#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 02, 2024; 9:56 GMT TreeBASE (cc) 1994-2008 Study reference: Cervantes-alcayde M.A., Olson M.E., Olsen K.M., & Eguiarte L.E. 2015. Apparent similarity, underlying homoplasy: morphology and molecular phylogeny of the North American clade of Manihot (Euphorbiaceae). American Journal of Botany, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16916] [ The following blocks are input data for analysis step 15396 ] BEGIN TAXA; TITLE TaxaForAnalysisStep15396; DIMENSIONS NTAX=33; TAXLABELS Cnidoscolus_egregius Manihot_aesculifolia_ Manihot_angustiloba Manihot_auriculata Manihot_brachyloba_ Manihot_caudata Manihot_chlorosticta_ Manihot_crassisepala_ Manihot_davisiae Manihot_esculenta_CLONE_1 Manihot_esculenta_CLONE_2 Manihot_esculenta_CLONE_3 Manihot_foetida_CLONE_1 Manihot_foetida_CLONE_2 Manihot_mcvaughii Manihot_michaelis_CLONE_1 Manihot_michaelis_CLONE_2 Manihot_oaxacana Manihot_obovata_ Manihot_pringlei_CLONE_1 Manihot_pringlei_CLONE_2 Manihot_pringlei_CLONE_3 Manihot_rhomboidea_CLONE_1 Manihot_rhomboidea_CLONE_2 Manihot_rhomboidea_CLONE_3 Manihot_rubricaulis_ Manihot_subspicata_CLONE_1 Manihot_subspicata_CLONE_2 Manihot_tomatophylla_CLONE_1 Manihot_tomatophylla_CLONE_2 Manihot_walkerae Manihot_websteri Manihotoides_pauciflora ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25602] TITLE Manihot_PEPC; LINK TAXA = TaxaForAnalysisStep15396; DIMENSIONS NCHAR=455; 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .] Cnidoscolus_egregius GAGTTATTTCCATGAGACAATCTGGAAGGGTGTCCCAAAGTTCTTGCGTCGTGTCGACACTGCCTTGAAGAACATAGGAATTGATGAAAGAGTTCCATACAATGCTCCTCTTATTCAGTTCTCTTCTTGGATGGGTGGTGATCGAGATGGTATGATCT--------------CTCTCTGTTGATGAAAAACTGAAGATATTTTAAG-TATCCAACAG-ATTCATTTGTT-TTTTG-------------------------------------------------------------------------TTCTTTTCTTTCTTTCTTTTT-AAATCTGCATCAATATATAACTTTTAAGTAGTTAAAAT-TTCT-CTCCCCCATGTGCTTATCATTTTCTTGACCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGACGTTT Manihot_aesculifolia_ GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAATTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTCCCCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_angustiloba GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCTTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTTT-AAACATGCATCAATGTAT-GCTTTTAATTAGCTAAAAT-TTGC-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGCCACAAGAGA-GTTT Manihot_auriculata GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAATTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTATT-AGTTG-------------------------------------------------------------------------TCCTTTCCTCTCTCTCTTTCT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_brachyloba_ GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGATGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTTTAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCTAAAACTTGCATTAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTGATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_caudata GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_chlorosticta_ GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGCCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGATGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGT-- Manihot_crassisepala_ GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_davisiae GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCTTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTTT-AAACATGCATCAATGTAT-GCTTTTAATTAGCTAAAAT-TTGC-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_esculenta_CLONE_1 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGCGACGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTTTAAA-TATCTATAAG-ATACATTTGTT-AGTTG-------------------------------------------------------------------------TCCT-CTCTCTCTCTCTTTCTAAAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_esculenta_CLONE_2 