#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 19, 2024; 5:17 GMT TreeBASE (cc) 1994-2008 Study reference: Burns J.H., Faden R.B., & Steppan S. 2011. Phylogenetic studies in the Commelinaceae subfamily Commelinoideae inferred from Nuclear Ribosomal and Chloroplast DNA Sequences. Systematic Botany, 36(2): 268-276. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10425] BEGIN TAXA; TITLE Untitled_Taxa_Block; DIMENSIONS NTAX=12; TAXLABELS Comm_benghalensis_1 Comm_benghalensis_2 Commelina_bracteosa Commelina_eckloniana Commelina_erecta_1 Commelina_erecta_2 Commelina_erecta_3 Commelina_foliacea Commelina_imberbis Commelina_lukei Commelina_mascarenica Commelina_nairobiensis ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M5229] TITLE Commelina_1_5S_NTS; LINK TAXA = Untitled_Taxa_Block; DIMENSIONS NCHAR=666; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Comm_benghalensis_1 ------CCCATTTTTGCCACGCGTGCCACTCAC?GACGGCCGAAAACCTACGC----------------------------------ATCTCTTTCTTTCTTTTTTCCCCAAA--------------------------------------?????????-AGGTATTGTCATCCCCGACCCAAAGCT?????????????????????????????????--------------------TATCATTTTATGTATCGT------------------------------------------------------CTTCACGG------------------------------------------------------------------------------------------------CTATTATATTCATTTTCCGGCCGCGTC-----------------------------------------------------------------------CTCCTCGGTGGTAAGGACACGCTTTGACGTGCCCCGCCGCCCCGTAGC-----------------------------------------GACGGCGACAACCATCGCCACCGAGAGCAT??AAATACATTCCGAGGCCTTTGGACTTCGGG Comm_benghalensis_2 ------CCCCTTTTTGCCACGCGTGCCACTCAC?GACGGCCGAAAACCTACGC----------------------------------ATCTCTTTCTTTCTTTTTTTCCCAAA--------------------------------------?????????-AGGTATTGTCATCCCCGACCCAAAGCT??????????????????????????????-----------------------TATCATTTTATGTATCGT------------------------------------------------------CTTCACGG------------------------------------------------------------------------------------------------CTATTATATTCATTTTCCGGCCGCGTC-----------------------------------------------------------------------CTCCTCGGTGGTAAGGACACGCTTTGACGTGCCCCGCCGCCCCGTAGC-----------------------------------------GACGGCGACAACCATCGCCACCGAGAGCAT??AAATACATTCCGAGGCCTTTGGACTTCGGG Commelina_bracteosa ------??????????????????????????????-------------------????-------------TGGGAAGTCCTTGTG-----------------------------------------------???TTGCA-CCCTTTTTGACACGAGT-????????????---------------TT??TACTAATC??CGACGCC???????????????????????????????-------------------??????----------------------------------------------------------------------------------------------A?CTT???????????TTTGCTCTGCGCCCTTTT-G????????-----------------------------------------------CTTG????GGCCTCTCTTGCTCC?????CCGTCCCGACGAAGGTG-------------------------------------------------------------------------------------------------------------GGCACCCGCGGCGATCTCAATCGAGAGCTC??AAATACATTCGTCGCCCTTTCGACTTCAAG Commelina_eckloniana ------CCCCTTTTTGCCCCGCGTGCCACTCGCCGACGACCGAAA?CCTACGC----------------------------------ATCTCTTTTTTCAAAAGATATTTATACCTAA-------------------------------------------------------------------------------------------ATTAAAATTTACTAACTATAAATATAATACAT------------------TATATATATATATATATATATATATATATATATATATATATATATATATATATA----------------------------------------------------------------------------------ATTTTATGTATCGTCTTGATGATTATTATATTCATTTTTCGGTT?????-----------------------------------------------------------------------?CCTTCATCGGCAAAGGCGTGACGTGG???GGCCCGCCGTGCCGTAAA-----------------------------------------GACGAAGATTAGCATCCCGATCGAGAGCAT??AAATACGTTCCGAGGCCTTAGGACTTCGGA Commelina_erecta_1 ------CCCCTTTTTGCCAGGCGTAGCACCAAT???-------------------CCGGCGGGAGTTTTTGG-------------------------------------------------------CCCCGCGCGCTTGCACCCCTTTTTG?CTCAGGC?????????????---------------GAAGCACAAATG??CGGCGCG???????????????????????????????-------------------?????-----------------------------------------------------------------------------------------------AGTTT???????????TTCGCACCGCGCGCTTTTTG????????-----------------------------------------------CGCG????GGCCCCGCTTGCTCCGAGTGCCGTCCCGACGGAGATG-------------------------------------------------------------------------------------------------------------????????CGGC?ACCCCGATCGGGAGCAC??AAATAGCTTCGGAGGCCATCGGACATCGGG Commelina_erecta_2 ------CCCCTTTTTGCCAGGCGTAGCACCAAT???-------------------CCGGCGGGAGTTTTTGG-------------------------------------------------------CCCCGCGCGCTTGCACCCCTTTTTG?CTCAGGC?????????????---------------GTAGCACAAATG??CGGCGCG???????????????????????????????