#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 21, 2024; 22:12 GMT TreeBASE (cc) 1994-2008 Study reference: Johnson L., & Cairns-heath H. 2010. Decrypting Cryptic Species: Morphological and Molecular Evidence for Recognizing Navarretia linearifolia as Distinct from N. sinistra (Polemoniaceae). Systematic Botany, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10286] BEGIN TAXA; TITLE M5078; DIMENSIONS NTAX=10; TAXLABELS Navarretia_capillaris_93114 Navarretia_capillaris_94062 Navarretia_linearifolia_linearifolia_94052 Navarretia_linearifolia_linearifolia_94081 Navarretia_linearifolia_linearifolia_97129 Navarretia_linearifolia_linearifolia_97157 Navarretia_sinistra_95040 Navarretia_sinistra_95047 Navarretia_sinistra_97146 Navarretia_sinistra_98004 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M4897] TITLE Navarretia_g3pdh; LINK TAXA = M5078; DIMENSIONS NCHAR=964; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Navarretia_capillaris_93114 ---------------------------------GCATTGATGTCTTGGCTA--GATGCTTGGTATTAATATTTTGTATGAATTGCCCTACAGCCACACAGAAGACTGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCTTTCAACATCATTCCCAGCAGCACCGGAGCTGCAAAGGTAGTTGCTTAACCTCT---------------------------------------------------------------------------TTCACCATCATGTTGTGTT-TAGCTATGGTTGTGTCTAATAGTGTTCACTGTGTTAT-GAG-TTGTCTGATTGATTAGGGCGTGTCTTTTGCAGGCTGTGGGAAAAGTGTTGCCGTCTTTGAATGGTAAGCTGACTGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCAGTTGTGGACCTTACTGTGAGACTTGCTAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGGGTTTCTGCAGCTTTCTTTCAAATTCGAAGCTATGGTTTGACTATGTGATCT-ATATGCTGATATTTGTGACAATGCAGGGAGGAATCTGAGGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Navarretia_capillaris_94062 CCATCACTGGTTGGTGATTCTTCAGGTTTCATTGCATTGATGTCTTGGCTA--GATGCTTGGTATTAATATTTTGTATGAATTGCCCTACAGCCACACAGAAGACTGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCTTTCAACATCATTCCCAGCAGCACCGGAGCTGCAAAGGTAGTTGCTTAACCTCT---------------------------------------------------------------------------TTCACCATCATGTTGTGTT-TAGCTATGGTTGTGTCTAATAGTGTTCACTGTGTTAT-GAG-TTGTCTGATTGATTAGGGCGTGTCTTTTGCAGGCTGTGGGAAAAGTGTTGCCGTCTTTGAATGGTAAGCTGACTGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCAGTTGTGGACCTTACTGTGAGACTTGCTAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGGGTTTCTGCAGCCTTCTTTCAAATTCGAAGCTATGGTT?GACTATGTGATCT-ATATGTTGATATTTGTGACAATGCAGGGAGGAATCTGAGGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACCGATTTTGTTGGTGATAGCAGGTAATGTTGCTCTTC-CTGATCTTAGTAATGTCATTGGACGAAGATTATCTTCCTCTAATGTAAGGG-----GGTAGACCTT-------GTTTCAAACTTAACC-CAAACTAATGAAGACACGAAGTTGTGAAGACTGCTCCTTC-----AGTGAACATTAA-AAATGTACTGCAATAAAATTA-CATATTAGTTAAACGCACGTGTTA------------------------CCCAGAAACTACAGGATTAGT--CTTGTAGCATCTGATTTCCATGG Navarretia_linearifolia_linearifolia_94052 