#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 May 17, 2024; 7:50 GMT

TreeBASE (cc) 1994-2008

Study reference:
Myllys L., Lohtander K., & Tehler A. 2001. β-tubulin, ITS and group I intron sequences
challenge the species pair concept in Physcia aipolia and P. caesia. Mycologia,
93(2): 335-343.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S702]

BEGIN TAXA;
        TITLE  TaxonLabelSet10488;
        DIMENSIONS NTAX=26;
        TAXLABELS
            Physcia_aipolia_10137
            Physcia_aipolia_3021a
            Physcia_aipolia_314
            Physcia_aipolia_400
            Physcia_aipolia_404
            Physcia_aipolia_5160
            Physcia_aipolia_7891
            Physcia_aipolia_7894b
            Physcia_aipolia_7894c
            Physcia_aipolia_7906
            Physcia_aipolia_7915
            Physcia_alnophila_380
            Physcia_alnophila_390
            Physcia_alnophila_399
            Physcia_alnophila_4286b
            Physcia_alnophila_7894a
            Physcia_caesia_10810
            Physcia_caesia_12019
            Physcia_caesia_190
            Physcia_caesia_316
            Physcia_caesia_3341b
            Physcia_caesia_346
            Physcia_caesia_3472a
            Physcia_caesia_3847
            Physcia_caesia_7887
            Physcia_caesia_7934
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3679]

