#NEXUS [MacClade 4.08 registered to Jean Burns, Washington University in St. Louis] BEGIN DATA; DIMENSIONS NTAX=20 NCHAR=471; FORMAT DATATYPE=DNA 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Tradescantia_spathacae TCCCTTTTT-------------GCTCCGTCTNNACGACGCACGCCCAACTTTCCTATGAGAACNNNNN------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACTTACTNTCTCATCACCTTCTCCTCTTAANNNNNTTTACTTTNTATTAATATAAAAGTAATAGAAATCAAATTTATTTTATTTNNNNNNNNNTTTCTCTTAATTTACCTTTTTTTNATTTCACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCGCATCTTCTGACNNNNCCCCGCCTATAGCACTACTATATTTCCTTACCATACTCTTTCGGA [290] Tradescantia_sp TCCCTTTTT-------------GCTCCGTCTNNACGACGCACGCCCAACTTTCCTATGAGAACNNNNN------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACTTACTNTCTCATCACCTTCTCCTCTTAANNNNNTTTACTTTNTATTAATATAAAAGTAATAGAAATCAAATTTATTTTATTTNNNNNNNNNTTTCTCTTAATTTACCTTTTTTTTATTTCACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCGCATCTTCTGACNNNNCCCCGCCTATAGCACTACTATATTTCCTTACCATACTCTTTCGGA [290] Tradescantia_brevifolia TCCCTTTTT-------------GCTCCATCT-N-CGCCNNNNNNNNNNNNNNNNNNNNNNNN-N-----N----------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACACGAANTATGCTCACCTTTTATTCTGTCTTATTTTGCTTCTNTATTNNNNTAATTGTAATTTACTTTTTATCTATTTCTATTNNNNNNNNNTGACTTTTAATTTGCTTTTNNNNNATTTTGCANNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGATTTTAGTCGCNNNNATGCGNNNATAACATTACTATATTTCAACATCATACTCTTTCGGA [284] Tradescantia_buckleyi TCCCTTTTT-------------GATCCATCTNNCCGCCGTCCATCCACCTTNNNNNNNNNNN-TCCCATGCCCCCTCGCC------------------------------------------------------------------------------------------------------------------------------------------------------------GGACACGAANTATATTCACCTTTTATTNNNNNNNNNNTTTCTTCTNTATTNNNNTAACTTTATTTTGATTTTTATTTATTTCTATTNNNNNNNNNTTTCTTTTAGTTCCCTTTTNNNNNCTTTTGCTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTGCATTTAATCGCNNNNATGCGNNNATAACATTACTATATTTCACCACCATACCCTTTCGGA [301] Tradescantia_roseolens TCCCTTTTT-------------GCTACATCTNNCCGTATTTCGTCCTCCTTNNNNNNNNNNN-NNNNNNTCCCACTCACC------------------------------------------------------------------------------------------------------------------------------------------------------------GGACACATGTTCTCTTTTTACTTTATCTAATCTCTTTTTTCTTNTNTNNNNNNNNNCTTTTACTTNNNNNNNNNNNNNNNTTTTATNNNNNNNNNTTACTTTTATTTTACTCTCNNNNNATTTTACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCNNNNNNNNNNNNNNNNACGNNNATGACATTTCTATATTTCATGTATATACTCTTTCGGA [301] Tradescantia_ohiensis TCCCTTTTT-------------GCTACATCTNNCCGTATTTCGTCCTCCTTNNNNNNNNNNN-NNNNNNTCCCACTCCCC------------------------------------------------------------------------------------------------------------------------------------------------------------GTACACATGCTCTCTTTTTACTTTATTTAATCTCTATTTTCTTNTNTTTTNNNNTCCTTTTTTTTNNNNNNNNNNNNACTTTTTATNNNNNNNNNTTACTTTTGTTTTACTCTCNNNNNATTTTACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATGTTATCACNNNNATGCGNNNATGACATTTCTTTATTTCATGTGTATACTCTTTCGGA [301] Tradescantia_occidentalis TCCCTTTTT-------------GCTACATCTNNCCGTGTTTCGTCCTCCTTNNNNNNNNNNN-NNNNNNTCCCACTCACC------------------------------------------------------------------------------------------------------------------------------------------------------------GGACACATGTTCTCTTTTTACTTTATTTAATCTTTATTTTCTTNTNTTTTNNNNTACTTTTATTTTACTCTCACTTTACTTTTTACNNNNNNNNNTTGCTTTCATCTTACTCTCNNNNNATTTTACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCTTGTTATCACNNNNATGCGNNNATGACATTTCTATATTTCATGTATATACTCTTTCGGA [301] Tradescantia_bracteata