CCATCACAGGTTGGCGATTATTCAGGTTTCATTACATTGATGTCTTGGCTATTGATGCTTGGTATTAATATTTCATATGAATT-CCCTGCAGCCACTCAAAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATTCCCAGCAGCACCGGAGCTGCAAAGGTAGTTG-----------------ATGATTCTATTGTCTTCGAGTTTCCTTGCCGAATCAGTTCCAACT-TGATGGTTACAAT-TTTGTAGCTTTACC-CGAAATGCCGTTTCAGTGATGGTTGTTTATAGTAGCATTCATAATGTCATTGAGGTAGTCTGGTTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGCAAGCTGACCGGCATGTCCTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTCGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTCTGCAGGCTTCTTTCAAATTTGTATCTACGGTTAGACTATGTGATCT-GTCTTCTGACATTTGCAACATTGCAGGGAGGAATCCGAGGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGACAGCAGGTAACATTGCTCTGC-CTAATTCGAATAATGTCTTTGGATGAAAATTATCATCCTTTAATGTAAGGG-------TAGACATG-------------AACTTACCC-CAAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTCTTAATAGTGATC------------------ATTA--TT--CA--TTAA-TAAACGCATG--TTATCTT-CTGTTGACGGTTAACTA--CCCAGAAACAACAGGATTAGC--CTTGTTGGATCTGATTTCCATGG Navarretia_linearifolia_linearifolia_94081 CCATCACAGGTTGGTGATTATTCCGGTTTCATTACATTGATGTCTTGGCTATTGATGCTTGGTCTTAATATTTCATATGAATT-CCCTGCAGCCACTCAAAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATTCCCAGCAGCACCGGAGCTGCAAAGGTAGTTG-----------------ATGATTCTATTGTCTTTGAGTTTCCTTGCCGAATCAGTTCCAACT-TAATGGTTACAAT-TTTGTAGCTTTACC-CGAAATGCCGTTTCAGTTATGGTTGTTTATAGTAGCATTCATAATGTCATTGAGATAGTCTGATTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCGTTGAATGGTAAGCTGACCGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCAGTTGTTGACCTTACTGTGAGACTTGCGAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTCTGCAGGCTTCTTTCAAATTTGTATCTACGGTTAGACTATGTGATCT-GTCTTCTGACATTTGCAACATTGCAGGGAGGAATCCGAGGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAACATTGCTCTGC-CTAATTTTAATAATGTCTTTGGATGAAAATTATCATCCTCTAATGTAATGG-------TAGACATG-------------ACCTTACCC-CAAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTCTTAATAGTGATC------------------ATTA--TT--CA--TTAA-TAAACGCATG--TTATCTT-CTGTTGACGGTTAACTG--CCCAGAAACAACAGGAATAGC--CTTATTGGATCTGATTTCCATGG Navarretia_linearifolia_linearifolia_97129 CCATCACAGGTTGGCAATTATTCAGGTTTCATTACATTGATGTCTTGGCTATTGATGCTTGGTCTTAATATTTCATATGAATT-CCCTGCAGCCACTCAAAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATTCCCAGCAGCACCGGAGCTGCAAAGGTAGTTG-----------------ATGATTCTATTGTCTTTGAGTTTCCTTGCTGAAACAGTTCCAACT-TAATGGTTACAAT-TTTGTAGCTTTACC-CGAAATGCCGTTTCAGTTATGGTTGTTTATAGTAGCATTCATAATGTCATTGAGGTAGTCTGATTGATCAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGCAAGCTGACCGGCATGTCCTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTCGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTCTGCAGGCTTCTTTCAAATTTGTATCTACGGTTAGACTATGTGATCT-GTCTTCTGACATTTGCAACATTGCAGGGAGGAATCCGAGGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAACATTGCTCTGC-CTAATTCTAATAATGTCTTTGGATGAAAATTATCATCCTCTAATGTAAGGG-------TAGACATG-------------AACTTACCC-CAAACTAATGAAGACACTAAGATGTGAATCTTGTTCCTTCTTAATAGTGATC------------------ATTA--TT--CA--TTAA-TAAACGCATG--TTATCTT-CTGTTGACGGTTAACTG--CCCAGAAACAACAGGATTAGC--CTTATTGGATCTGATTTCCATGG