#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 18, 2024; 13:12 GMT TreeBASE (cc) 1994-2008 Study reference: Davis J., Simmons M., Stevenson D., & Wendel J. 1998. Data decisiveness, data quality, and incongruence in phylogenetic analysis: and example from the monocotyledons using mitochondrial atpA sequences. Systematic Biology, 47(2): 282-310. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S398] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=20; TAXLABELS Acorus Alstroemeria Anigozanthos Canna Catopsis Curculigo Eriocaulon Flagellaria Gymnostachys Nypa Oryza Piper Saruma Smilax Symplocarpus Tacca Trillium Vellozia Veratrum Xanthorrhoea ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2089] TITLE atpA; LINK TAXA = Taxa1; DIMENSIONS NCHAR=110; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 A T G C" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110] [ . . . . . . . . . . .] Acorus 1GAT?AGTGAGCCTAGAATTTGAAACGCAAATTTAAGC????GAAGATAGTATTTACGCAA?AAAGCTTTC?ATTT?TAATAATT?TATCAC?CGTAAT?TTGAACATTA Alstroemeria 0AAGCGTTTGACTTGGGGCACCGGGTGCAGTTATAGTACCTCGGAGGTAAAAAGAGCGCAATGGAGCATCTGACCTACAATGGTCTCGTCACTCGTCAATAGTCAGGAGA Anigozanthos 0AATCGTTGGACTTGGGGTACCAGGTTAATTTATAGGACCTCAGAGGTAATGTGAGCGCAATGGAGCATCTGACCTATAATGGTCTCATCACTCGTCAAGATTCAGG?TC Canna ?AAGCGTTTGACTTGGGGCACCAGGTTAATATATAG?AG?????AGGCAATGTGTGCGCAATGGAGCATCTCACCTACAATGGTCTCGTCACTCGTCAAGATTCAGGAGC Catopsis 1AAGCGTTTGACCTGGCACACGAGGTTAATTTATAGGA????GGAAGCAATGTGTGCGCTAAGGAGCATCTGACCTTC?TTAGTCTCGTCACTCGTCATTAGTCTGGAGC Curculigo 0AAGCGTTTGACTTGGGGCACGAAGTTAAT?TATAGGCCCTCGGAGGCAATGTTTACGCAATGGAGCTTTTGACCTACATAGA?TTCATCATACGCAAATAGTCAG?ATC Eriocaulon 1A?GC?TGTGAC?TGGGGCTT?AAGTGCATTAATAAGA????GGTAGGAAAGTGTGCACTAAGGAGCATCTGACTTATAATAGTCTC?TCACTCGTCAAGTGTCAGTACC Flagellaria 0GAGCGTTTGACTTGGCACACCAGGTTAATTTATAGGACAAAGGTAGGGATGTGTGCGCTAAGGAGCATCTGACTTTTAATAGTTTCGTCACTCGTCAAGAGTCAGGACC Gymnostachys 0AGTGAGTTGGCTTGGGGCATGAGGTTAATATTTAGGACCTCGGAGGTAATGTGTGCGCCATGGAGC?TCCGACTAATAATAGCCACGTCACTTTTAAATAGTCAC?T?C Nypa 0AAGCGTTTGACTTGGC?CACGAGGTTAATTTATAGTACCTCAGAGGCAATGTGTGAGCTATGGAGCATCTGACCTACAATGGTCTCGTCACTCGCCAATAGTCAGAAG? Oryza 0AAGCGTTTGACTTGGCACACCAGGTTAATAAATAGGACAAAGGTAGTAATGTGAGCGCTAAGGAGCATTTGACTTATATTAGTTTCGTCACTCGTCAATAGGAAGGTCC Piper 0AGTGATGTAATTCGAAG?ATGTGGTTACTTGTCGGAACCGAGGAGATAATGTTTGCGTTCTGGAGCTCTCCTCCTTCA??AGTCTCGCTTTTTACACATAAGAACGAGC