TCCCTTTTT-------------GCTACTTCCNNCCGTATTTCGTCCTCCTTNNNNNNNNNNN-NNNNNNTCCCACTCACC------------------------------------------------------------------------------------------------------------------------------------------------------------GGACACATGTTCTCTTTTTACTTTATTTAATCTCTATTTTCTTCTNTTTTNNNNTCCCTTTGTTTTNNNNNNNNNNNACTTTTTATNNNNNNNNNTTACTTTTATTATACTCTCNNNNNATTTTACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATGTTATCACNNNNATGCGNNNATGACATTTCTATATTTCATGTGTATACTCTTTCGGA [301] Tradescantia_sillamontana TCCCTTTTT-------------GCTCCGTCTNNCCTTCNTCCGTCCGCCTTNNNNNNNNNNN-TACCGTAGCCCCTCACC------------------------------------------------------------------------------------------------------------------------------------------------------------GAACACGAANTNNNNTCACTTTTTCTTNNNNNNNNNNNNNNNNNNNTATTNNNNTCAATTTACTTCTTATATTNTCTATTGTCAATNNNNNNNNNTTCCTTTTAATTCACTTTTNNNNNAATTTACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATATTATAACCATAAAATAGCGATAGCATTGCTATATTTCATGAACGTACTCTTTCGGA [301] Tradescantia_pallida TCCCTTTTT-------------GCTCCATCTNNCCGCCGTCCGTCCACCTTANNNNNNNNNN-TAAAATGTCCCCTCACC------------------------------------------------------------------------------------------------------------------------------------------------------------GAACACGAANTATATTCACCCTTTATTNNNNNNNNNNTTTCCTCTNTATTNNNNTAACTTTAATTTGCCTTTTATTTATTTCTGATNNNNNNNNNTTGCTTTTAGGTTACCTTTNNNNNATTTTGCTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATTTAGTCGCNNNNATGCGNNNATAACATTACTATATTTCATCGTCATACTCTTTCGGA [301] Tradescantia_zebrina TCCCTTTTTT------------GCTCTTTTNNTTNNNNNNNNTTAAACTTNNNNNNNNNNNNNNNNNN-NTTCGGTCA--------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTCACTTCTTATCCCCTTTTTACCCAAGNNNNNNTTAATTAATTATTTAACCAACCCAATTCTTNNNNNNNNNNNTTTTTTATNNNNNNNNNTATTTCTCGCCGTCCCCACNNNNNATATTACCAATAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-TCATCCTCATATTATAACNNNNTAGCAACGATAGCATTACTACATTTTCTTGCCATTCTCCTTCGGA [299] Tradescantia_zanonia TCCCTTTTT-------------GCTAATCTT-NNTCNNNNNNNTTCTCCTT-NNNNNNNNNNN------NCTCGCC----------------------------------------------------------------------------------------------------------------------------------------------------------------AAATTTACTNTTTAATCGCTTATTTTACACTAATTAATTATTTCCGTTTTTTATTACTCGTATCCCCNNNNNNNNNNGCCATCTTTNNNNNNNNNAAAACAATAACTTACTTTTNNNNNATTTTCCTATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATCTTATCTCNNNNTCGCGAATATACTATTACTATATTTCCGTAATATACTCTTTCGGA [290] Tradescantia_hirsutiflora TCCCTTTTT-------------GGNACACNNNNNNNNNNNTTGTTCACTTTNNNNNNNNNNNNNNNNN------------TTACTTT-----------------------------------------------------------------------------------------------------------------------------------------------------NNATTTATTCTCTTTTTTCATTTTTTTTNCTTTTATTTTGCTTTTNTATTNNNNTGCTTTTATTTTCNNNNNNNNNNNCTTTTTATNNNNNNNNNTTACTTTTATTTTACTCTCNNNNNATTTCACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATGTTATCGCNNNNATGCGNNNATGACATTTCTATATTTCATGAACATACTCTTTCGGA [297] Tradescantia_andersoniana TCCCTTTTT-------------GGNACACNNNNNNNNNNNTTGTTCGCTTTNNNNNNNNNNNNNNNNN------------TTACTTT-----------------------------------------------------------------------------------------------------------------------------------------------------NNATTTATTCTCTTTTTTCATTTTTTTTTCTTTTATTTTACTTTTNTATTNNNNTGCTTTTATTTTCNNNNNNNNNNNCTTTTTATNNNNNNNNNTTACTTTTATTTTACTCTCNNNNNATTTTACTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCATGTTATCACNNNNATGCGNNNATGGCGTTTCTATATTTCATGATTATACTCTTTCGGA [297] Tradescantia_standleyi