#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 22, 2024; 11:40 GMT TreeBASE (cc) 1994-2008 Study reference: Vondrak J., Frolov I., Riha P., Hrouzek P., Palice Z., Nadyeina O., Halici G., Khodosovtsev A., & Roux C. 2013. New discoveries in biodiversity of Teloschistaceae lichen crusts in Central Europe north of the Alps. Fungal Diversity, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13908] [ The following blocks are input data for analysis step 10823 ] BEGIN TAXA; TITLE TaxaForAnalysisStep10823; DIMENSIONS NTAX=17; TAXLABELS Caloplaca_citrina_DQ173226 Caloplaca_citrina_DQ173239 Caloplaca_sp._aff._C._ulcerosa_USA_2 Caloplaca_sp._aff._C._ulcerosa_USA1_GU080298 Caloplaca_sp._aff._C._ulcerosa_USA3 Caloplaca_substerilis_Austria1_GU080299 Caloplaca_substerilis_Austria2 Caloplaca_substerilis_Bulgaria Caloplaca_substerilis_Czech_Republic Caloplaca_substerilis_Slovakia Caloplaca_ulcerosa_EU639623 Caloplaca_ulcerosa_EU639623_2 Caloplaca_ulcerosa_GU080293 Caloplaca_ulcerosa_GU080294 Caloplaca_ulcerosa_GU080295 Caloplaca_ulcerosa_GU080296 Caloplaca_ulcerosa_GU080297 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M16007] TITLE ITS_Caloplaca_ulcerosa_group; LINK TAXA = TaxaForAnalysisStep10823; DIMENSIONS NCHAR=519; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Caloplaca_citrina_DQ173226 AGAGAGGGACGTGCGGTTGCTTGCGGCCCACGGCCCGGGGGGG--TTCCCCTCTACTCTTCAACCCTATGCGTACCAACCTCTGTTGCTTCGGCGAGCGCCGGGGGG-TCT-ATACGCCTCGGCCCCGGCTTCGGTCGGTGAGTTCTCGCCGAAGACCCAATTCC-AATCTATTTGCAGTCCCGTCCGAGCGCATCCAT-AAA-TCCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCGTTCGCTTCCCC--ATTCGGGG-GGGCGCGCCTGTAAACTAGTGGCGGCCCCGGGGGGACCTCAAGCGTAGTAGAACCTT-TT-CGCTTGGGAGGTGCCA-CCCAGGGCTCGGCCGTCAA Caloplaca_citrina_DQ173239 AGAG-GGGACATGCGGCTGCTCGCGGCCCATGTCCCGGGGGAGC-TTCCCC-CAACTCTTCAACCCCATGTGTACCTACCTCTGTTGCTTCGGCGAGCGCGGGGGGGCTCTCGGGCGCCCCCGCCCCGGCTTCGGTCGGTGAGTTCTCGCCCGAAGCCCAACCTT-ATCCTGTTTGCAGCCATGTCCGAGCGCACCGATAAAAATTCCATCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCGTTCGCTTCCTTCTTTTGGGGG-AGGCGTGCCCGTAAACTAGTGGCGACCCCGGGGGGATCTCAAGCGCAGTTGAACCTT-AT-CGCTTGCAAGATGCCGCCCCGGGATCCGGCCGTCAA Caloplaca_sp._aff._C._ulcerosa_USA_2 AGAGCGGG-CAGGC--TT---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACTGTTGCTTCGGCGAGCGTTGGGGCGCCTC---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGTTCTCGCCCGAGGCTCAACCCC-ATTCTGTTCACAGTGATGTCCGAGTACACCGATTAAA--TCAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGCATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-ACGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCTGTCA-CGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGGAAA Caloplaca_sp._aff._C._ulcerosa_USA1_GU080298 AGAGCGGG-CAGGC--TT---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACTGTTGCTTCGGCGAGCGTTGGGGCGCCTC---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGTTCTCGCCAGAGGCTCAACCCC-ATTCTGTTCACAGTGATGTCCGAGTACACCGATTAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGCATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-ACGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCTTTCA-CGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGGAAA Caloplaca_sp._aff._C._ulcerosa_USA3 