#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 05, 2024; 11:35 GMT TreeBASE (cc) 1994-2008 Study reference: Wynns J.T., & Asmussen-lange C. 2014. A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales). American Journal of Botany, 101(4): 1-18. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15161] [ The following blocks are input data for analysis step 12903 ] BEGIN TAXA; TITLE TaxaForAnalysisStep12903; DIMENSIONS NTAX=25; TAXLABELS Herzogiella_seligeri_Denmark Isopterygiopsis_muelleriana_Scotland Plagiothecium_cavifolium_Denmark Plagiothecium_cavifolium_Denmark_B Plagiothecium_cavifolium_Germany Plagiothecium_curvifolium_Denmark Plagiothecium_curvifolium_Germany Plagiothecium_denticulatum_Denmark Plagiothecium_denticulatum_var_obtusifolium_Germany Plagiothecium_draytonii_HI_USA Plagiothecium_euryphyllum_Yunnan_China Plagiothecium_handelii_Yunnan_China Plagiothecium_laetum_Germany Plagiothecium_latebricola_Denmark Plagiothecium_neckeroideum_Yunnan_China Plagiothecium_nemorale_Germany Plagiothecium_nemorale_Iran Plagiothecium_nemorale_aquatic_Germany Plagiothecium_piliferum_WA_USA Plagiothecium_platyphyllum_Finland Plagiothecium_ruthei_Denmark Plagiothecium_succulentum_Denmark Plagiothecium_undulatum_Denmark Pseudotaxiphyllum_elegans_Germany Taxiphyllum_sp_Yunnan_China ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M20452] TITLE 'psbA-trnH Wynns & Asmussen Lange'; LINK TAXA = TaxaForAnalysisStep12903; DIMENSIONS NCHAR=179; 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 ] [ . . . . . . . . . . . . . . . . . ] Herzogiella_seligeri_Denmark CTTCTGTAAATAGTTAATATTTTCGTTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTTTTTTTATTTATTTTTAATAAATAAATTAGAAAAA-------------------AAGGCGGACGTG Isopterygiopsis_muelleriana_Scotland CTTCTGTAAATAGTTAATATTTTCGTTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGACCTTAGGAAATAAATTCCTAAGGTCATTATTTTT---TTATTTATTTCCAATAAATAAATTGGAAAAA-------------------AAGGCGGACGTG Plagiothecium_cavifolium_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTCATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_cavifolium_Denmark_B CTTCTGTAAATAGTTAATATT--AGTTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTCATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_cavifolium_Germany CTTCTGTAAATAGTTAATATT--AGTTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTCATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_curvifolium_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTAATATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTAT---TTATTTATTTTCGGTAAATAAATTTAAAAAA-----------------AAAAGGCGGACGTG Plagiothecium_curvifolium_Germany CTTCTGTAAATAGTTAATATT--AGTTATAAATTTAATATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTAT---TTATTTATTTTCGGTAAATAAATTTAAAAAA-----------------AAAAGGCGGACGTG Plagiothecium_denticulatum_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACCATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTCATTTTCGGTAAATAAATTAAAAAAA------------------AAGGGCGGACGTG Plagiothecium_denticulatum_var_obtusifolium_Germany CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACCATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTTCTAAGATCATTATTTTT---TTATTCATTTTCGGTAAATAAATTAAAAAAA----------------AAAAAGGCGGACGTG Plagiothecium_draytonii_HI_USA CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTTT---TTATTCATTTTCGATAAATAAATTAGAAAAA-------------------AAGGCGGACGTG Plagiothecium_euryphyllum_Yunnan_China CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTACATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTTT---TTATTTATTTTCGATAAATAAATTAGAAAAA--------------------AGGCGGACGTG Plagiothecium_handelii_Yunnan_China CTTCTGTAAATAGTTAATATTTTAATTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTTT---TTATTTATTGAAAATAAATAAATTAGAAAGATTAATAAATTAAGAAAAAAAAGGCGGACGTG Plagiothecium_laetum_Germany CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAGGATCATTATTTTT---TTATTCATTTTCGGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_latebricola_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTTT--TTATTCATTTTCGGTAAATAAATAAATAAAT------------AAATAAAAAGGCGGACGTG Plagiothecium_neckeroideum_Yunnan_China CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTTT---TCATTCATTTTCGGTAAATTAATTAAAAAAA---------------AAAAAAGGCGGACGTG Plagiothecium_nemorale_Germany CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTTATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_nemorale_Iran CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTTATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_nemorale_aquatic_Germany CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTTATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_piliferum_WA_USA CTTCTGTAAATAGTTAATATTTTAATTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGACCTTAGGAATTTATTTCCTAAGGTCATTATTTTT---TTATTTATTTTCAATAAATAAATTAAGAAAA------------------AAAGGCGGACGTG Plagiothecium_platyphyllum_Finland CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACCATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTTCTAAGATCATTATTTTT---TTATTCATTTTCGGTAAATAAATTAAAAAAA----------------AAAAAGGCGGACGTG Plagiothecium_ruthei_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACCATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAAATCCTAAGATCATTATTTTT---TTATTCATTTTCGGTAAATAAATTTAAAAAA-----------------AAAGGGCGGACGTG Plagiothecium_succulentum_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATCTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAAATAAATTCCTAAGATCATTATTTTT---TTATTTATTTT-GGTAAATAAATTAAAAAAA------------------AAAGGCGGACGTG Plagiothecium_undulatum_Denmark CTTCTGTAAATAGTTAATATT--AGTTATAAATTTACTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGATCTTAGGAATTTATTTCCTAAGATCATTATTTTT---TTATTCATTTTCGATAAATAAATTAGAAAAA-------------------AAGGCGGACGTG Pseudotaxiphyllum_elegans_Germany CTTCTGTAAATAGTTAATATTTTAGTTATAAATTTATTATATAAATTTATATAAATAGGATAACAACTTGAAAATAATGACCTTAGGAAATAAATTCCTAAGGTCATTATTT--------------CAAAATAAATAAATTAGAAAAA----------------AAAAAGGCGGACGTG Taxiphyllum_sp_Yunnan_China CTTCTGTAAATAGTTAATATTTTAATTATAAATTTATTCTATAAATTTATAAAAATAGGATAACAACTTGAAAATAATGACCTTAGGAATTTATTTACTAAGGTCATTATTCTTTTTTTATTTGTTGAAAATGAATAGATTGGAAAAA--------------------AGGCGGACGTG ; END; [ The following blocks are output data for analysis step 12903 ] BEGIN TREES; TITLE trnHpsbA_Wynns_UNINF_EXCL; LINK TAXA = TaxaForAnalysisStep12903; TREE PAUP_4 = [&R] (Herzogiella_seligeri_Denmark:3.0,Isopterygiopsis_muelleriana_Scotland:2.0,(((((((Plagiothecium_cavifolium_Denmark:0.0,Plagiothecium_cavifolium_Germany:0.0,Plagiothecium_cavifolium_Denmark_B:0.0):1.0,(((Plagiothecium_denticulatum_Denmark:0.0,Plagiothecium_ruthei_Denmark:1.0):1.0,(Plagiothecium_denticulatum_var_obtusifolium_Germany:0.0,Plagiothecium_platyphyllum_Finland:0.0):1.0):1.0,(Plagiothecium_nemorale_Germany:0.0,Plagiothecium_nemorale_Iran:0.0,Plagiothecium_nemorale_aquatic_Germany:0.0,Plagiothecium_succulentum_Denmark:0.0):1.0):1.0,Plagiothecium_latebricola_Denmark:0.0):3.0,((Plagiothecium_curvifolium_Denmark:0.0,Plagiothecium_curvifolium_Germany:0.0):4.0,Plagiothecium_laetum_Germany:0.0):1.0,Plagiothecium_neckeroideum_Yunnan_China:0.0):2.0,Plagiothecium_draytonii_HI_USA:0.0,Plagiothecium_undulatum_Denmark:0.0):1.0,Plagiothecium_euryphyllum_Yunnan_China:0.0):4.0,((Plagiothecium_handelii_Yunnan_China:2.0,Taxiphyllum_sp_Yunnan_China:2.0):3.0,Plagiothecium_piliferum_WA_USA:1.0):1.0):3.0,Pseudotaxiphyllum_elegans_Germany:3.0):1.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr70069] END; BEGIN TREES; TITLE trnHpsbA_Wynns_UNINF_EXCL; LINK TAXA = TaxaForAnalysisStep12903; TREE PAUP_5 = [&R] (Herzogiella_seligeri_Denmark:3.0,Isopterygiopsis_muelleriana_Scotland:2.0,(((((((((Plagiothecium_cavifolium_Denmark:0.0,Plagiothecium_cavifolium_Germany:0.0,Plagiothecium_cavifolium_Denmark_B:0.0):1.0,Plagiothecium_latebricola_Denmark:0.0):1.0,(((Plagiothecium_denticulatum_Denmark:0.0,Plagiothecium_ruthei_Denmark:1.0):1.0,(Plagiothecium_denticulatum_var_obtusifolium_Germany:0.0,Plagiothecium_platyphyllum_Finland:0.0):1.0):1.0,(Plagiothecium_nemorale_Germany:0.0,Plagiothecium_nemorale_Iran:0.0,Plagiothecium_nemorale_aquatic_Germany:0.0,Plagiothecium_succulentum_Denmark:0.0):1.0):0.0):3.0,((Plagiothecium_curvifolium_Denmark:0.0,Plagiothecium_curvifolium_Germany:0.0):4.0,Plagiothecium_laetum_Germany:0.0):0.0):1.0,Plagiothecium_neckeroideum_Yunnan_China:0.0):2.0,Plagiothecium_draytonii_HI_USA:0.0,Plagiothecium_undulatum_Denmark:0.0):1.0,Plagiothecium_euryphyllum_Yunnan_China:0.0):4.0,((Plagiothecium_handelii_Yunnan_China:2.0,Taxiphyllum_sp_Yunnan_China:2.0):3.0,Plagiothecium_piliferum_WA_USA:1.0):1.0):3.0,Pseudotaxiphyllum_elegans_Germany:3.0):1.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr70070] END; BEGIN TREES; TITLE trnHpsbA_Wynns_UNINF_EXCL; LINK TAXA = TaxaForAnalysisStep12903; TREE PAUP_3 = [&R] (Herzogiella_seligeri_Denmark:3.0,Isopterygiopsis_muelleriana_Scotland:2.0,(((((((((Plagiothecium_cavifolium_Denmark:0.0,Plagiothecium_cavifolium_Germany:0.0,Plagiothecium_cavifolium_Denmark_B:0.0):1.0,Plagiothecium_latebricola_Denmark:0.0):1.0,((Plagiothecium_denticulatum_Denmark:0.0,Plagiothecium_ruthei_Denmark:1.0):1.0,(Plagiothecium_denticulatum_var_obtusifolium_Germany:0.0,Plagiothecium_platyphyllum_Finland:0.0):1.0):1.0,(Plagiothecium_nemorale_Germany:0.0,