-------------------?????-----------------------------------------------------------------------------------------------AGTTT???????????TTCGCACCGCGCGCTTTTTG????????-----------------------------------------------CGCG????GGCCCCGCTTGCTCCGAGTGCCGTCCCGACGGAGATG-------------------------------------------------------------------------------------------------------------????????CGGC?ACCCCGATCGGGAGCAC??AAATAGCTTCGGAGGCCATCGGACATCGGG Commelina_erecta_3 ------CCCCTTTTTGCCAGGCGTAGCACCAAT???-------------------CCGGCGGGAGTTTTTGG-------------------------------------------------------CCCCGCGCGCTTGCACCCCTTTTTG?CTCAGGC?????????????---------------GTAGCACAAATG??CGGCGCG???????????????????????????????-------------------?????-----------------------------------------------------------------------------------------------AGTTT???????????TTCGCACCGCGCGCTTTTTG????????-----------------------------------------------CGCG????GGCCCCGCTTGCTCCGAGTGCCGTCCCGACGGAGATG-------------------------------------------------------------------------------------------------------------????????CGGC?ACCCCGATCGGGAGCAC??AAATAGCTTCGGAGGCCATTGGACATTGGG Commelina_foliacea ------CCCCTTTTTGGCCCGCGTGCCGCTCAC-GACGACCTAAA-CCTACGTTA----------------------------------CTCTTTTGCCCGTCTCTCTCGGGATC????--------??????????????????????????????--------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTTTCATCATCGGCGTCGTCCTCGTGCTGGGCGAAG--------------------------------------------------------------------------------------?????????????---------------------------------------------------------CTCTGACGTGGGGCCCGCTTGCCA?CCCTTGCCGTACCGACGAAGACG-----------------------------------------??????AGCATCCC???CGAACGAGAGCAC??AAATACTTTCCGTGGCCTCTGGACTTCGGG Commelina_imberbis ------??????????????????????????????-------------------????-------------TGGGAAGTCCTTGTG-----------------------------------------------???TTGCACCCCTTTTTGGCGCGCGTT????????????---------------GCACTTCTAACGACTGACAAT???????????????????????????????-------------------?????-----------------------------------------------------------------------------------------------CTCCCTCAAT?????TTTTTCTCCACGCGCTTT???????????-----------------------------------------------?????????GGC-------------------------------------------------------------------------------------------------GCCGGCCCGC??TTGCTCCCCATACGACGCTCAGTCATCCCTTGC--------------TCACCGTC?ATACCAT??AAATACATTCCGTGGCCACTGGACTTTGGG Commelina_lukei ------CCCCTTTTTGAACCGCGTGCCACTCAC-GACGACCGAAA-CATACGCTA------------------------------------CTTTTTTTTTTTTTTTTTCTTGAGCGTCTCGACATC?????????????????????????????????-----------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTTTC?CCTCCTGCTTCGTCATCGG?GAAG{GT}CGGA{CG}-------------------------------------------------------------------------------------TTTTTA????????---------------------------------------------------------CTT{CT}GACCCGCGGGCCGCTTGCTAGCCTTT{CG}CCGTACCGACGACTACA-----------------------------------------??????TATATACATTACG{AG}ACATTGACACTTATATACATTACGGGTCCTCAGGACTTCGGG Commelina_mascarenica ------??????????????????????????????-------------------????-------------TGGGAAGTCCTCGTG-----------------------------------------------???TTGCACCCCTTTTTGGCTCGCGCT????????????---------------GCACTTTTAACGACCGGCACC???????????????????????????????-------------------?????-----------------------------------------------------------------------------------------------CGTCCGTTGCACCC?CTTTGCTACACGCGCTTTTCA????????-----------------------------------------------CCTTTAACGGCC-------------------------------------------------------------------------------------------------GATATCACGCCTTTCTCCCCCGTAAGTCACTCGTTCCTCCCTTGC--------------TCCCCGTC?AGAGCAC??AAATACATTCCGACCACATTGGACTCCGGG Commelina_nairobiensis ------??????????????????????????????-------------------????-------------???------------???????????-------------------------------------------????????????????????????????????---------------????????????????????????????????????????????????????-------------------???????????????????------------------------------------------------------------------------------------------??????????????-----------------------------------??????????????????????????-------??????????????????????-----------------------TGGGAAGTCCTTGTGTTGCA-----------------------------------------------------------------------------------------??CAAAGATGAGCATCACCGTCGAGAGCAT??AAATACATTCCGATGCCTTGGGACTTCGGG ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Commelina_1_5S_NTS) = N: 1-666; CODONPOSSET CodonPositions (CHARACTERS = Commelina_1_5S_NTS) = N: 1-666; END;