AGAGCGGG-CAGGC--TT---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACTGTTGCTTCGGCGAGCGTTGGGGCGCCTC---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGTTCTCGCCAGAGGCTCAACCCC-ATTCTGTTCACAGTGATGTCCGAGTACACCGATTAAA--TCAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGCATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-ACGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCTTTCA-CGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGGAAA Caloplaca_substerilis_Austria1_GU080299 AGAGCGGG-CAGGC--TT---TACGGCC-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACCGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCCCGGCCGGTGAGTTCTCGCCAGAGGCCCAACCCC-ATCCTGTTCACAGTAACGTCCGAGTACACCGATCAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCATCCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-GT-TCCAGGG-CGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCG-CCTGCGGCCCGGCCGGAAA Caloplaca_substerilis_Austria2 AGAGCGGG-CAGGC--TT---TACGGCC-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACCGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCCCGGCCGGTGAGTTCTCGCCAGAGGCCCAACCCC-ATCCTGTTCACAGTAACGTCCGAGTACACCGATCAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCATCCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-GT-TCCAGGG-CGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCG-CCTGCGGCCCGGCCGGAAA Caloplaca_substerilis_Bulgaria AGAGCGGG-CAGGC--TT---CGCGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCCACCCTGTGCGTATCAACCCCTGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCCCGGTCGGTGAGTTCTCGCCAGAGGCCCAACCCC-ATCCTGTTCACAGTGACGTCCGAGTACACCGATTAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTC{AC}AGCTTTGCTTGGTATTGGGCGTTCGCCTCCC-GCGTC-AGGG-CGGTGCGCCCGCAAATTAGTGGCGG-TCCGGGG{AG}GACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCGCCCTGCGGCTCGGCCGGAAA Caloplaca_substerilis_Czech_Republic AGAGCGGG-CAGGC--TT---CGCGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCCACCCTGTGCGTATCAACCCCTGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCCCGGTCGGTGAGTTCTCGCCAGAGGCCCAACCCC-ATCCTGTTCACAGTGACGTCCGAGTACACCGATTAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCGTTCGCCTCCC-GCGTC-AGGG-CGGTGCGCCCGCAAATTAGTGGCGG-TCCGGGGAGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCG-CCTGCGGCTCGGCCGGAAA Caloplaca_substerilis_Slovakia AGAGCGGG-CA{AG}GC--{AC}T---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCGACTCTTCAACCCTGTGTGTACCAACCATTGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCTCGGTCGGTGAGTTCTCGTCAGAGGCCCAACCTC-ATTCTGTTCACAGTGACGTCCGAGTACACCGATTAAA--CCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTGCTGGGC-TTCGCCTCCCCGTGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCGGGGAGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCG-CCCGCGGTCCTGCCGGAAA Caloplaca_ulcerosa_EU639623 AGAG-GGG?CAGGC--TT---CGCGGCC-GCGCCCTCGGGGGGAAACCCCCGTAACTCTTCAACCCACTGTGTATCTACCTTCGTTGCTTCGGCGAGCGTTGGGGCGCCTT---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGCTCTCGCCCGAGGCCCAACCTCAAGTCTGTTTAGAGTACCGTCCGAGCACA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCCAGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCT--CAACGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGTGAA Caloplaca_ulcerosa_EU639623_2 