#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 09, 2025; 22:33 GMT

TreeBASE (cc) 1994-2008

Study reference:
Watanabe K., Ohi-toma T., & Murata J. 2008. Multiple hybridization in the Aristolochia
kaempferi group (Aristolochiaceae): evidence from reproductive isolation and
molecular phylogeny. American Journal of Botany, null.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S2058]

[ The following blocks are input data for analysis step 4286 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep4286;
        DIMENSIONS NTAX=23;
        TAXLABELS
            Aristolochia_K580homo_K325homo_K61_1_Setu2_2_AM2_1
            Aristolochia_cucurbitifolia_AC2_allele2
            Aristolochia_kaempferi_K158_allele1
            Aristolochia_kaempferi_K158_allele2
            Aristolochia_kaempferi_K61allele2_K437allele2
            Aristolochia_kaempferi_K642homo_K160homo
            Aristolochia_liukiuensis_K32_allele1
            Aristolochia_liukiuensis_K32_allele2
            Aristolochia_manshuriensis_SEST21_allele1
            Aristolochia_manshuriensis_SEST21_allele2
            Aristolochia_mollissima_AM2_allele2
            Aristolochia_moupinensis_Mou2_allele1
            Aristolochia_moupinensis_Mou2_allele2
            Aristolochia_saccata_Asa_homo
            Aristolochia_shimadai_AS2_allele1
            Aristolochia_shimadai_AS2_allele2
            Aristolochia_shimadai_K282_allele1
            Aristolochia_shimadai_K282_allele2
            Aristolochia_shimadai_K437_allele1
            Aristolochia_shimadai_Setu2allele1_AC2allele1
            Aristolochia_tanzawana_K95homo_K555homo_K653homo
            Aristolochia_westlandii_SETS36_allele1
            Aristolochia_westlandii_SETS36_allele2
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3185]

