#NEXUS [MacClade 4.08 registered to Jean Burns, Washington University in St. Louis] BEGIN DATA; DIMENSIONS NTAX=12 NCHAR=666; FORMAT DATATYPE=DNA MISSING=? GAP=- ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Commelina_lukei ------CCCCTTTTTGAACCGCGTGCCACTCAC-GACGACCGAAA-CATACGCTA------------------------------------CTTTTTTTTTTTTTTTTTCTTGAGCGTCTCGACATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTTTCNCCTCCTGCTTCGTCATCGGNGAAGKCGGAS-------------------------------------------------------------------------------------TTTTTANNNNNNNN---------------------------------------------------------CTTYGACCCGCGGGCCGCTTGCTAGCCTTTSCCGTACCGACGACTACA-----------------------------------------NNNNNNTATATACATTACGRACATTGACACTTATATACATTACGGGTCCTCAGGACTTCGGG [278] Commelina_foliacea ------CCCCTTTTTGGCCCGCGTGCCGCTCAC-GACGACCTAAA-CCTACGTTA----------------------------------CTCTTTTGCCCGTCTCTCTCGGGATCNNNN--------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTTTCATCATCGGCGTCGTCCTCGTGCTGGGCGAAG--------------------------------------------------------------------------------------NNNNNNNNNNNNN---------------------------------------------------------CTCTGACGTGGGGCCCGCTTGCCANCCCTTGCCGTACCGACGAAGACG-----------------------------------------NNNNNNAGCATCCCNNNCGAACGAGAGCACNNAAATACTTTCCGTGGCCTCTGGACTTCGGG [268] Comm_benghalensis_1 ------CCCATTTTTGCCACGCGTGCCACTCACNGACGGCCGAAAACCTACGC----------------------------------ATCTCTTTCTTTCTTTTTTCCCCAAA--------------------------------------NNNNNNNNN-AGGTATTGTCATCCCCGACCCAAAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--------------------TATCATTTTATGTATCGT------------------------------------------------------CTTCACGG------------------------------------------------------------------------------------------------CTATTATATTCATTTTCCGGCCGCGTC-----------------------------------------------------------------------CTCCTCGGTGGTAAGGACACGCTTTGACGTGCCCCGCCGCCCCGTAGC-----------------------------------------GACGGCGACAACCATCGCCACCGAGAGCATNNAAATACATTCCGAGGCCTTTGGACTTCGGG [305] Comm_benghalensis_2 ------CCCCTTTTTGCCACGCGTGCCACTCACNGACGGCCGAAAACCTACGC----------------------------------ATCTCTTTCTTTCTTTTTTTCCCAAA--------------------------------------NNNNNNNNN-AGGTATTGTCATCCCCGACCCAAAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----------------------TATCATTTTATGTATCGT------------------------------------------------------CTTCACGG------------------------------------------------------------------------------------------------CTATTATATTCATTTTCCGGCCGCGTC-----------------------------------------------------------------------CTCCTCGGTGGTAAGGACACGCTTTGACGTGCCCCGCCGCCCCGTAGC-----------------------------------------GACGGCGACAACCATCGCCACCGAGAGCATNNAAATACATTCCGAGGCCTTTGGACTTCGGG [302] Commelina_eckloniana ------CCCCTTTTTGCCCCGCGTGCCACTCGCCGACGACCGAAANCCTACGC----------------------------------ATCTCTTTTTTCAAAAGATATTTATACCTAA-------------------------------------------------------------------------------------------ATTAAAATTTACTAACTATAAATATAATACAT------------------TATATATATATATATATATATATATATATATATATATATATATATATATATATA----------------------------------------------------------------------------------ATTTTATGTATCGTCTTGATGATTATTATATTCATTTTTCGGTTNNNNN-----------------------------------------------------------------------NCCTTCATCGGCAAAGGCGTGACGTGGNNNGGCCCGCCGTGCCGTAAA-----------------------------------------GACGAAGATTAGCATCCCGATCGAGAGCATNNAAATACGTTCCGAGGCCTTAGGACTTCGGA [323] Commelina_erecta_3 ------CCCCTTTTTGCCAGGCGTAGCACCAATNNN-------------------CCGGCGGGAGTTTTTGG-------------------------------------------------------CCCCGCGCGCTTGCACCCCTTTTTGNCTCAGGCNNNNNNNNNNNNN---------------GTAGCACAAATGNNCGGCGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNN-----------------------------------------------------------------------------------------------AGTTTNNNNNNNNNNNTTCGCACCGCGCGCTTTTTGNNNNNNNN-----------------------------------------------CGCGNNNNGGCCCCGCTTGCTCCGAGTGCCGTCCCGACGGAGATG-------------------------------------------------------------------------------------------------------------NNNNNNNNCGGCNACCCCGATCGGGAGCACNNAAATAGCTTCGGAGGCCATTGGACATTGGG [301] Commelina_erecta_2 ------CCCCTTTTTGCCAGGCGTAGCACCAATNNN-------------------CCGGCGGGAGTTTTTGG-------------------------------------------------------CCCCGCGCGCTTGCACCCCTTTTTGNCTCAGGCNNNNNNNNNNNNN---------------GTAGCACAAATGNNCGGCGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNN-----------------------------------------------------------------------------------------------AGTTTNNNNNNNNNNNTTCGCACCGCGCGCTTTTTGNNNNNNNN-----------------------------------------------CGCGNNNNGGCCCCGCTTGCTCCGAGTGCCGTCCCGACGGAGATG-------------------------------------------------------------------------------------------------------------NNNNNNNNCGGCNACCCCGATCGGGAGCACNNAAATAGCTTCGGAGGCCATCGGACATCGGG [301] Commelina_erecta_1 ------CCCCTTTTTGCCAGGCGTAGCACCAATNNN-------------------CCGGCGGGAGTTTTTGG-------------------------------------------------------CCCCGCGCGCTTGCACCCCTTTTTGNCTCAGGCNNNNNNNNNNNNN---------------GAAGCACAAATGNNCGGCGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNN-----------------------------------------------------------------------------------------------AGTTTNNNNNNNNNNNTTCGCACCGCGCGCTTTTTGNNNNNNNN-----------------------------------------------CGCGNNNNGGCCCCGCTTGCTCCGAGTGCCGTCCCGACGGAGATG-------------------------------------------------------------------------------------------------------------NNNNNNNNCGGCNACCCCGATCGGGAGCACNNAAATAGCTTCGGAGGCCATCGGACATCGGG [301] Commelina_bracteosa ------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNN-------------TGGGAAGTCCTTGTG-----------------------------------------------NNNTTGCA-CCCTTTTTGACACGAGT-NNNNNNNNNNNN---------------TTNNTACTAATCNNCGACGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNNN----------------------------------------------------------------------------------------------ANCTTNNNNNNNNNNNTTTGCTCTGCGCCCTTTT-GNNNNNNNN-----------------------------------------------CTTGNNNNGGCCTCTCTTGCTCCNNNNNCCGTCCCGACGAAGGTG-------------------------------------------------------------------------------------------------------------GGCACCCGCGGCGATCTCAATCGAGAGCTCNNAAATACATTCGTCGCCCTTTCGACTTCAAG [294] Commelina_mascarenica ------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNN-------------TGGGAAGTCCTCGTG-----------------------------------------------NNNTTGCACCCCTTTTTGGCTCGCGCTNNNNNNNNNNNN---------------GCACTTTTAACGACCGGCACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNN-----------------------------------------------------------------------------------------------CGTCCGTTGCACCCNCTTTGCTACACGCGCTTTTCANNNNNNNN-----------------------------------------------CCTTTAACGGCC-------------------------------------------------------------------------------------------------GATATCACGCCTTTCTCCCCCGTAAGTCACTCGTTCCTCCCTTGC--------------TCCCCGTCNAGAGCACNNAAATACATTCCGACCACATTGGACTCCGGG [294] Commelina_imberbis ------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNN-------------TGGGAAGTCCTTGTG-----------------------------------------------NNNTTGCACCCCTTTTTGGCGCGCGTTNNNNNNNNNNNN---------------GCACTTCTAACGACTGACAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNN-----------------------------------------------------------------------------------------------CTCCCTCAATNNNNNTTTTTCTCCACGCGCTTTNNNNNNNNNNN-----------------------------------------------NNNNNNNNNGGC-------------------------------------------------------------------------------------------------GCCGGCCCGCNNTTGCTCCCCATACGACGCTCAGTCATCCCTTGC--------------TCACCGTCNATACCATNNAAATACATTCCGTGGCCACTGGACTTTGGG [294] Commelina_nairobiensis ------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNN-------------NNN------------NNNNNNNNNNN-------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------NNNNNNNNNNNNNNNNNNN------------------------------------------------------------------------------------------NNNNNNNNNNNNNN-----------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNN-------NNNNNNNNNNNNNNNNNNNNNN-----------------------TGGGAAGTCCTTGTGTTGCA-----------------------------------------------------------------------------------------NNCAAAGATGAGCATCACCGTCGAGAGCATNNAAATACATTCCGATGCCTTGGGACTTCGGG [295] ; END; BEGIN PAUP; exclude 82-121 204-353 390-411 439-444 490-509; END; BEGIN TREES; [! >Data file = Commelina1_5S_Fig2 >Heuristic search settings: > Optimality criterion = likelihood > 238 characters are excluded > Likelihood settings: > User-specified substitution rate matrix = > - 1.000000 2.463000 1.000000 > 1.000000 - 1.000000 1.577300 > 2.463000 1.000000 - 1.000000 > 1.000000 1.577300 1.000000 - > Assumed nucleotide frequencies (set by user): > A=0.21080 C=0.29130 G=0.19510 T=0.30280 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = 1.8368 > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the GTR+G model > Number of distinct data patterns under this model = 202 > 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 = 1964292564 > 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 = 509 > Score of best tree(s) found = 1398.74467 > Number of trees retained = 1 > Time used = 10.83 sec ] TRANSLATE 1 Commelina_lukei, 2 Commelina_foliacea, 3 Comm_benghalensis_1, 4 Comm_benghalensis_2, 5 Commelina_eckloniana, 6 Commelina_erecta_3, 7 Commelina_erecta_2, 8 Commelina_erecta_1, 9 Commelina_bracteosa, 10 Commelina_mascarenica, 11 Commelina_imberbis, 12 Commelina_nairobiensis ; TREE * PAUP_1 = [&R] (1,2,(((((3,4),(5,12)),((6,(7,8)),9)),10),11)); END; BEGIN CODONS; CODONPOSSET * CodonPositions = N: 1-666; CODESET * UNTITLED = Universal: all ; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ; END; BEGIN MacClade; Version 4.0 87; LastModified -1011026637; FileSettings treewindow '0' '0' '1' '1'; Singles 000; 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' '445' 000; ListWindow Taxa closed Geneva '9' '50' '10' '257' '384' 100000000; ListWindow Trees open Geneva '9' '50' '25' '129' '379' ; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490' ; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490' ; ListWindow ExSets closed Geneva '9' '50' '10' '276' '490' ; ListWindow CharSets closed Geneva '9' '50' '10' '276' '490' ; ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490' ; ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490' ; 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