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Caloplaca_ulcerosa_GU080293 AGAG-GGGTCCGGC--TT---CGCGGCC-GCGCCCTCGGGGGGAAACCCCCGTAACTCTTCAACCCCGTGTGTATCTACCTCTGTTGCTTCGGCGAGCGTCGAGGCGTCTT---GCGCCCCGGCCCCGGCCTCGGCCGGCGAGTTCTCGCCAGAGGCCCAACTTCAAGCCTGTTCAGAGTACTGTCCGAGCACA-CGATCAAA--CGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGAGCCTTCGTCCCCC-CCCCCGTGGG-CGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGATCTCAAGCGCAGTA-AATCT--CAACGCTTTCGAGGTATCG-CCTGCGGCCCGGCCGTGAA Caloplaca_ulcerosa_GU080294 AGAG-GGGTCAGGC--TT---CGCGGCC-GCGCTCTCGGGGGGAAACCCCCGTAACTCTTCAACCCAGTGTGTATCTACCTCCGTTGCTTTGGCGAGCGTTGGGGCGCTTT---GCGCCTCGGCCCCGGCCCCGGCCGGTGAGCTCTCGCCAGAGGCCCAGCCTCAAGTCTGTTTAGAGTACCGTCCGAGCATA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCTCGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCT--CAACGCTTGCGAGGTGTCG-CCTGCGGCCCGGCCGTGAA Caloplaca_ulcerosa_GU080295 AGAG-GGGTCAGGC--TT---CGCGGCC-GCGCCCTCGGGGGGAAACCCCCGTAACTCTTCAACCCACTGTGTATCTACCTTCGTTGCTTCGGCGAGCGTTGGGGCGCCTT---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGCTCTCGCCCGAGGCCCAGCCTCAAGTCTGTTTAGAGTACCGTCCGAGCACA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCCAGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCT--CAACGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGTGAA Caloplaca_ulcerosa_GU080296 AGAG-GGGTCGGGC--TT---?GCGGCC-GCGCACTCGGGGGGAAACCCCCGCAACTCTTCCACCCACTGTGTATCTACCTTCGTTGCTTCGGCGAGCGTTGGGGCGCCTT---GCGCCTCGGCCCCGGCCCCGGTCGGTGAGCTCTCGCCCGAGGCCCAGCCTCAAGTCTGTTTAGAGTACCGTCCGAGCATA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCCCGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCT--CAACGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGTGAA Caloplaca_ulcerosa_GU080297 AGAG-GGGTCAGGC--TT---CGCGGCC-GCGCCCTCGGGGGGAAACCCCCGTAACTCTTCAACCCA{CG}TGTGTATCTACCT{CT}CGTTGCTTCGGCGAGCGTTGGGGCGC{CT}TT---GCGCCTCGGCCCCGGCC{CT}CGG{CT}CGGTGAGCTCTCGCC{AC}GAGGCCCAGCCTCAAGTCTGTTTAGAGTACCGTCCGAGCACA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCCAGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGC----------------------------------------------------- ; END; [ The following blocks are output data for analysis step 10823 ] BEGIN TREES; TITLE Bayesian_inference_of_ITS_Caloplaca_ulcerosa_group; LINK TAXA = TaxaForAnalysisStep10823; TREE Bayesian_inference = [&R] (Caloplaca_citrina_DQ173226:0.385437,Caloplaca_citrina_DQ173239:0.318955,(((Caloplaca_sp._aff._C._ulcerosa_USA1_GU080298:0.009916,(Caloplaca_sp._aff._C._ulcerosa_USA_2:0.029119,Caloplaca_sp._aff._C._ulcerosa_USA3:0.009517)0.98:0.019252)0.99:0.058582,((Caloplaca_substerilis_Austria1_GU080299:0.009738,Caloplaca_substerilis_Austria2:0.009498)1.00:0.110188,((Caloplaca_substerilis_Bulgaria:0.009913,Caloplaca_substerilis_Czech_Republic:0.009688)1.00:0.108887,Caloplaca_substerilis_Slovakia:0.137393)0.68:0.033927)0.94:0.084101)1.00:0.168712,(Caloplaca_ulcerosa_GU080293:0.203143,(Caloplaca_ulcerosa_GU080294:0.074747,((Caloplaca_ulcerosa_EU639623_2:0.018196,Caloplaca_ulcerosa_GU080295:0.009419,Caloplaca_ulcerosa_GU080297:0.011001)0.80:0.027253,Caloplaca_ulcerosa_GU080296:0.063253)0.96:0.04906)1.00:0.09025)1.00:0.186931)1.00:0.480282); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr60887] END;