#NEXUS BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=17; TAXLABELS 'Caloplaca_citrina_DQ173226' 'Caloplaca_citrina_DQ173239' 'Caloplaca_ulcerosa_EU639623' 'Caloplaca_aff_ulcerosa_USA1_GU080298' 'Caloplaca_aff_ulcerosa_USA 2' 'Caloplaca_aff_ulcerosa_USA3' 'Caloplaca_substerilis_Austria1_GU080299' 'Caloplaca_substerilis_Austria2' 'Caloplaca_substerilis_Bulgaria' 'Caloplaca_ulcerosa_GU080293' 'Caloplaca_ulcerosa_GU080294' 'Caloplaca_ulcerosa_EU639623' 'Caloplaca_ulcerosa_GU080295' 'Caloplaca_ulcerosa_GU080296' 'C. Caloplaca_ulcerosa_GU080297' 'Caloplaca_substerilis_Czech_Republic' 'Caloplaca_substerilis_Slovakia' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=519; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX '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_ulcerosa_EU639623' AGAGCGGG-CAGGC--TT--TTACGGCT-ACGCTC-GAGCGGGCAACCCCCGCAACTCTTCAACCCCGTGTTTACCACCCACTGTTGCTTCGGCGAGCGCCGGAACGCCCC---GCGCCCCGGCCCCGGCCTCGGTCGGTGAGTTCTCGCCAGAGGCCCAACCCC-ATTCTGTTCACAGTGACGTCCGAGTACACCGATTAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCGTTCGCCTCCC-GTGTC-AGGG-CGGCGCGCCCGCAAACTAGTGGCGG-TCCAGGGAGACTTCAAGCGCAGTA-AACCTTTCA-CGCTT------------------------------- 'Caloplaca_aff_ulcerosa_USA1_GU080298' AGAGCGGG-CAGGC--TT---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACTGTTGCTTCGGCGAGCGTTGGGGCGCCTC---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGTTCTCGCCAGAGGCTCAACCCC-ATTCTGTTCACAGTGATGTCCGAGTACACCGATTAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGCATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-ACGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCTTTCA-CGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGGAAA 'Caloplaca_aff_ulcerosa_USA 2' AGAGCGGG-CAGGC--TT---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCAACCCTGTGTTTACCAACCACTGTTGCTTCGGCGAGCGTTGGGGCGCCTC---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGTTCTCGCCCGAGGCTCAACCCC-ATTCTGTTCACAGTGATGTCCGAGTACACCGATTAAA--TCAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGCATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGC-TTCGCCCCCC-ACGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCTGTCA-CGCTTTCGAGGTGTCG-CCTGCGGCCCGGCCGGAAA 'Caloplaca_aff_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--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCMAGCTTTGCTTGGTATTGGGCGTTCGCCTCCC-GCGTC-AGGG-CGGTGCGCCCGCAAATTAGTGGCGG-TCCGGGGRGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCGCCCTGCGGCTCGGCCGGAAA '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_EU639623' AGAG-GGG?CAGGC--TT---CGCGGCC-GCGCCCTCGGGGGGAAACCCCCGTAACTCTTCAACCCACTGTGTATCTACCTTCGTTGCTTCGGCGAGCGTTGGGGCGCCTT---GCGCCTCGGCCCCGGCCTCGGTCGGTGAGCTCTCGCCCGAGGCCCAACCTCAAGTCTGTTTAGAGTACCGTCCGAGCACA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCCAGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGCGCAGTA-AATCT--CAACGCTTTCGAGGTGTCG-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 'C. Caloplaca_ulcerosa_GU080297' AGAG-GGGTCAGGC--TT---CGCGGCC-GCGCCCTCGGGGGGAAACCCCCGTAACTCTTCAACCCASTGTGTATCTACCTYCGTTGCTTCGGCGAGCGTTGGGGCGCYTT---GCGCCTCGGCCCCGGCCYCGGYCGGTGAGCTCTCGCCMGAGGCCCAGCCTCAAGTCTGTTTAGAGTACCGTCCGAGCACA-CGATTAAA--TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCCTTCGTCTCCC-TCCCAGAGGG-CGGCGTGCCCGTAAACTAGTGGCGG-TCCAGGGAGACCTCAAGC----------------------------------------------------- 'Caloplaca_substerilis_Czech_Republic' AGAGCGGG-CAGGC--TT---CGCGGCT-GCGCCC-GGGCGGGCAACCCCCGCAACTCTTCCACCCTGTGCGTATCAACCCCTGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCCCGGTCGGTGAGTTCTCGCCAGAGGCCCAACCCC-ATCCTGTTCACAGTGACGTCCGAGTACACCGATTAAA--TCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTATTGGGCGTTCGCCTCCC-GCGTC-AGGG-CGGTGCGCCCGCAAATTAGTGGCGG-TCCGGGGAGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCG-CCTGCGGCTCGGCCGGAAA 'Caloplaca_substerilis_Slovakia' AGAGCGGG-CARGC--MT---CACGGCT-GCGCCC-GGGCGGGCAACCCCCGCGACTCTTCAACCCTGTGTGTACCAACCATTGTTGCTTCGGCGAGCGTTGGGGCGCCCC---GCGCCCCGGCCCCGGCCTCGGTCGGTGAGTTCTCGTCAGAGGCCCAACCTC-ATTCTGTTCACAGTGACGTCCGAGTACACCGATTAAA--CCAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCCTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCAACCCTCAAGCTTTGCTTGGTGCTGGGC-TTCGCCTCCCCGTGTC-AGGGGCGGCGTGCCCGCAAATTAGTGGCGG-TCCGGGGAGACTTCAAGCGCAGTA-AATCTTTCA-CGCTTCCGAGGTCTCG-CCCGCGGTCCTGCCGGAAA ; END; BEGIN TREES; Title 'Trees from "ulcerosaDoomsday.MrB"'; LINK Taxa = Taxa; TRANSLATE 1 'Caloplaca_citrina_DQ173226', 2 'Caloplaca_citrina_DQ173239', 3 'Caloplaca_ulcerosa_EU639623', 4 'Caloplaca_aff_ulcerosa_USA1_GU080298', 5 'Caloplaca_aff_ulcerosa_USA 2', 6 'Caloplaca_aff_ulcerosa_USA3', 7 'Caloplaca_substerilis_Austria1_GU080299', 8 'Caloplaca_substerilis_Austria2', 9 'Caloplaca_substerilis_Bulgaria', 10 'Caloplaca_ulcerosa_GU080293', 11 'Caloplaca_ulcerosa_GU080294', 12 'Caloplaca_ulcerosa_EU639623', 13 'Caloplaca_ulcerosa_GU080295', 14 'Caloplaca_ulcerosa_GU080296', 15 'C. Caloplaca_ulcerosa_GU080297', 16 'Caloplaca_substerilis_Czech_Republic', 17 'Caloplaca_substerilis_Slovakia'; TREE Bayesian_inference = (1:0.385437,2:0.318955,(((4:0.009916,(5:0.029119,6:0.009517)0.98:0.019252)0.99:0.058582,((7:0.009738,8:0.009498)1.00:0.110188,((9:0.009913,16:0.009688)1.00:0.108887,17:0.137393)0.68:0.033927)0.94:0.084101)1.00:0.168712,(10:0.203143,(11:0.074747,((12:0.018196,13:0.009419,15:0.011001)0.80:0.027253,14:0.063253)0.96:0.04906)1.00:0.09025)1.00:0.186931)1.00:0.480282); END;