#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 September 19, 2025; 8:17 GMT TreeBASE (cc) 1994-2008 Study reference: Budke J.M., & Goffinet B. 2006. Phylogenetic Analyses of the Timmiaceae (Bryophyta: Musci) Inferred from Nuclear and Chloroplast Sequence Data. Systematic Botany, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1520] [ The following blocks are input data for analysis step 2951 ] BEGIN TAXA; TITLE TaxaForAnalysisStep2951; DIMENSIONS NTAX=34; TAXLABELS Bryobrittonia_longipes Diphyscium_foliosum Ditrichum_flexicaule Encalypta_armata Funaria_hygrometrica Timmia_austriaca_1 Timmia_austriaca_2 Timmia_austriaca_3 Timmia_austriaca_4 Timmia_austriaca_5 Timmia_austriaca_6 Timmia_megapolitana_1 Timmia_megapolitana_2 Timmia_megapolitana_3 Timmia_megapolitana_4 Timmia_megapolitana_subspecies_bavarica_1 Timmia_megapolitana_subspecies_bavarica_2 Timmia_megapolitana_subspecies_bavarica_3 Timmia_megapolitana_subspecies_bavarica_4 Timmia_megapolitana_subspecies_bavarica_5 Timmia_megapolitana_subspecies_bavarica_6 Timmia_megapolitana_subspecies_bavarica_7 Timmia_megapolitana_subspecies_bavarica_8 Timmia_megapolitana_subspecies_bavarica_9 Timmia_norvegica_1 Timmia_norvegica_2 Timmia_norvegica_3 Timmia_norvegica_4 Timmia_norvegica_5 Timmia_norvegica_variety_excurrens_1 Timmia_norvegica_variety_excurrens_2 Timmia_sibirica_1 Timmia_sibirica_2 Timmia_sibirica_3 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1126] TITLE 'trnL-trnF region'; LINK TAXA = TaxaForAnalysisStep2951; DIMENSIONS NCHAR=691; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Bryobrittonia_longipes ???????????????????????????AAAAACTTACTAAATGCGAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA----TTTTTATTAAAAATAAGATAGGTGCAGAGACTCGATGGAAGC-TATCCTAACGCATAATAGTTTAATATTTATTT-AATTAAGTTTATTAATTGATAAAA-----------CTAAAATGAAACTAAAA-------TTTTTTAATA----------------------------------------------------------------TTTTGAATATT------------AAGCAAGGATAAAGAGA-GAGTCCAATTTTACATGTTAATGTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAACTAGTA-----------------------------------------------------------------------AAATTTTT------------------G-TATATTTAATAGCACGTATAAAT-G---TACAAAATTCTAAA----------CAAATAATTTTTATTGACATAAACTTCTAATTTATGTTAAAATAATCCAAATA--AAAAA? Diphyscium_foliosum ???????????????????????????AAAAACTCACTAAATGCTAGCTTTCAGATTCAGGGGAACTTAGGTTGAAAAA-AGTATAAGCGATCCTGAGCCAAATCTTA-------TTTCAAAAACAAGCATAGGTGCAGAGACTCAATGGAAGC-TATTCTAACGAATAATATTTTGAAATTTAATT-AATAATAAAATAATTATAAA--------TTTAT--TATTAAATTTACTGATA------AAAAACGACAAAACAAGAAGATATTTTACTAAGAGTAAAAAAAGTAAAAAACTTTATTTAAACTGTAATTTTGTCTATTAAGTATT------------AAACGAGGATAAAGATA-GAGTCCAAATTTACATGTTAATTTTAGCAACAATTTGAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AGATCATTT---------------------------AAAAAATTATTGAAAATAGAAAAATAAAATATACTTTTT-----ATATT----CTATATATGTATAT---G-TATATATATATGAAA-TATAAAAA-GTATAGAAAAATATAAAGATAAATTTTTTT---------GTTGACATAAGCTTCTAAATTATG????????????????????????? Ditrichum_flexicaule CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTGCTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCGATCCTGAGCCAAATCTTA--------CTTTAAAAGTAAGATAGGTGCAGAGACTCGATGGAAGC-TATCCTAACGCAAAATTTTTTAAGATTTATTT-AATTGAATTTT-----------------------------------CTGGATTAATAG-AAATAAAAAAAATTTAA--------------------------------------------------------CTATAATATTATTTTTTAAATAGCAAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAACTATGA-------------------------------------------------------------TTTTTTTTTT--------------------------------------------------------------------------------------------ATTGACATAGGCTTCCAGTTTATGTTAGGATAGCCCAAACG--AAAAAA Encalypta_armata ??????????????????CTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTTGGTTGAAAAAAAATATAAGCAATCCTGAGCCAAATTTTC--------TTTTAAAAGTAAGATAGGTGCAGAGACTCGATGGAAGC-TATCCTAACGTATAATATTTTTATATTTATTT-AATTATTGAT--------------------------------GAAACTAAAT------TTAAACTGAAATTTTATTA--------------------------------------------------------TTTTGAATATT------------AAGCAAGGATAAAGATA-GAGTCCAATTTTACATGTTAATTTTAACAACAATTTAAATTGTAGTAGAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAA------------------------------------------------------------------CTTT-------ATTAGTTTT---GTACATTTCTATTTGTTATATATAATAGCA------------TATACAAA--TGTACAAAATTATAAACAAATATTTTTTATTGACATAAACTTTTAATTTATGTTAAAATAATTTGAACA--AAA-AA Funaria_hygrometrica