GAGTTATTTCCATGAGACAATCTGGAAGGGTGTCCCGAAGTTCTTGCG{CT}CGTGTTGACACTGCTTTGAAGAACATAGGGATTAATGAAAGAGTTCCTTACAATGCTCCTCTTATTCAATTTTCTTCTTGGATGGGTGGTGACCGTGATGGTGTGATCTTTCTCTATTAGTAT---------------------------------------------------------------TACCATTTTTATCCATTAGATTTTTTCTCTTTTAAGATTTTTT--CTCTTTTATATATTTTTTT-TCTCTTT-------------------------ATATATATATATATAT--------------------------CCTCCCC---TGTTTATCATTTTCGTGATCTGAGATGCAGGTAAT-CCAAGGG-TTACTCCTGAGGTCACAAGGGATGTCT Manihot_esculenta_CLONE_3 GAGTTATTTCCACGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTTTAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTCTCTCTCTCTCTCTTTAAAACATGCATCAATATAT-GCTTTTA-TTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_foetida_CLONE_1 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTATT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATTTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_foetida_CLONE_2 GGGTTATTTCCACGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATGTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTCTCTCTCTCTCTCTTT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_mcvaughii GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGT{AG}TGATCT--------------CTTTGTATTGATGAAAA-CTGAA{GT}ATA{CG}TATA{AG}A-TATCTAT?AGCATCCAATTGTTTAGT{AC}T------------------------------------------------------------------------GTCCTTTTCTCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTA?GTAAAATATTGTACTG-TCC?TGTGCTTATCATTTTCTTGATCTGAGATGCA?G?AAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_michaelis_CLONE_1 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATGTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_michaelis_CLONE_2 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGGTGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCTTTTTCTCTCTCTCTCTCT-AAACATGTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_oaxacana GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGATGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTC-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGCAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_obovata_ ???TTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGCT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCTAAAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGCCACAAGAGATGTTT Manihot_pringlei_CLONE_1 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTATAAATTATCTATAAT-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCTAAAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_pringlei_CLONE_2 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTATAAATTATCTATAAT-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCTAAAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_pringlei_CLONE_3 GAGTTATTTCCATGAGACAATCTGGAAGGGTGTCCCGAAGTTCTTGCGTCGTGTTGACACTGCTTTGAAGAACATAGGGATTAATGAAAGAGTTCCTTACAATGCTCCTCTTATTCAATTTTCTTCTTGGATGGGTGGTGATCGTGATGGTGTGATCTTTCTCTATTAGTAT---------------------------------------------------------------TACCATTTTTATCCATTAGA-----------------TTTTTT--CTCTTT----------------------------------------------ATATATATATATATAT--------------------------CCTCCCC---TGTTTATCATTTTCTTGATC-GAGATGCAGGTAAT-CCAAGGG-TTACTCCTGAGGTCACAAGGGATGTCT Manihot_rhomboidea_CLONE_1 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTTTCT-AAACATGTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_rhomboidea_CLONE_2 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCATGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGTTATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTTTCT-AAACATGTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_rhomboidea_CLONE_3 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGGAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTTTCT-AAACATGTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCGTGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_rubricaulis_ GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTTT-AAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_subspicata_CLONE_1 