TCCCTTTTTTTTTCTTTTTTTCGCTCC-N----------------------------------------------------------NNNNNNNNNNNNNN----------------NNNNNNNNNNN------------------------------------------------------------------------------------------------------------NNATATCCGNNNNNNTCACCCGTCAATNNNNNNNNNNNNNATTTCNTAATNNNNTAAATAAATNNNNNNNNNNNNNNATTTTTCTTNNNNNNNNNTTAATTTTACCCTTTTTTTNNNNNATTTTATTNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTACCCCTTATTTACNATATCACGATTACAGCATAACTATATTTCTCTACCACACTCTTTCGGA [288] Tradescantia_soconuscana TCCCTTTTTT------------GCTTTCT----------------------------------------------------------AAATTTGCATTTACTCACCCTTAGTTTAATTATCACTTTCTTTTTGCTA----------------------------------------------------------------------------------------------------AATACTACTTTTATTCACTTTTTGCATAATTATTACTTCTTTTTGCTAAAAATTCACTTCTTCGTCAATTTATTATATTATCTTTGCTAAATTATCAATATTTATCCGTCGTCTCCAAATATTACCAATAAAAACTTACCCCTTTCATCCCACAGTACGTAAATACTATATTTTACTTATTATGACNNNNTCCCGAAAATAACATTACTTCATTTACTTACTATACTCTTTCGGA [301] Tradescantia_fluminensis_2 TCCCTTTTT-------------GCTCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------NNNNNN----NNNNNNNNNNN-----------------------------------------------AGATATACGACGTCCTTCCATCTTGCCGGATGGGACTAGCCGCTCGCTCACCGGACAGGAACGCACGCTT------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNN----------------------------------------------------------------------------------------------------------------------------------------------ATTGCATCCCGTAACNNNTTCCCGACGAAAGCATTACTGCATTCCATCACCTTACCCTTTCGGA [229] Tradescantia_fluminensis_1 TCCCTTTTT-------------GCTCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------NNNNNN----NNNNNNNNNNN-----------------------------------------------AGATATACGACGTCCTTCCATCTTGCCGGATGGGACTAGCCGCTCGCTCACCGGACAGGAACGCACGCTT-----------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----------------------------------------------------------------------------------------------------------------------------------------------ATTGCATCCCGTAACNNNTTCCCGACGAAAGCATTACTGCATTCCATCACCTTACCCTTTCGGA [236] Tradescantia_fluminensis_3 TCCCTTTTT-------------GCTCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------NNNNNN----NNNNNNNNNNN-----------------------------------------------AGATATACGACGTCCGTCCATCTTGCCGGATGGGACTAGCCGCTCGCTCACCGGACAGGAACGCACGCTT----------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----------------------------------------------------------------------------------------------------------------------------------------ATTGCATACCGTAACNNNTTCCCGACGAAAGCATTACTGCATTCCATCACCTTACCCTTCCGGA [242] Tradescantia_blossfeldiana NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------NNNNNN-----------NNNN---NNNNNNN---------------------------------------------------------------------------------------------------------NNNNN----------------TGCAACACGAGGACTTCCCAGGGGGTCACCNNNNNNNNNNNNNNNNNNNNNNNNNN--------------------------------------------------------------------------------------------------------------------------------------------------CATCCCAGTACTACNNNNTCTCGCCCANAGCACGCTTAACTTCGGAGTTCTGATGGGATCCGG [183] ; END; BEGIN PAUP; exclude 64-69 81-136 207-236 367-407; END; BEGIN TREES; [! >Data file = 5S_Trade_ML.Paup >Heuristic search settings: > Optimality criterion = likelihood > 133 characters are excluded > Likelihood settings: > User-specified substitution rate matrix = > - 1.000000 6.773500 1.000000 > 1.000000 - 1.000000 1.326900 > 6.773500 1.000000 - 1.000000 > 1.000000 1.326900 1.000000 - > Assumed nucleotide frequencies (set by user): > A=0.23580 C=0.26130 G=0.08430 T=0.41860 > Among-site rate