CTTAAAAAATAATTTGAGCTTTAATAAAAAAACTTATTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATCTTC------TATATTTTTAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGCATAAT----------------------------------------------------TTTTTTTTT-----------------------------------------------------------AATTTATACAAAATTTAA-------------TTAAATTAAA------------AATCGAGGGTAAAGAGA-GAGTCCAATTTTACATGTTAAATTTAGCAACAATTCAAATTGTAGTAAAAAGAAAATCCGTTGGCTTAAGTGACCGTGAGGGTTCAAGTCCCTCTTCCCCCA------AAAGTATTTAATAAAAAAAAGTTAATGTACTTTCTAAAAATTA--------------------------TTTTTTT------------------------------------------------------------------------------------------------ATTGACACAAACTTTTAATTTATGTTAGTATGTT-CACGTA--AAACAA Timmia_austriaca_1 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATATTTTAAGATTTTTTT-AATTAAATAATTAATTAATAGAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA------------------------------------------------------------CCTTTCTTTTT--------------------------------------------------------------------------------------------ATTGACATAAGCTCCTAGTTTATGTTACGATAGCCGAAACA--AAACAA Timmia_austriaca_2 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATATTTTAAGATTTTTTT-AATTAAATAATTAATTAATAGAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA------------------------------------------------------------CCTTTCTTTTT--------------------------------------------------------------------------------------------ATTGACATAAGCTCCTAGTTTATGTTACGATAGCCGAAACA--AAACAA Timmia_austriaca_3 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATATTTTAAGATTTTTTT-AATTAAATAATTAATTAATAGAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA------------------------------------------------------------CCTTTCTTTTT--------------------------------------------------------------------------------------------ATTGACATAAGCTCCTAGTTTATGTTACGATAGCCGAAACA--AAACAA Timmia_austriaca_4 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATATTTTAAGATTTTTTT-AATTAAATAATTAATTAATAGAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA------------------------------------------------------------CCTTTCTTTTT--------------------------------------------------------------------------------------------ATTGACATAAGCTCCTAGTTTATGTTACGATAGCCGAAACA--AAACAA Timmia_austriaca_5 ????????????????AGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATATTTTAAGATTTTTTT-AATTAAATAATTAATTAATAGAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA------------------------------------------------------------CCTTTCTTTTT--------------------------------------------------------------------------------------------ATTGACATAAGCTCCTAGTTTATGTTACGATAGCCGAAACA--AAACAC Timmia_austriaca_6 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATATTTTAAGATTTTTTT-AATTAAATAATTAATTAATAGAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA------------------------------------------------------------CCTTTCTTTTT--------------------------------------------------------------------------------------------ATTGACATAAGCTCCTAGTTTATGTTACGATAGCCGAAACA--AAACAA Timmia_megapolitana_1 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTTATTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGACTTTTTTTAATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAACGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_2 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTTATTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGACTTTTTTTAATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAACGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_3 ?????????????????????????????????????????TGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTTATTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGACTTTTTTTAATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAACGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_4 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTTATTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGACTTTTTTTTATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAATTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAACGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAGTTTATGTTACGATAACCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_1 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_2 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_3 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_4 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_5 ????????????????????????????AAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_6 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_7 ????????????????????????????????CTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_8 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAATAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_megapolitana_subspecies_bavarica_9 