#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 November 11, 2026; 16:28 GMT

TreeBASE (cc) 1994-2008

Study reference:
Hibbett D. 2002. Shiitake mushrooms and molecular clocks: historical biogeography
of Lentinula. Journal of Biogeography, 28(2): 231-241.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S735]

[ The following blocks are input data for analysis step 1137 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep1137;
        DIMENSIONS NTAX=11;
        TAXLABELS
            Agaricus_bisporus
            Albatrellus_syringae
            Boletus_satanas
            Bondarzewia_berkleyi
            Dacrymyces_chrysospermus
            Gomphus_floccosus
            Lentinula_boryana_R50
            Lentinula_edodes_TMI1148
            Lentinula_novaezealandieae_TMI1449
            Pleurotus_ostreatus
            Thelephora_sp
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2309]

	TITLE clock_calibration;
	LINK TAXA = TaxaForAnalysisStep1137;
	DIMENSIONS NCHAR=412;
	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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410  ]
[                                               .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .  ]
Agaricus_bisporus                      GGGAAAATAATGATATTACCTT-GCTATAAG?GTTGTCCAAATAACTGGTGCCAGAAG?CTCGGTAACGCCAGAAACGCAAACGTTAGTCGTCCTAATCAGGCGTAAAGGGTGAGTAGGCTGCTTTAAAAGCTAGAATCAAACAGAGGATAA--ACCGAACAATGTTTAGAGTAGGGA-TGAAATCCTTAAATACTAA-ATGGAGTACTAATGGTGAAAA-CTTTTATCT-AATAATGATTGACGCTGAGGAACGAAGGTGAGAATAGA-AAATAGGATTGGAGACCC-AGATATCCCTCACTGTCAACGATGAATGGTGGTTG-TTAGTT--CTAGTAACGATGTTAACGCGATAACCAT?-CCGCCTTGCGAGTACGGTTGCAAAACTGAAA-CCAAAAAAATTAGTCGT
Albatrellus_syringae                   GGGAAAATATTGATATTACCTT-ACTAATAGTGTCGTCCAA--AACTGGTGCCAGAAGACTCGGTAAGGCCAGAGACGCAAACGTTAATCGTCTTAATCAGGCGTAAAGGGTTTGTAGGCAGCTTTTAAAGATAGAATCAAATAGAGGATAGTTACCAAATCATGCTTAGAGGAGGGC-TGATATCCTAAGATACTAA-GTGGAATACTAGGAGCGTAAG-CTTTTTATCCAATAATGATTGACGCTGAGAAACGAAGGTGAGGATAGG-AAATAGGATTAGATACCC-AGATACCCCTCTCTGTCAACGATGAATGGTAGTTA-TTAGTTTTTTAGTGACGATGTTAACGCGTTAACCATT-CCGCCTTGTGAGTACGACTGCAAAGTTGAA?-A??AAAAAATTAGTCGG