variation: > Assumed proportion of invariable sites = 0.0334 > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = 1.5975 > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the GTR+G+I model > Number of distinct data patterns under this model = 233 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected > without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, > delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via stepwise addition > Addition sequence: random > Number of replicates = 1 > Starting seed = 1835091775 > Number of trees held at each step during stepwise addition = 1 > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Initial 'MaxTrees' setting = 100 > Branches collapsed (creating polytomies) if branch length is less than or equal to 1e-08 > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30868 > Score of best tree(s) found = 2197.63275 > Number of trees retained = 12 > Time used = 02:01:44.1 ] TRANSLATE 1 Tradescantia_spathacae, 2 Tradescantia_sp, 3 Tradescantia_brevifolia, 4 Tradescantia_buckleyi, 5 Tradescantia_roseolens, 6 Tradescantia_ohiensis, 7 Tradescantia_occidentalis, 8 Tradescantia_bracteata, 9 Tradescantia_sillamontana, 10 Tradescantia_pallida, 11 Tradescantia_zebrina, 12 Tradescantia_zanonia, 13 Tradescantia_hirsutiflora, 14 Tradescantia_andersoniana, 15 Tradescantia_standleyi, 16 Tradescantia_soconuscana, 17 Tradescantia_fluminensis_2, 18 Tradescantia_fluminensis_1, 19 Tradescantia_fluminensis_3, 20 Tradescantia_blossfeldiana ; TREE PAUP_1 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),((17,18,19),20)),15),((11,16),12))); TREE PAUP_2 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),((17,18,19),20)),((11,16),12)),15)); TREE PAUP_3 = [&R] (1,2,((((((3,4),10),(((5,(6,8)),7),(13,14))),9),((17,18,19),20)),(((11,16),12),15))); TREE PAUP_4 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),(17,18,19,20)),15),((11,16),12))); TREE PAUP_5 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),(17,18,(19,20))),15),((11,16),12))); TREE PAUP_6 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),((17,18),19,20)),15),((11,16),12))); TREE PAUP_7 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),(17,18,19,20)),((11,16),12)),15)); TREE PAUP_8 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),(17,18,(19,20))),((11,16),12)),15)); TREE PAUP_9 = [&R] (1,2,(((((((3,4),10),(((5,(6,8)),7),(13,14))),9),((17,18),19,20)),((11,16),12)),15)); TREE PAUP_10 = [&R] (1,2,((((((3,4),10),(((5,(6,8)),7),(13,14))),9),(17,18,19,20)),(((11,16),12),15))); TREE PAUP_11 = [&R] (1,2,((((((3,4),10),(((5,(6,8)),7),(13,14))),9),(17,18,(19,20))),(((11,16),12),15))); TREE PAUP_12 = [&R] (1,2,((((((3,4),10),(((5,(6,8)),7),(13,14))),9),((17,18),19,20)),(((11,16),12),15))); END; BEGIN CODONS; CODONPOSSET * CodonPositions = N: 1-471; CODESET * UNTITLED = Universal: all ; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ; END; BEGIN MacClade; Version 4.0 87; LastModified -1011025483; FileSettings editor '0' '0' '1' '1'; Singles 100; Editor 00011001111111100100010010 '0' '24' Geneva '9' '100' '1' all; EditorPosition '46' '6' '963' '1611'; TreeWindowPosition '46' '6' '981' '1630'; ListWindow Characters closed Geneva '9' '50' '10' '273' '399' 000; ListWindow Taxa closed Geneva '9' '50' '10' '276' '490' 100000000; ListWindow Trees closed Geneva '9' '50' '10' '276' '490' ; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490' ; ListWindow WtSets 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