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGTTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AATATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAATAATGTTTTAAGATTTTTTT-TATTAAATAATTAATTAATAAAAAGAAATTTAA-------------CTAAAACTTTAT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTATTTTTAGCAACAATTTAAATTGTGGTAAAAAGAAAATCCGTTGGCTTTATTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAATCTAA------------------------------------------------------------CTTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGCTTCTAATTTATGTTACGATAGCCGAGACG--AAACAA Timmia_norvegica_1 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AATTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_norvegica_2 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_norvegica_3 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_norvegica_4 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_norvegica_5 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_norvegica_variety_excurrens_1 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_norvegica_variety_excurrens_2 ??????????????TGAGCTTTAGTAGAAAAACTTA-TAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAAATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AATTAAGTAATTAATTAATAAAAGTAAATTTAA-------------CTAAAATTTTCT--------------------------------------------------------------------------CTTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCTTAATTTATGTTACGATAACCGAAACG--AAACAA Timmia_sibirica_1 ???????????????????????????????????????????????CTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGGCCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_sibirica_2 CTTAAA---TAATTTGAGCTTTAGTAGAAAAACTTACTAAATGCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AGTTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAACAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCA------AAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGTCGAAACG--AAACAA Timmia_sibirica_3 ??????????????????????????????????????????GCTAGCTTTCAGATTCAGGGAAACTTAGGTTGAAAAA-AGTATAAGCAATCCTGAGCCAAATTTTA------TTCTTTAAAAATAAGATAGGTGCAGAGACTCAATGGAAGC-TATCCTAACGAAGAATATTTTAAGATTTTATT-AATTAAGTAATTAATTAATAAAAATAAATTTAA-------------CTAAAA---------------------------------------------------------------------------------TTTTATATATT------------AAGCGAGGATAAAGATA-GAGTCCAATTTTACATGTTACTTTTAGCAATAATTTAAATTGTAGTAAAAAGAAAATCCGTTGGCTTTAGTGACCGTGAGGGTTCAAGTCCCTCTACCCCCAACCCCAAAAGTCTAA-------------------------------------------------------------TTTTTTT-----------------------------------------------------------------------------------------------CTTGACATAAGTTCCTAATTTATGTTACGATAGCCGAAACG--AAAC?? ; END; BEGIN SETS; CHARSET trnL (CHARACTERS = 'trnL-trnF region') = 1-691; CHARSET messytrnL (CHARACTERS = 'trnL-trnF region') = 222-234 247-320 465-470 480-642; CHARSET spacer (CHARACTERS = 'trnL-trnF region') = 465-691; CHARSET 3.exon (CHARACTERS = 'trnL-trnF region') = 413-464; CHARSET trnLStems (CHARACTERS = 'trnL-trnF region') = 371-376 379-382 387-396 401-405 407-412 1-6 13-27 33-41 47-69 71-73 81-83 85-88 90-100 103-108 126-131 133-161 350-355 363-368; CHARSET trnLLoopsFreeSpacer (CHARACTERS = 'trnL-trnF region') = 7-12 28-32 42-46 70 74-80 84 89 101-102 109-125 132 162-349 356-361 369-370 377 383-386 397-400 406 471-479 540-550 643-683 686-691; CHARSET intron (CHARACTERS = 'trnL-trnF region') = 1-412; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'trnL-trnF region') = N: 1-691; CODONPOSSET CodonPositions (CHARACTERS = 'trnL-trnF region') = N: 1-691; END; [ The following blocks are output data for analysis step 2951 ] BEGIN TREES; TITLE Tb7724; LINK TAXA = TaxaForAnalysisStep2951; TREE 'Fig. 1. trnL-trnF region rr' = [&R] (((Timmia_austriaca_1,Timmia_austriaca_2,Timmia_austriaca_3,Timmia_austriaca_5,Timmia_austriaca_4,Timmia_austriaca_6),(((Timmia_megapolitana_subspecies_bavarica_1,Timmia_megapolitana_subspecies_bavarica_2,Timmia_megapolitana_subspecies_bavarica_8,Timmia_megapolitana_subspecies_bavarica_3,Timmia_megapolitana_subspecies_bavarica_4,Timmia_megapolitana_subspecies_bavarica_5,Timmia_megapolitana_subspecies_bavarica_9,Timmia_megapolitana_subspecies_bavarica_6,Timmia_megapolitana_subspecies_bavarica_7),(Timmia_megapolitana_1,Timmia_megapolitana_4,Timmia_megapolitana_2,Timmia_megapolitana_3)),(((Timmia_norvegica_2,Timmia_norvegica_3,Timmia_norvegica_4,Timmia_norvegica_5,Timmia_norvegica_variety_excurrens_1,Timmia_sibirica_2,Timmia_sibirica_1),Timmia_norvegica_1),Timmia_norvegica_variety_excurrens_2,Timmia_sibirica_3))),Ditrichum_flexicaule,Diphyscium_foliosum,(Encalypta_armata,Bryobrittonia_longipes),Funaria_hygrometrica); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2421] END;