Plagiothecium_nemorale_Iran:0.0,Plagiothecium_nemorale_aquatic_Germany:0.0,Plagiothecium_succulentum_Denmark:0.0):1.0):3.0,(Plagiothecium_curvifolium_Denmark:0.0,Plagiothecium_curvifolium_Germany:0.0):4.0,Plagiothecium_laetum_Germany:0.0):1.0,Plagiothecium_neckeroideum_Yunnan_China:0.0):2.0,Plagiothecium_draytonii_HI_USA:0.0,Plagiothecium_undulatum_Denmark:0.0):1.0,Plagiothecium_euryphyllum_Yunnan_China:0.0):4.0,((Plagiothecium_handelii_Yunnan_China:2.0,Taxiphyllum_sp_Yunnan_China:2.0):3.0,Plagiothecium_piliferum_WA_USA:1.0):1.0):3.0,Pseudotaxiphyllum_elegans_Germany:3.0):1.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr70068] END; BEGIN TREES; TITLE trnHpsbA_Wynns_UNINF_EXCL; LINK TAXA = TaxaForAnalysisStep12903; TREE PAUP_2 = [&R] (Herzogiella_seligeri_Denmark:3.0,Isopterygiopsis_muelleriana_Scotland:2.0,(((((((((((Plagiothecium_cavifolium_Denmark:0.0,Plagiothecium_cavifolium_Germany:0.0,Plagiothecium_cavifolium_Denmark_B:0.0):1.0,Plagiothecium_latebricola_Denmark:0.0):1.0,((Plagiothecium_denticulatum_Denmark:0.0,Plagiothecium_ruthei_Denmark:1.0):1.0,(Plagiothecium_denticulatum_var_obtusifolium_Germany:0.0,Plagiothecium_platyphyllum_Finland:0.0):1.0):1.0):1.0,(Plagiothecium_nemorale_Germany:0.0,Plagiothecium_nemorale_Iran:0.0,Plagiothecium_nemorale_aquatic_Germany:0.0,Plagiothecium_succulentum_Denmark:0.0):0.0):3.0,(Plagiothecium_curvifolium_Denmark:0.0,Plagiothecium_curvifolium_Germany:0.0):3.0):1.0,Plagiothecium_laetum_Germany:0.0):1.0,Plagiothecium_neckeroideum_Yunnan_China:0.0):2.0,Plagiothecium_draytonii_HI_USA:0.0,Plagiothecium_undulatum_Denmark:0.0):1.0,Plagiothecium_euryphyllum_Yunnan_China:0.0):4.0,((Plagiothecium_handelii_Yunnan_China:2.0,Taxiphyllum_sp_Yunnan_China:2.0):3.0,Plagiothecium_piliferum_WA_USA:1.0):1.0):3.0,Pseudotaxiphyllum_elegans_Germany:3.0):1.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr70067] END; BEGIN TREES; TITLE trnHpsbA_Wynns_UNINF_EXCL; LINK TAXA = TaxaForAnalysisStep12903; TREE PAUP_1 = [&R] (Herzogiella_seligeri_Denmark:3.0,Isopterygiopsis_muelleriana_Scotland:2.0,(((((((((((Plagiothecium_cavifolium_Denmark:0.0,Plagiothecium_cavifolium_Germany:0.0,Plagiothecium_cavifolium_Denmark_B:0.0):1.0,Plagiothecium_latebricola_Denmark:0.0):1.0,((Plagiothecium_denticulatum_Denmark:0.0,Plagiothecium_ruthei_Denmark:1.0):1.0,(Plagiothecium_denticulatum_var_obtusifolium_Germany:0.0,Plagiothecium_platyphyllum_Finland:0.0):1.0):1.0):1.0,Plagiothecium_nemorale_Germany:0.0,Plagiothecium_nemorale_Iran:0.0,Plagiothecium_nemorale_aquatic_Germany:0.0,Plagiothecium_succulentum_Denmark:0.0):3.0,(Plagiothecium_curvifolium_Denmark:0.0,Plagiothecium_curvifolium_Germany:0.0):3.0):1.0,Plagiothecium_laetum_Germany:0.0):1.0,Plagiothecium_neckeroideum_Yunnan_China:0.0):2.0,Plagiothecium_draytonii_HI_USA:0.0,Plagiothecium_undulatum_Denmark:0.0):1.0,Plagiothecium_euryphyllum_Yunnan_China:0.0):4.0,((Plagiothecium_handelii_Yunnan_China:2.0,Taxiphyllum_sp_Yunnan_China:2.0):3.0,Plagiothecium_piliferum_WA_USA:1.0):1.0):3.0,Pseudotaxiphyllum_elegans_Germany:3.0):1.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr70066] END;