Boletus_satanas                        GAGAAAATAATGATATTATCTT-ACTATTAGTGTCGTCTAA--ATTTGGTGCCAGAAGACTCGGTAAGACCTTAGACGCAAACGTTAATCGTCATAATCAGGCGTAAAGGGTGTGTAGGCGGCTTTTAAAGCTAGAATCTAAAAGAGGGTAA--GCTAAACAACATAATTAATTGGGACTGACAACTTATAATAAT---GTGGAGTACTAAAGGTTAAAG-CTATTTATCTACTTAAGATTGACGCTCAGAAACGAAGGGGAGAATAAGAAACTTAGATTAGAGACCT-AATTATCTCTCTCAGTCAACGATGAATGGTAGTTA-TTAAAA--TTAGTGACGAGGTTAACACGATGACCATT-CCGCCTTGTTAGTAAGACTGCAAAGTTGAAAA-CAAAAAAATTAGTCGG
Bondarzewia_berkleyi                   GGGAGAATAATGATGTTACCTT-ATTAATAGTGTCGCCCAA--AGCTGGTGCCAGAAGACTCGGTAAGGCCAGAGACGCAAACGTTAGTCGTCCTAATCAGGCGTAAAGGGTTTGTAGGCAGCTTTTAAAGCTAGAATCAAATAGAGGTTAT--ATTAAATAATACTTAGTGTAGGGC-CGATATCCTTAGATACTAA-GGGGAATATTAAGGGCGAAAG-CTTTTTTCC-ACTAATGATTGACTCTGAGAAACGA-GGTGAGGATAGG-AAATAGGATTAGATACCCAAATTACCCCTCTCTGTCAACGATGAATGGTGGCTA-CTAGTG--TTGGTGGCGATGTTAACACGATAACCATT-CCGCCTTGTGAGTACGACTGCAAAGTTGAAAA-CCAAAAAATTAGTCGG
Dacrymyces_chrysospermus               GGGAAA-TAATGATATATCCGTTACTATCAGTGTCGTCCAA--AGCTGGTGCCAGAAGACTCGGTAAGGCCAGAGACGCAAACGTTAGTCGTCATAAACAGGCGTAAAGGGTTCGTAGGCATCTTTTAAAGATAGAATCTAATGGAGTTTGA--ACCGCTAAATGCTTTAAGTAGGGA-TGAAATATTTAGAGATAAG-GTAGAATGCTCAAGGCGTAAG-CAGCCTCTCATGTAAAGATTGACGCTGAGGAACTAAGGAGAGCCCCAGGAAAAAGGATTAGATACCC-AAGTACCCTCTC-TGCCAACGATGAATGGTACTCA-TTAGCAAATTAGTGGGAAAGTTAACACGTGAACCATT-CCGCCTTGTGAGTACGG?CGCAAAG?CTGAAAACAAAAAAATTAG----
Gomphus_floccosus                      GTAAAAATAATGATGTTACTTT-ACTATTAGTGTTGTCAAA--GTCTGGTGCCAGAAGACTCGGTAAGGCCAGAGACGCAAGCGTTAATCATCTTGATCAGGCGTAAAGGGTTTGTAGGCGGCTTAAAAAGCTAGAATCAGATAGAGGTCAC-CGTGAGAGAACACTTGGAGTAGGGT-TGATATCTGTAGATACCAATGTGGAATTCTAATTAGCGAAGGCTCTTTTCCAAATAATGATTGACGCTGATAAACGAAGGTGAGGAACGA-CAATAGGATTAGATACCC-TGGCATCCCTCTCTGTCAACGATGAATGGTAGTGG-CTAGTTCTCTAGTGGCGAGGTTAACACGTTAACCATT-CCGCCTTGTGAGTACAATTGCAAAGTTGAA?-ACCAAAAAATTAGTCGG
Lentinula_boryana_R50                  GGACAAAATATGATATTACTTT-ACTATAAGTGTTGTCCAA--ATCTGGTGCCA?AAGACTCGGTAACGCCAGAAACGCGAACGTTAGTCACATTAACCAGGCGTAAAGGGTTCGTAGGCAGTTTTTTAAGATAGAATCAAATTGAGGATAA--GCCGAATAATGCTTAGAGTAGGGA-TTAAATCCTTAGATACTAG-GTGGAATACTAATGGTGAAAG-CTTTTTATCTAATAATGATCGACGCTGAGGAACGAAGGTGAGAATAGA-AAATAGGATTAGAGACCC-AGATATCTCTCACTGTCAACGATGAATGGTGGAATGTTAGTTTTCTAGTACCGATGTTAACGCGATAACCATT-CCGCCTTGAGAGTACGGTCGCAAGACTGAAA-CCAAAAAAATTA-----