	TITLE 'PI intron (MP)';
	LINK TAXA = TaxaForAnalysisStep4286;
	DIMENSIONS NCHAR=261;
	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       250       260 ]
[                                                               .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Aristolochia_K580homo_K325homo_K61_1_Setu2_2_AM2_1     GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_cucurbitifolia_AC2_allele2                GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACAGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_kaempferi_K158_allele1                    GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGATCACTGATAGTGGGGCATGGTCTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_kaempferi_K158_allele2                    GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTTCCAAAGAAATGAACCAGTAATATTAACAAGGTTTCTACATGTGATTTGTATATTAAACTACATAAGTTTTCCATTTTGACAG
Aristolochia_kaempferi_K61allele2_K437allele2          GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACATTGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_kaempferi_K642homo_K160homo               GTATGCCATTTCTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACAGATGATGGTTTCACTGCTGTTATGGTGATCCAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_liukiuensis_K32_allele1                   GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACAGATGATGGTTTCACTGCTGTTATGGTGATCCAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTTATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACCACACAAGTTTTCTATTTTGACAG
Aristolochia_liukiuensis_K32_allele2                   GTATGCCCTTACTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACAGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAATTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_manshuriensis_SEST21_allele1              GTATGCTCTTTCTTTTTCATAATAAACTGATTAAACTTTCCTTATCTCTTAAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTCCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTCAAAATGCTTCTGAGCTTGGGCCTGTTCCACATTCAGTTTTTTAAAGTTCCCAAAGAAATGAACCAGTGATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACTACACAAGTTTTCCATTTTGACAG
Aristolochia_manshuriensis_SEST21_allele2              GTATGCTCTTTCTTTTTCATAATAAACTGATTAAACTTTCCTTATCTCTTAAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTCTCCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTCAAAATGCTTCTGAGCTTGGGCCTGTTCCACATTCAGTTTTTTAAAGTTCCCAAAGAAATGAACCAGTGATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACTACACAAGTTTTCCATTTTGACAG
Aristolochia_mollissima_AM2_allele2                    GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTTATATTAACAAGGTTTCTACTTGTGACTTGTATATTAAACCACACAAGTTTTCTATTTTGACAG
Aristolochia_moupinensis_Mou2_allele1                  GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTCACAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTT----C-----CCCAAAGAAATGAACTAGTAATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACTACACAAGTTTTCCATTTTGACAG
Aristolochia_moupinensis_Mou2_allele2                  GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTCACAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTT----C-----CCCAAAGAAATGAACCAGTAATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACTACACAAGTTTTCCATTTTGACAG
Aristolochia_saccata_Asa_homo                          GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAC--CTGTGGTCACTGATAGTGGGATATGGTCGTCACAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTT----C-----CCCAAAGAAATGAACCAGGAATATTAACAAGGTTTCTACTTGTGATTTGTATATTAAACTACACAAGTTTTCCATTTTGACAG
Aristolochia_shimadai_AS2_allele1                      GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATTGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_shimadai_AS2_allele2                      GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATTACTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAATTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_shimadai_K282_allele1                     GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTCATCTCTTGAACTGATAATGGTTTCACTGCTGTTATGGTGATCTAAATTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATAAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_shimadai_K282_allele2                     GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTCTTCATCTCTTGAACTGATAATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_shimadai_K437_allele1                     GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTT--AAAGTTCCCACAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_shimadai_Setu2allele1_AC2allele1          GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTTTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_tanzawana_K95homo_K555homo_K653homo       GTATGCCCTTTCTTTTTCATAATAAACTGATTAAACTCTTTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTTACAATGCCTCTGAGCTTGGGCATTTTCCATATTCAGTTTT--AAAGTTCCCACAGAAATGAACCAGTAATATTAACAAGGTTTATACTTGTGATTTGTATATTAAACTACACAAGTTTTCTATTTTGACAG
Aristolochia_westlandii_SETS36_allele1                 GTATGCCCTTTCTTTTTCATAATAAACTGATTGAACTCCCTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTCAAAATGCTTCTGAGCTTGGGCATTTTCCATATTCAGTTT---C-----CCCAAAGAAATGAACCAGTAATATTAACAAGGTTTCTACTTGTGATTCGTATATTAAACCACACAAGTTTTCCATTTTGACAG
Aristolochia_westlandii_SETS36_allele2                 GTATGCCCTTTCTTTTTCATAATAAACTGATTGAACTCTCTTTATCTCTTGAACTGATGATGGTTTCACTGCTGTTATGGTGATCTAAACTGTTCAATTCTGTGGTCACTGATAGTGGGATATGGTCTTCAAAATACTTCTGAGCTTGGGCATTTTCCATATTCAGTTTTT-AAAGTTCCCAAACAAATGAACCAGTAATATTAACAAGGTTTCTACTTGTGATTCGTATATTAAACCACACAAGTTTTCCATTTTGACAG
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = 'PI intron (MP)') = 
		N: 1-261;
CODONPOSSET  CodonPositions (CHARACTERS = 'PI intron (MP)') = 
		N: 1-261;
END;
[ The following blocks are output data for analysis step 4286 ]
BEGIN TREES;
      TITLE Tb9058;
      LINK TAXA = TaxaForAnalysisStep4286;
      TREE Fig._3_PI_intron = [&R] (((Aristolochia_saccata_Asa_homo,Aristolochia_moupinensis_Mou2_allele2,Aristolochia_moupinensis_Mou2_allele1),((Aristolochia_westlandii_SETS36_allele1,Aristolochia_westlandii_SETS36_allele2),(Aristolochia_manshuriensis_SEST21_allele2,Aristolochia_manshuriensis_SEST21_allele1))),((Aristolochia_kaempferi_K642homo_K160homo,Aristolochia_tanzawana_K95homo_K555homo_K653homo,Aristolochia_K580homo_K325homo_K61_1_Setu2_2_AM2_1,Aristolochia_kaempferi_K61allele2_K437allele2,Aristolochia_shimadai_K437_allele1,Aristolochia_kaempferi_K158_allele1,Aristolochia_shimadai_Setu2allele1_AC2allele1,(Aristolochia_shimadai_K282_allele2,Aristolochia_shimadai_K282_allele1),Aristolochia_shimadai_AS2_allele1,Aristolochia_shimadai_AS2_allele2,(Aristolochia_liukiuensis_K32_allele1,Aristolochia_mollissima_AM2_allele2),Aristolochia_liukiuensis_K32_allele2,Aristolochia_cucurbitifolia_AC2_allele2),Aristolochia_kaempferi_K158_allele2));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1053]


END;