GAGTTATTTCCATGAGACAATCTGGAAGGGTGTCCCGAAGTTCTTGCGTCGTGTTGACACTGCTTTGAAG{AG}ACATAGGGATTAATGAAAGAGTTCCTTACAATGCTCCTCTTATTCAATTTTCTTCTTGGATGGGTGGTGATCGTGATGGTGTGATCTTTCTCTATTAGTAT---------------------------------------------------------------TACCATTTTTATCCATTAGA---TTTCTCTTTTA---TTTTTTTTCTCTTT------------------------------------------------ATATATATATATAT--------------------------CCTCCCC---TGTTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCAAGGG-TTACTCCTGAGGTCACAAGGGATGTCT Manihot_subspicata_CLONE_2 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTATAAATTATCTATAAT-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCTAAAACATGCATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_tomatophylla_CLONE_1 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTATT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATTTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_tomatophylla_CLONE_2 GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGGAAAACATAGGGATTAATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTATAAG-ATCCATTTATT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCT-AAACATTTATCAATATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAAT-CCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT Manihot_walkerae GAGTTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAAACTGAAGATATTATAAA-TGTCTATAAG-ATCCATTTGTT-AGTTG-------------------------------------------------------------------------TCCTTTTCTCTCTCTCTCTCTAAAACATGCATCAACATAT-GCTTTTAATTAGTTAAAAT-TTGT-CTG-TCCATGTGCTCATTATTTTCTTGATCTGAGATCCAGGTAAT-CCTAGGG-TTACTCCAGAGGTCACAAGAGATGTTT Manihot_websteri GAGTTATTTCCATGAGACAAT{CT}TGGAAGGGTGTCCC{AG}AAGTTCCTGCGT{AC}GTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGT{AG}TGATCT--------------CT{CT}TGTATTGATGAAAA-CTGAAGATATCATAAA-TATCTATCA{CG}-ATCCATTTTTT-AGTTC-------------------------------------------------------------------------GCCTTTTC{AT}CTCTC{AT}C{AT}C{AT}T{AT}-AAACATGCATCAATATAT-GCTCTTAAT{AG}AGT{AG}AAAAT-?TGT{AG}CT{CG}-TCCACCTGCTTATCATTCTCTTGATCTGAGATGCAGGTAAT-CCTAGGGCTTACTCCTGAGGTCACAAGAGATGTTT Manihotoides_pauciflora GA{AG}TTATTTCCATGAGACAATTTGGAAGGGTGTCCCAAAGTTCCTGCGTCGTGTTGACACTGCTTTGAAAAACATAGGGATTGATGAAAGAGTTCCTTATAATGCTCCTCTCATTCAATTTTCTTCGTGGATGGGTGGTGATCGTGACGGTATGATCT--------------CTTTGTATTGATGAAAA-CTGAAGATATTATAAA-TATCTAT{AC}A{CG}-ATCCATTTTTT-AGTTG-------------------------------------------------------------------------TCCCTTTCTCTCTCTCTCTCT-AAACATGCATCAATATAT-GCTTTTAATTA{GT}TTAAAATATTGTACTGCTCCATGTGCTTATCATTTTCTTGATCTGAGATGCAGGTAATCCCTAGGG-TTACTCCTGAGGTCACAAGAGATGTTT ; END; [ The following blocks are output data for analysis step 15396 ] BEGIN TREES; TITLE Data_Supplement_S5._First_preliminary_analysis_with_all_the_sequences_of_PEPC_from_Manihot_; LINK TAXA = TaxaForAnalysisStep15396; TREE First_Bayesian_separate_analysis_of_all_the_sequences_of_PEPC = [&R] ((Cnidoscolus_egregius:0.04667437,(Manihot_pringlei_CLONE_3:0.001656013,Manihot_subspicata_CLONE_1:0.001622959,Manihot_esculenta_CLONE_2:0.006227684):0.03792565):0.02071234,(Manihot_caudata:0.001393014,Manihot_chlorosticta_:0.00381247,Manihot_crassisepala_:0.001398574,Manihot_mcvaughii:0.01165069,Manihot_oaxacana:0.005840322,Manihot_obovata_:0.005383688,Manihotoides_pauciflora:0.004717504,Manihot_rubricaulis_:0.001587287,Manihot_walkerae:0.01354956,Manihot_websteri:0.02465017,Manihot_brachyloba_:0.009356998,Manihot_esculenta_CLONE_1:0.009946918,(Manihot_aesculifolia_:0.003320177,Manihot_auriculata:0.005440862):0.005433134,(Manihot_angustiloba:0.003271928,Manihot_davisiae:0.001439795):0.009460648,(Manihot_foetida_CLONE_2:0.005816397,Manihot_esculenta_CLONE_3:0.00291058):0.005411861,(Manihot_pringlei_CLONE_1:0.001399139,Manihot_pringlei_CLONE_2:0.001382627,Manihot_subspicata_CLONE_2:0.001396578):0.003358706,(Manihot_michaelis_CLONE_1:0.001450699,Manihot_michaelis_CLONE_2:0.00555903,(Manihot_foetida_CLONE_1:0.001387404,Manihot_tomatophylla_CLONE_1:0.001398769,Manihot_tomatophylla_CLONE_2:0.00539447):0.005592463,(Manihot_rhomboidea_CLONE_1:0.001445103,Manihot_rhomboidea_CLONE_2:0.005517152,Manihot_rhomboidea_CLONE_3:0.005488105):0.003394519):0.003340601):0.02071234); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr80813] END;