Lentinula_edodes_TMI1148               GGAAAAAATATGATATTACTTT-ACTAAAAGTGTTGTCCAA--ATCTGGTGCCAAAAGACTCGGTAACGCCAGAAACGCGAACGTTAGTCACATTAACCAGGCGTAAAGGGTTCGTAGGCAGTTTTTTAAGATAGAATCAAATTGAGGATAA--GCCGAATAATGCTTAGAGTAGGGA-TTAAATCCTTAGATACTAG-GTGGAATACTAATGGTGAAAG-CTTTTTATCTAATAATGATCGACGCTGAGGAACGAAGGTGAGAATAGA-AAATAGGATTAGAGACCC-AGATATCTCTCACTGTCAACGATGAATGGTGGAAAGTTAGTTTTCTAGTACCGATGTTAACGCGATAACCATT-CCGCCTTGAGAGTACGGTCGCAAGACTGAAA-CCAAAAAAATTA-----
Lentinula_novaezealandieae_TMI1449     GGAAAAAATATGATATTACTTT-ACTAAAAGTGTTGTCCAA--ATCTGGTGCCAAAACACTCGGTAACGCCAGAAACGCGAACGTTAGTCACATTAACCAGGCGTAAAGGGTTCGTACGCACTTTTTTAAGATAGAATCAAATTGAGGAT?A--GCCGAATAATGCTTAGAGTAGGGA-TTAAATCCTTAGATACTAG-GTGGAATACTAATGGTGAAAG-CTTTTTATCTAATAATGATCGACGCTGAGGAACGAAGGTGAGAATAGA-AAATAGGATTAGAGACCC-AGATATCTCTCACTGTCAACGATGAATGGTGGAAAGTTAGTTTTCTAGTACCGATGTTAACGCGATAACCATT-CCGCCTTGAGAGTACGGTCGCAAGACTGAAA-CCAAAAAAATTA-----
Pleurotus_ostreatus                    GGGAAAAAAATGATATTACCTC-ACTAAAAGTGTTGTCCAA--ATCTGGTGCCAGAAGACTCGGTAAGACCAGAAACGCAAACGTTAGTCATCTTAATCAGGCGTAAAGGGTATGTAGGCAGCTTTTAAAGCTAGAATCTAATAGAGGAAAA--ACCAAATAATACTTAGAGTAGGGA-TGATATCCATAGATACTAA-GGGGAATACTAAGGGCGAAAG-CTTTTTTTCTATTAAAGATTGACGCTGAGAAACGAAGGTGAGAATAGG-AAATAGGATTAGATACCC-AGATACCTCTCACTGTCAACGATGAATGGTGGTTG-TTAGTT--CTGATGGCGATGTTAACACGATAACCATT-CCGCCTTGCGAGTACGGTTCCCAAACTGAAACCCCAAAAAATTAGTCGG
Thelephora_sp                          GGGAAGATAATGACATTACCTT-ACTATTAGTGTTGTCCAA--ATCTGGTGCCAGAAGACTCGGTAAGGCCA?AAACGCGAACGTTAGTCGTCCTAATCAGGCGTAAAGGGTGTGTAGGCAGCTTTAAAAGCTAGAATCAAATAGAGGATAT--ATTAAATAATATTTAGAGGAGGTC-TTATATCCTTAGATACTAA-ATGGAATATTAAGAGTGAAAG-CTTTTTATCTACTAAAGATTGACGCTGAGAAACGAAGGTGAGTATAGG-AAATAGGATTAGATACCC-AGATACCACTCTCTGTCAACGATGAATGGTGGTTG-CCAATTATTAGGTGGCTCTGTTAACACTATAACCATTTCCGCCATGTTAGTATGACTGCAAAGTTGAAAA-CAAAAAAATTAGTCGG
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = clock_calibration) = 
		N: 1-412;
CODONPOSSET  CodonPositions (CHARACTERS = clock_calibration) = 
		N: 1-412;
END;
[ The following blocks are output data for analysis step 1137 ]
BEGIN TREES;
      TITLE Tb5913;
      LINK TAXA = TaxaForAnalysisStep1137;
      TREE Fig._5 = [&R] (Dacrymyces_chrysospermus,((((((Agaricus_bisporus,(Lentinula_boryana_R50,(Lentinula_edodes_TMI1148,Lentinula_novaezealandieae_TMI1449))Lentinula),Pleurotus_ostreatus),Gomphus_floccosus),Thelephora_sp),Bondarzewia_berkleyi),Boletus_satanas));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3807]


END;