Saruma 0AGTGATGTAATTTGAAGCATGTGGTTACTTGTCGGAACCGAGGAGATAATGTTTGCGTTCTGGAGCTCTCCTCCTTCATTAGTCTCGCTTTTTACACATAAGAACGA?C Smilax 0AAGCGTTTGACTTGGGGCACCGGGTGCAGTTATAGTACCTCGGAGGTAAAATGTGCGCAATGGAGCATCTGACCTACAATGGTCTCGTCACTCGCCAATAGTCACTACC Symplocarpus 0AGGGAGTTGACTCGGGGCACGAGGTTAATTTTTAGGACCTCGGAGGTAATGTGTGCGCCATGGAGCATCCGACTAATAATAGCCACGTCACTTTTAAATAGTCAGGTGC Tacca 0AAGCGTGTGACTTGGGGCATGAGGTTAATTTTTAGTAGCTCGGAGGCAATATGTGCACAATGAAGCATCTGACCT?CGTTGGTCTCGTCACTCGTCAAGAGTCACTA?C Trillium 0AAGCGTTTGACTTGGGGCAC?GAATGCAGTTATAGGACCTCGAAGGCAGAATGTGCGCCATAGGCTATCTGATCTACA?TGGT?TCGTCACTCGTAAATAGTCTGGAG? Vellozia 0AAGCGTTTGACTTGGCGC?CCAGGCTAATTTATAGGACCTCGGAGGTAATGAGTGCGCAATGGGCTTTTTCACTTATGATAGTTTTGTCACTCGTCAATAGTCAGGATC Veratrum 0AAGCGTTTGA?TTGGGGCACCGAATGCAAATATAGGCCAAAGGAGG?GAAATGTGAGCTATGGGCTATTCCACCTACAATGGTCTCGTCACTCGCCAATAGTCAGGA?C Xanthorrhoea 0AATCGTTTGACTTAGGACACGAAGTTAATATATAGGACCTCGGAGGCAATGTGTGCGCAATGGAGCTTCTGACCTACATAAGTCTCGTCACACGCCAATAGTCAGGATC ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2091] TITLE RS; LINK TAXA = Taxa1; DIMENSIONS NCHAR=42; FORMAT DATATYPE=Standard SYMBOLS= "0 1" MISSING=? GAP= -; MATRIX [ 10 20 30 40 ] [ . . . . ] Acorus 0110001111110111000110000?0111100111?11011 Alstroemeria 010001?011000110011???01010111100111111011 Anigozanthos 11100100??0011110010001001?110100111101111 Canna 011000000100111100100111000110101110?01011 Catopsis 011000?1110?111100101011010110100111111111 Curculigo 01100100?100?11111110001010110100111111011 Eriocaulon 0100010?1000?111???01011010110?00011?01000 Flagellaria 011001000100111100100010110110100101111110 Gymnostachys 01100110?111?11101001001110110100111111011 Nypa 011001001?0011110?100111010110100111111011 Oryza 1??0010?010??01?001000110???10?0?101???000 Piper 01111000?110?10101011000?01101010111011010 Saruma 01111000?110010101011000?01101010111?11010 Smilax 111001001?000111101?0001010110?00111111011 Symplocarpus 0010010010000111010?1?00010111?00111111011 Tacca 0110??00?101?01101110001010110100110110011 Trillium 00000100?100011110110010?1100010000101?011 Vellozia 011001001100?11101110001010111101111111011 Veratrum 011001011100011001110011010001100101111011 Xanthorrhoea 011001001100011101110000010110?00111110011 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2090] TITLE