	TITLE 'group I intron (Figure 2b)';
	LINK TAXA = TaxonLabelSet10488;
	DIMENSIONS NCHAR=258;
	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        ]
[                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .        ]
Physcia_aipolia_10137       AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCACCGACT???CTAAATACATGCGCGGCTTGCACCTTTAGG-TGGCAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTCTGGG-CCCGATCCGACCAGCAGCCAGCTTA???AGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCG-CCTGTG??CCTGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_aipolia_3021a       AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT???CTAAATACATGCGCGGCTT-CACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGATCTCTGGCCTGTGAGCCCGAT??GACCAGCAGCCAGCTTT--CG?C??TGGTTCACAGATCAATCGACGGTGG????????????????????????????????????????????????????GACACTGCGGA-GG
Physcia_aipolia_314         AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT???CTAAACACATGCGCGGCTTGCACCTTTAGG-TCGCAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGGCTGTTAG-CCCAATCCGACCAGCAGCCAGATTCCACATC??TGGTTCACAGATCATTCGACGGTGGCCCTATGGCTAAAATATGACCGGTCCCCG?CTTTTGGCCCTGGA-TTTAGCGGAACCTGCGGAAGG
Physcia_aipolia_400         AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCACGTCGACT???CTAAATATATGCGCGGCTTGCCCCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGCCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACGGC??TGGTTCACAGATCAATCGACGGTGGCCTTGTGGCTAAAATATGACCGGTCCCCGGCTTTCGGCCCCGGA--TTTGCGGAACCTGCGGAAGG
Physcia_aipolia_404         AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT???CTAAACATATGCGCGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTTAAGTGCTGAGAGGATTTCGGGCTTTCAG-CCCAATCCGACCAGCAGCCAGATTCCACATC??TGGTTCACAGATCATTCGACGGTGGCCTTATGGTTAAAATATGACCGGTCCCTGGCTTTCGGCCCCGGA--TTTGCGGAACCTGCGGAAGG
Physcia_aipolia_5160        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCACCGACT???CTAAATATATGCACGGCTTGCACCTTTAGGGTGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGGG-CCCCATCCGACCAGCAGCCAGCTTA???AGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCGCCCTTTG??CCTGGAATTTTGCGGAACCTGCGGAAGG
Physcia_aipolia_7891        ?????????????TAGGTGAA-GGTTTGCCTACCGAAATCTCTCACGTCGACT???CTAAATATATGCGCGGCTTGCCC?TTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGCCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACGGC??TGGTTCACAGATCAATCGACGGTGGCCT-GTGGCTAAAATATGACCGGTCCCCGGCTTTCGGCCCCGGA--TTTGCGGAACCTGCGGAAGG
Physcia_aipolia_7894b       ???????TTTCCGTAGGTGAA-GGTTTGCCTACCGAAACCTCTCGCATCGACT???CTAAACACATGCGCGGCTTGCACCTTTGGG-TGGTAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGGCTGTGAG-CCCGGACCGACCAGCAGCCAGCTTTCACAGC??TGGTTCACAGATCAATCGACGGTGGCCCTTCGGCTAAAATATGACCGGTCCTCG?CTCTCTGCC?TAGA-ATTTGCGGAACCTGCGGAAGG
Physcia_aipolia_7894c       ??????GTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCACGTGGACT???CTAAATATATGCGCGGCTTGCCCCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGCCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACGGC??TGGTTCACAGATCAATCGACGGTGGCCTTGTGGCTAAAATATGACCGGTCCCCG?CTTTCGGCCCCGGA--TTTGCGGAACCTGCGGAAGG
Physcia_aipolia_7906        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCACGTCGACT???CTAAATATATGCGCGGCTTGCCCCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGCCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACGGC??TGGTTCACAGATCAATCGACGGTGGCCTTGTGGCTAAAATATGACCGGTCCCCG?CTTTCGGCCCCGGA--TTTGCGGAACCTGCGGAAGG
Physcia_aipolia_7915        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCACCGACT???CTAAATACATGCGCGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCAGGCTCTGGG-CCCGATCCGACCAGCAGCCAGCTTA???AGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCG?CCTGTGGCCCTGGAATTTTGCGGAACCTGCGGAAGG
Physcia_alnophila_380       AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGATATCTTTCGCATCGACT???CTAAATACATGCGCGGCTTGCATCTTCAGGGTGCGAGC-GACACCGTTTAAGTGCTGAGAGGATTTCGCGCTGTGAG-CTCGATCCGACCAGCAGCCAGTTTTGACAATCTGGGTTCACAGATCATTCGACGGTGGCCCCATGGCTAAAATATGACCGGTCCCCGGCTTTCAGCCCAGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_alnophila_390       AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGATATCTTTCGCATCGACT???CTAAATACATGCGCGGCTTGCATCTTCAGGGTGCGAGC-GACACCGTTTAAGTGCTGAGAGGATTTCGCGCTGTGAG-CTCGATCCGACCAGCAGCCAGTTTTGACAATCTGG-TTCACAGATCATTCGACGGTGGCCCCATGGCTAAAATATGACCGGTCCC?G?CTTTCAGCC?AGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_alnophila_399       AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGATATCTTTCGCATCGACT???CTAAATACATGCGCGGCTTGCATCTTCAGG-TGCGAGC-GACACCGTTTAAGTGCTGAGAGGATTTCGCGCTGTGAG-CTCGATCCGACCAGCAGCCAGTTTTGACAATCTGG-TTCACAGATCATTCGACGGTGGCCCCATGGCTAAAATATGACCGGTCCCCGGCTTTCAGCCCAGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_alnophila_4286b     AACAAG-TTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTAGCTCCGACT???CTAAATAAATGCGCGGCTTGCATCTCTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGAATTTGGGCTTTAA---CTCGATTCGACCAGCAGCCAGTTTTGACA-TCTGG-TTCACAGATCATTCAACGGTGGCCTAT-GGCTAAAATATGACCGGT?CCCCGCTTTCAG??CAGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_alnophila_7894a     ?????GGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATTTTTCGCATCGACT???CTAAATACATGCGCGGCTTGCATCTTTAGG-TGCGAGC-GACACCGTTTAAGTGCTGAGAGGATTTCGCGCTGTGAG-CTCGATCCGACCAGCAGCCAGTTTGGACAATCTGG-TTCACAGATCATTCGACGGTGGCCCCATGGCTAAAATATGACCGGTCCCCG?CTTTCGGCCCAGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_10810        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAACCCCTCGCAGCATCGACTCTAAATACATGCGTGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACAGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCGGCCTTTG??CCTGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_12019        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT-CTCTAAATACATGCGCGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTCCGGGCTGTTAG-CCCGATCCGACCAGCAGCCAGCTTTCGCAGC??TGGTTCACAGATCAATCGACGGTGGCCTTGTGGCTAAAATATGACCGGTCCC?GGCCTTTG?CC?TGGA-TTTCGCGGAACCTGCGGAAGG
Physcia_caesia_190          ????????????GTAG-TGAA-GGTTTGCCTACCGAAACCCCTCGCAGCATCGACTCTAAATACATGCGTGGCTTGCACCTTTA?G-TG??AGC?GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGAG-CCCT-TCCGACCAGCAGCCAGCTTTCACAGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCGGCCTTTGGCC?TGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_316          AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT-CTCTAAATACATGCGCGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTCCGGGCTGTTAG-CCCGATCCGACCAGCAGCCAGCTTTCGCAGC??TGGTTCACAGATCAATCGACGGTGGCCTTGTGGCTAAAATATGACCGGTCCCCGGCCTTTG?CC?TGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_3341b        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT???CTAAATCCATGCGCGGCTCGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGATTTCGGGCTGTTAG-CCCGATCCGACCAGCGGCCAGTTTTCACAGC??TGGTTCACAGATCAATCGACGGTGGCCCTATGGCTAAAATATGACCGGTCCCCGGCCTTTG??CCTGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_346          ???????TTTCCGTAGGTGAA-GGTTTGCCTACCGAAACCCCTCGCAGCATCGACTCTAAATACATGCGTGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACAGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCGGCCTTTGGCC?TGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_3472a        AACAAGGTTTCCGTAGGTGAA-GGTTTGCCTACCGAAACCCCTCGCAGCATCGACTCTAAATACATGCGCGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACAGTTTTGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCGGCCTTTG??CCTGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_3847         AACAAG-TTTCCGTAGGTGAA-GGTTTGCCTACCGAAACCCCTCGCAGCATCGACTCTAAATACATGCGCGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACAGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCG-CCTTTG??CCTGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_7887         ??????GTTTCCGTAGGTGAA-GGTTTGCCTACCGAAACCCCTCGCAGCATCGACTCTAAATACATGCGTGGCTTGCACCTTTAGG-TGCGAGC-GACACCGTTCAAGTGCTGAGAGGGTTTCGGGCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACAGT??TGGTTCACAGATCAATCGACGGTGGCCTTATGGCTAAAATATGACCGGTCCCCGGCCTTTGGCC?TGGA-TTTTGCGGAACCTGCGGAAGG
Physcia_caesia_7934         ??????GTTTCCGTAGGTGAA-GGTTTGCCTACCGAAATCTCTCGCATCGACT???CTAAATACATGCGCGGCTTGCACCTTTAGG-TGCGAGC-AACACCGTTCAAGTGCTGAGAGGGTTCCGGGCTGTGAG-CCCGATCCGACCAGCAGCCAGCTTTCACAGC??TGGTTCACAGATCAATCGACGGTGGCCTTGTGGCTAAAATATGACCGGTCCC?GGCCTTTG?CCCTGGA-TTTTGCGGAACCTGCGGAAGG
;
END;