50        60        70        80        90        100       ]
[                                              .         .         .         .         .         .         .         .         .         .       ]
Cenchrus_brownii                      AGAAGCGGGCACTATCACTCATTACGTGA?AGTCGACGACATGCCAGGATGCGAGTTACCCAGCTGTGAAAGGGCGATCCTATCCCGCACTCTC???ACGAGCGACA
Cenchrus_ciliaris                     AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGACATGCCAGGATGCGAGTTACCCAGCTGTGAAATGGCGATCCTATCCCGCACTCTC???ACGAGCGACA
Cenchrus_echinatus                    AGAAGCGGGCACTATCACTCATTACGTGA?AGTCGACGACATGCCAGGATGCGAGTTACCCAGCTGTGAAAGGGCGATCCTATCCCGCACTCTC???ACGAGCGACA
Cenchrus_incertus                     AGAAACGGGCACTATCGCTCATTACGTGA?GGTCGACGACATGCCAGGATGCGAGTTACCCAGCTGTGAAATGGCGATCCTAACCCGCACTCTC???ACGAGCGCCA
Cenchrus_myosuroides                  AGAAACGGGCACTATCGCTCATTACGTGA?GGTCGACGACATGCCAGGATGCGAGTTACCCAGCTGTGAAATGGCGATCCTAACCCGCACTCTC???ACGAGCGACA
Cenchrus_pilosus                      AGAAGCGGGCACTATCACTCATTACGTGA?AGTCGACGACATGCCAGGATGCGAGTTACCCAGCTGTGAAAGGGCGATCCTATCCCGCACTCTC???ACGAGCGACA
Cenchrus_setigerus                    AGAAGCGGGCACTGTCACTCATTACGTGA?GATCGACGACATGCCAGGATG????????????????????????????????????????????????????????
Chasmanthium_latifolium               GACAGCGTACTAGACCAATCAGATTGATGTGG???ACTGATTCCCAGGCTGTCGACA?CACCACGGCGGAG?GGCGTCTAGCTTGTG???TTAACCGACGCGCGCAG
Ixophorus_unisetus                    AACAGCGTGCACTATCGCTCATTATGTGG?AACCAACTGCCGCCCAGGCTA??AGGTACCCAACTGTGGAA?AGCGATCCTATCCTGCGCTCTA???ACGAGCGCCA
Panicum_repens                        GGCAGCGTGCTATACCAATCATATTTTGGAGA???????????????????TCGGGAAAACAACTGTGGAATGGCGACCATATCCTGCGC?CT?TCAACGAGCGCCA
Paspalidium_geminatum                 AGCAGCGTGCACTGTCACTCATAATGTGG?GATCAGCTGCCGCCCAGGCTG?????????CAACAGTGGAATGGCGATCATATCCTGCGCTCTC???ACGAGCGCCA
Pennisetum_alopecuroides              AGAAGCGGGCACTATCACTCATAACGTGG?GATCGACGGCATCCCAGTCTGTGAGTTACCCAACTGTGAAATGGCGATCCTATCCTGCGCTCTT???ACGAGCGCCA
Pennisetum_chilense                   AGAAGCGGGCACTATCGCTCGTAACGTGG?GATCGAC???ATCCCAG????TAAGTTACCCAACTGTGATATGGCAATCCTATCCTGCGCTCTA???ACGAACGCCA
Pennisetum_clandestinum               AGCAGCGGGCACTATCACTCGTCACGTGG?GATCAACGGCATGCCAGGCTG??????ACCCAACTGTGAAATGGCGATCCTATCCTACGCTCTC???ACAAGCGCTA
Pennisetum_flaccidum                  AGAGGCGGGCACTATCACTCATTACTTGG?GATCGACGGCATGCCAGGATG???????????????????AAGGCGATCCTATCCCGCGC?CTA???ACGAGCGCTA
Pennisetum_frutescens                 AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGGCATGCCAGGATGTGAGTTACCCAGCTGTGAAATGGAGATCCTATCCCGCACTCTC???ACGAGCGACA
Pennisetum_glaucum                    AGAGGCGGGCACTATTACTCATAACGTGG?GATCGACGGTATGCTAGGCGGTGAGTTACCCAATTGTAAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCA
Pennisetum_lanatum                    AGCAGCGTGCACTATCACTCATAATGTGG?GA??AACTGCCGCCCAAGCTGTCAGTTACCCAGCAGTGGAATGGCGATCCTATCCTGCGCTCTT???ACGAGCGCCA
Pennisetum_latifolium                 AGAAGCGGGCACTATCACTCGTAACGTGG?GATCGAC???ATGCCAGGCTGTAAGTTACCCAACTGTGATATGGCAATCCTATCCTGCGCTCTC???ACGAACGCCA
Pennisetum_macrourum                  ?GCAGCGGGGACTATCGCTCGTAACGTGG?GATCAATGGCATGCCAGGCTG???????CCTAACTGTGAAATGGAGATCCTATCCTACGCTCTC???ACAAGCGCTA
Pennisetum_montanum_Morrone_4931      AGAAGCGGGAACTATCACCCGTAACGTGG?GATCGAC???ATGCCAGGCTG??AGTTGC???????????ATGGCAATACTATCCT????TCTA???ACGAACGCCA
Pennisetum_montanum_Morrone_sn        AGAAGCGGGAACTATCACCCGTAACGTGG?GATCGAC???ATGCCAGGCTGTAAGTTGCCCAACATTGATATGGCAATACTATCCTGCGCTCTC???ACGAACGCCA