rbcL; LINK TAXA = Taxa1; DIMENSIONS NCHAR=242; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 ] [ . . . . . . . . . . . . . . . . . . . . . . . . ] Acorus TCCATGAATTCAACC?AGTGTCGCCCCCGCCCGTTGGAATATCCGTGCCCTGGCTTCCGTCCACGCT?GGAGGTTCCATGCGGCCAAACTACGGCGAGTCTATAGGAATAATGTGTGCCAAGCAGTTTCGTATGCGATTACCCCTTGGCTCG?TAGCCAAGGATAGACTTACAAGTTTACTATTGCACCTCGCGGTCGCTTACAATATCGATGGACACCATTGT?????????????????? Alstroemeria CCCCCGAACTTAGCCAAGTGTTGTT?CTGACTATTGGAATATCCGTTTCCTGGCGTCCGTCCACGCCTAAAGGCTCCGCACAGCCGGAATACGACGCATTCACTGGAGCAGCGGGTATGTATTAGTTTCAACGGCGTATCCCCTCTAGTTCATCAGCTAAGGATGGATTTTCAAGTTTACTACTGCGATTCGCAGTCGCTTAT?GTATCAGTAGGTAAGATAGTCCCGAGACGCGCGAAG?G Anigozanthos CTCGTGAGCTTAGCTAAGA?TTGTTATCGCCC?TTGGAATGTCCGTTCCCTGGTATCATTCAATG?CCAAGGGCTCCATACAGTCGGAATACAACAAACTCAAAGGAGTAACGCGTTTGTATCAATCTCGTTGGCGCATTCCCCTCAGTTCATTATCTAAGGGCGGATTTATAAGCTTACTATCGTGGTTTGCAACTGTCTACAAGATCAGTGGATA?GACGCCT?TGAAATACCCAGAGCA Canna TTCC??AACTCAACCAAGTGTTGTT?TCGCGCGTTGGTATATCCGTTCCTCGGCGTCCGTCTATGTCCGAGGGTTCCATATAACCACAATACAACGAATTCAATTAGATAACGTGTTCGTATCAATTTCGTTTGCGCATTCCCCCTACTCCATTAGCTAAG?GTGGATTTATAAGCT?ACTATA?CGATTTGCAGCCGTCTACA?TCTAGGTGGA?AAGATAGCCT???????????????? Catopsis ?TCGCGAACTCAGCTAAGTGATTTTACCACCCGTCGGAATATCCATTCCCCGGCGTCATTCAACGTTCAAGGGTTTCATACAGCCAGAACGCAACGAATGCAAAGGGGTAACATGTGCATATCAGTTTCGTTGGCGCATCCTCCTCAGTTCATTAGCTAAGGATGGGTTTTCTAGTCTACTATAATGATTT?CAACCGTTTGCAATATCGGTGAATACGATAGCCCTGAAACCTCCGAAGCA Curculigo TTCCCGAACTTAGCTGAGAGTTGTTACCGGCCATTGGAACATCCGTTCCCCGGCGTCCGTCTAAGTTCAAAGGTTCCGTACAACCAGAATACGACGAATTCAAAGGAGTAACGAGTGCGCAGCAGTTTCATCTCCGATTCCCCCTCAGTTCATTGGGCAAGGATGGGTTTACAAGCTTACTATTGCGATTCACAGCCGCTTACAACATAGACAGATAAACTAGCCTAGAGACGCAGAGAGCA Eriocaulon CTCACGAGTCC?TGTAGCTGTCTTCATAGCCTGTTGAAATACTTGTTCTTTAATACTCGTCAATATCTAAGGATTCCATATAGCTA?AACACAACAAATTC?AAGGGATAGCGTGTCTGTATCAGTTTTGATGGTACAGCCTCCTCGATTCATGAGCCAGGGATGGGTTCTC?GCC?TATC?CAACGGTCTGCAG?CGTTTGCAGTACCAGTGAACAAGATTGC?????????????????? Flagellaria TTCGCGAACTGAACTGAGTGTCTTTATCGCCTGTTGGAATATTCATTCCCCGGCGTCATTCAACCTTCAAGGGTTCTATACAGCCAGAATACAACGAATTCGCAGAGGTAGCGTA?CCACAGCAGTTTCGTTGGTGCATCCTCCC?AGTCCGATGGCTAAGGATGGATTTTTTAGC?TACTGTCGGGATTTGCAACCGTTC?CAATATCAGTGAGTAAGATTGCTCAGAACCGCGCGACGAA Gymnostachys CCCCTGGACTCAACTAGGTATTGTCACCGGCCGTTGAAACATCCGTGCTTCGGCTTTCGTCCACGCTCAGAAGTTCCAGACGACCAGACCACGGCGAATCCATAGGGATAACGTATGTGTGTTAGCCTTGTAGGTGTATACCCCTCGGTTCATTAGCTAAATGTGGGTTTACAAGTTTAATATCGCGATTCGTGGCCGCTTACAACATCGGCGGATAAGATAGCTCTGAGACAC???????? Nypa CTCCCGAACTCAGCTGAGAGTTGTTACCAACCGTCGGAATATCCGTTCCCCGGCGCCCTTCCACATTCAAGGGTTTCATACAGCCGGAACACGACGAATTCAAAGGGGTAACGTGTGCATATCAGTTTCATTGGCGCATCTCCCTCAGTTCATTAGG?AGGGATGGGTTTTCAAGCCTACTATAACGATTCGCAGCTGTCTACAACATCGGTGGATAAGATAGCCTCGAGACCC???????? Oryza TTTGCGAGCTGGGCCAAGTATTTTTCTCGCCCGTTGGTATGTCCGCTCCCCGGCGTCC?TCAATGTTTAAGGACTTTATATAATTAAGACACAACAAATGC?AATAGCTGGCGGACTTGTAT?GATTTTGTCGGTGCATCCCCTC?AGTCTATGAGCTAAAGACAGATCTTTTGCCCTGACATAAGGAT?TGCAATTATTTATTATACCGGT?AGTAAGA?TGCTCAAAACCGCGCGAAACA Piper TCCATGAGCCCAGCTGAGTGTTGCCACCGCCCGCTGGAACGTCCATATTCCGATGTTATATCGCGTCCAGAGGTCCCATACCGCCGGACCACGGCGCACTCAAAGAGATAACGTACCCGTATCGGCTCCGTAGGCGCATACCCCTCGGCTCGTCAGCTCAGGAT?CGCTTTC?AGCTAACTGTCGCGATCTGCGGCCACTTACAA?CTCGGTGGATGAGATAGC?????????????????? Saruma TCCCTGAACTCAGCTGAGTGTTGCCACCGCCTGCTGGATCATCTGTACCCCGGCATTCGTCCAT?CTTAGAGGTTCCATG?CGCCAGACCACGGTGCATTCAAATAGACAGCGTACCCGTATCAGTTTCGTAGGCGCAT?TCCCTTGACCTGTTAGCTCAGGA?ACGCTTTCAAGCTAACTATCGTGACTCGCGGCCGCTTACAATATAGGTGGGTAAGATGCCT?TAAGACATAGAGC?TG Smilax TCCCTGAATTCAGCTAAG?G?TGTTACAGAGCGTTGGAATACCCGTTCCCCAGTGTTATTCCACACTCAAAGGTTCCACACAGCCAGA?CACAACGAATGCACTGGGGTAACGTGTGCGCATTAGTTTCGT?GCTACATATCCCTCAGTCCATCAGCTAAGGATGGACCTTCAAG?TTACTATTGCACCCTACAGCCGCCCACAGTATCAGCG????????????????????????????? Symplocarpus TCCCTGGACTCAACTAA?TATTTTCACCGGCCGTTAGATCGTCCGTGCTTCGGCTTTCGTCAACACCCAGAGGTTCCAGATGACCAGA?CACGGCGAATTCAAAGGGATAATGTATCTGTGTCAGCTCCGTAGGTGCATACCCCTCGGTCCATTATCTAAGTATGGGTTTACAAGTTTACTATCGCGATTCGTGGCCGCTTACAACATCGGCGGATAACATAGC?????????????????? Tacca TCTCCGAACTCGGCCAA?TATTGTTACCAAGTGCT?G?ATATCCATTCCCCGACGTTATTCCACGTTCAAGGGTCCCATGCAGCCACAACA?GAT?AGTGTGCAGGAGCGACGTGTATGTAT?AGCTTCGTATGCGCATCTT?CTCAGTTCATTAGCTAAGGGTGGGCTTACAAGCTTACTGTAACGATTCGCAGTCGCTTGCAATATCGGTGGATAAGATAGCTCTGAGACACACAACACA Trillium CCCCCAAACTCAGGTAGCTGATGTTACCGAGCGCTGGAATATTCGTGCCCCAGCGTTCGTCAACGCTTGAAGGCTCCA?ATAGCCAAGACATGACGAATTCAAAGGGGTAGCGCGTGCGTATTAGTTTCGTTGGCGCATCCCCTTCAGTTCATTAGCTAGGGATGGACTTTCAAGTTTGCTATCGCGATTCGCAGCCGCCTATAATATCAGTAGATAAGATTGCCCTGCG???????????? Vellozia ??CCCGAACTCAGCTAAGAGTTGTTACTGAGCGTTGGAATATTCACTCCCCAGCGTT?TATCGAGTTTGAAGGTTTTATATAGCCGGAATACAACGAACTCAAAGAGATAACATATCCGTATCAGCTTCG?TGGCGCATTCCACCCAGTCCATTATCTCAAGATGGACTTTCAAGTTTACTATCATGATTCGCAGCCGCTTACTAG?TCAATAGATAAAATAGCCCTGAGATACACAAAGTA