Pennisetum_nervosum                   AGAAGCGGGCACTATTACTCATAACGTGG?GATCGACGGTAT?????????TGAGTTACCCAACTGTGAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCA
Pennisetum_polystachion               AGAAGCGGGCACTATCTCTCGTTACGTGA?GATCGACGGC??????GGATGTGAGTTAACCAACTGTGAAATGGCAATCCTAACCCGCACTCTA???ACGAGTGACA
Pennisetum_purpureum_Morrone_4220     AGAAGCGGGCACTATTACTCATAACGTGG?GATCGACGGTATGCTAGGCGGTGAGTTACCCAACTGTGAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCA
Pennisetum_purpureum_Morrone_4473     AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGACATGCCAGGATG????????CCAGCTGTGAAATGGCGATCCTATCCCGCAC???????ACGAGCGACA
Pennisetum_ramosum                    AGAAGCGGGCACTATCACTCATTACGTGA?GATCGACGGCATGCCAGGATGTGAGTTACCCAGCTGTGAAATGGCGATCCTATTCCGCACTTTA???ACGAGCGACA
Pennisetum_setaceum                   AGAAGCGGGCACTATCACTCATGACGTGA?GGTCGACGACATGCCAGGATGCGAGTTACC??GCTTTGAAATGGCGATACTATCCCGCACTCTC???ACGAGCGACA
Pennisetum_sieberianum                AGAGGCGGGCACTATTACTCATAACGTGG?GATCGACGGTATGCTAGGCGGTGAGTTACCCAATTGTAAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCA
Pennisetum_squamulatum                AGAAGCGGGCACTATTACTCATAACGTGG?GA??GACGGTATGCTAGGCGGTGAGTTACCCAACTGTGAAATAGTGATCCTATCCTGCGCTCTT???TCGAGCGCCA
Pennisetum_tristachyon                AGAAGCGGGCACTATCACTCGTCACGTGG?GATCGAC???ATGCCAG????TAAGTTACCCAACTGTGATATGGCAATCCTATCCTGCGCTCTC???ACGAACGCCA
Pennisetum_unisetum                   AGAAGCGGGCACTATCACTTATAACGTGG?GA????TAGCATGCCAAGCT?TAAGTTACCCAACAGTGAAAT???????????CCTGCGCTCTA???ACGAGTGCCA
Pennisetum_villosum_Doust_1500        AGCAGAAGTCACTGTCGC??ATAACGTGG?GATCAACGGCATGCCAGGCTGTAAGTTACCCAACTGTGAAA?GACGATCCTATCCTGCGTGCTC???ATGAGCGCCA
Pennisetum_villosum_PI_304750         AGCAGAAGTCACTGTCGC??ATAACGTGG?GATCAACGGCATGCCAGGCTG??????????AACTGTGAAA?GACGATCCTATCCTGCGTGCTC???ATGAGCGCCA
Pseudoraphis_paradoxa                 AGCAGCGTGCACTATCACTCATTATGAGG?GATCAACTGCCGCCCAGGCTGTCAGTTACCCAACAGTGGAATGGCGATCCTATCCTGCGCTCTC???ACGAGCGCCA
Sacciolepis_vilvoides                 GGCAGCGTGCTAGACCAATCAGATTGAGGAGACTAGCTGCTGCCCTGGCTGTCGAGAAA?CAACTGCGGAA?GGCGACCAGATCCTGAGCTCT?TAAACGAGCTACG
Setaria_lachnea                       AGCAGCGTGCACTATCACTCATAATGTGG?GATCAACTGCCGCCCAGGCTGTCAGGTACCCAACTGTGGAATGGCGATCCTATCCTGCGCTCTC???ACGAGCGCCA
Setaria_sulcata                       GGCAGCGTGCACTATCACTCATAATGTGG?GATTAACTGCCGCCCAGTCTGTCGGTTACCCAACTTTGGAA?GGCGTTCCTATCCT????TCTA???ACGAGCGCCA
Stenotaphrum_secundatum               AGCAGCGTGCACTATCACTCATAATGTGG?GATCAACTGCCGCCCAGGC??TCAGGTACCTAACTGTGGAATGGCCATCCTATCCTGCGCTCTC???ACGAGCGCCA
Urochloa_panicoides                   GGCAGCGTGCTATACCAATCATAATGTGGAGATCAACTGCTGCTCAGGCTG??????AAACAACAGTGGAATGGCAACCATATCCTGAGCTCTC???ACGAGCACCA
Zea_mays                              GGCAGC??????????AATTATATTGATGTGGTCAACTGCTGCTCTGGCTATC?????AACCACTGCGGAGTGGCGACCATCTCGTGCACTCACCAGACGCGCACCG
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = 'PI trnL-F + PI rpl16') = 
		N: 1-107;
CODONPOSSET  CodonPositions (CHARACTERS = 'PI trnL-F + PI rpl16') = 
		N: 1-107;
END;
[ The following blocks are output data for analysis step 4457 ]
BEGIN TREES;
      TITLE Tb9229;
      LINK TAXA = TaxaForAnalysisStep4457;
      TREE 'PI trnL-F + PI rpl16' = [&R] (Chasmanthium_latifolium,(Zea_mays,(Sacciolepis_vilvoides,(Panicum_repens,(Urochloa_panicoides,(Ixophorus_unisetus,Paspalidium_geminatum,Pseudoraphis_paradoxa,Setaria_sulcata,Setaria_lachnea,Stenotaphrum_secundatum,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_latifolium,Pennisetum_tristachyon,(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:Tr373]


END;