Veratrum CCCCCAAACTTAACTAAC?GTT?TTACTGAGCGTTAGAATATCCGTTCCCCGACGTTATTCCACGCCTAAAAGTTCCACACAGCCACAACATGACGAATGCAAAGGAATAACGCGTGCCAATCAGTTCCGTTGCCGCAGCCCACCCACTCCATTAGCTAGG?ATGGACTCTCAAGTTTACTATCACAATTCGCAGCCGCCTGCAATATCAGTGGATGAGACTGCCCTGCG???????????? Xanthorrhoea TTC?CGAACTCATCTAAGTGTT?CCACTGGCCGTTGAAATATCCGTTCCCCGGCATCCTTCCA?CCCCAAAGGCTCCATACAACCAAAACGCGACGAATGTAAAGGACTAACGAATCCGTATCAGTTTCGTTGGTGCATCCCCCTCAGTTCGATAGCCAAGGATGGATTTTCAAGCTTATTATA?CGATTCACAACCGCTTACAAC?TCGATGGATAAGCCTGCCCTGAACCACACGAAGAA ; END; BEGIN TREES; TITLE Tb5249; LINK TAXA = Taxa1; TRANSLATE 1 Piper, 2 Saruma, 3 Acorus, 4 Gymnostachys, 5 Symplocarpus, 6 Alstroemeria, 7 Curculigo, 8 Vellozia, 9 Trillium, 10 Veratrum, 11 Smilax, 12 Tacca, 13 Xanthorrhoea, 14 Nypa, 15 Catopsis, 16 Anigozanthos, 17 Canna, 18 Eriocaulon, 19 Flagellaria, 20 Oryza; TREE Fig._3a = [&R] (1,2,(3,((4,5),(12,((8,((6,11),(9,10))),((7,13),(14,((16,17),(15,(19,(18,20))))))))))); END; BEGIN TREES; TITLE Tb5247; LINK TAXA = Taxa1; TRANSLATE 1 Piper, 2 Saruma, 3 Acorus, 4 Gymnostachys, 5 Symplocarpus, 6 Alstroemeria, 7 Curculigo, 8 Vellozia, 9 Trillium, 10 Veratrum, 11 Smilax, 12 Tacca, 13 Xanthorrhoea, 14 Nypa, 15 Catopsis, 16 Anigozanthos, 17 Canna, 18 Eriocaulon, 19 Flagellaria, 20 Oryza; TREE Fig._2a = [&R] (1,2,(3,((4,5),(12,((8,((6,11),(9,10))),((7,13)Asparagales,((16,17),(14,(15,(19,(18,20))Commelinanae))))))))Liliopsida); END; BEGIN TREES; TITLE Tb5248; LINK TAXA = Taxa1; TRANSLATE 1 Piper, 2 Saruma, 3 Acorus, 4 Gymnostachys, 5 Symplocarpus, 6 Alstroemeria, 7 Curculigo, 8 Vellozia, 9 Trillium, 10 Veratrum, 11 Smilax, 12 Tacca, 13 Xanthorrhoea, 14 Nypa, 15 Catopsis, 16 Anigozanthos, 17 Canna, 18 Eriocaulon, 19 Flagellaria, 20 Oryza; TREE Fig._2b = [&R] (1,2,(3,((4,5),(8,((7,13),((12,((6,11),(9,10))),((16,17),(14,(15,(18,(19,20))))))))))); END; BEGIN TREES; TITLE Tb5250; LINK TAXA = Taxa1; TRANSLATE 1 Piper, 2 Saruma, 3 Acorus, 4 Gymnostachys, 5 Symplocarpus, 6 Alstroemeria, 7 Curculigo, 8 Vellozia, 9 Trillium, 10 Veratrum, 11 Smilax, 12 Tacca, 13 Xanthorrhoea, 14 Nypa, 15 Catopsis, 16 Anigozanthos, 17 Canna, 18 Eriocaulon, 19 Flagellaria, 20 Oryza; TREE Fig._3b = [&R] (1,2,(3,((4,5),((8,(20,(18,19))),(15,(14,((12,(7,13)),((16,17),((6,11),(9,10)))))))))); END;