Navarretia_linearifolia_linearifolia_97157 CCATCACAGGTTGGCGATTATTCAGGTTTCATTACATTGATGTCTTGGCTATTGATGCTTGGTATTAATATTTCATATGAATT-CCCTGCAGCCACTCAAAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATTCCCAGCAGCACCGGAGCTGCAAAGGTAGTTG-----------------ATGATTCTATTGTCTTCGAGTTTCCTTGCCGAATCAGTTCCAACT-TGATGGTTACAAT-TTTGTAGCTTTACC-CGAAATGCCGTTTCAGTGATGGTTGTTTATAGTAGCATTCATAATGTCATTGAGGTAGTCTGGTTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGCAAGCTGACCGGCATGTCCTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTCGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTCTGCAGGCTTCTTTCAAATTTGTATCTACGGTTAGACTATGTGATCT-GTCTTCTGACATTTGCAACATTGCAGGGAGGAATCCGAGGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGACAGCAGGTAACATTGCTCTGC-CTAATTCGAATAATGTCTTTGGATGAAAATTATCATCCTTTAATGTAAGGG-------TAGACATG-------------AACTTACCC-CAAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTCTTAATAGTGATC------------------ATTA--TT--CA--TTAA-TAAACGCATG--TTATCTT-CTGTTGACGGTTAACTA--CCCAGAAACAACAGGATTAGC--CTTGTTGGATCTGATTTCCATGG Navarretia_sinistra_95040 CCATAACTGGTTAGTGATTCTTCAGGTTTCATTACATTGATGTCTTGGCTA--GCTGATTGGTCTTAAAATTTTGTATGAATTGCCCTGCAGCCACACAGAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATTATTCCCAGCAGCACCGGTGCTGCAAAGGTAGTTGCTTCACCTCTTGCACAC------------------AGTTTTCTTGCCAAAGCAGTT-GAACTATAATAGCTAC--TGTTTGAATCTTCACCATCATGTTGTGTTTTAGCTGTGGTTGTGTCTAATAAGGTTCACTGTGTT-CTGAG-TTGTCTGATTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGTAAGCTGACCGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTGGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTGTGCAGGCTTCTTTCAAATTTGAATCTATGGCTAGACTACGTGATCTCGTCTTCTGACATTTGCAACATTGCAGGGAGGAATCTGAAGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAACAT----------------------------------------ATCATCCTTTAATGTA---------------CATG-------GCTTCAAACTTAACCTCGAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTTTTTATAGTAATC------------------ATTAAATTA-CATATTAGTTAAACAGATG--TTATCTT-CTTTTGTCGGTTAACTG--CCCAGAAACAACAGGATTAGG--GTTATTGCATCTGATTTCCATGG Navarretia_sinistra_95047 CCATAACTGGTTAGTGATTCTTCAGGTTTCATTACATTGATGTCTTGGCTA--GCTGATTGGTCTTAAAATTTTGTATGAATTGCCCTGCAGCCACACAGAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATTATTCCCAGCAGCACCGGTGCTGCAAAGGTAGTTGCTTCACCTCTTGCACAC------------------AGTTTTCTTGCCAAAGCAGTT-GAACTATAATAGCTAC--TGTTTGAATCTTCACCATCATGTTGTGTTTTAGCTATGGTTGTGTCTAATAAGGTTCACTGTGTT-CTGAG-TTGTCTGATTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGTAAGCTGACCGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTGGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTGTGCAGGCTTCTTTCAAATTTGAATCTATGGCTAGACTACGTGATCTCGTCTTCTGACATTTGCAACATTGCAGGGAGGAATCTGAAGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAACAT----------------------------------------ATCATCCTTTAATGTA---------------CATG-------GCTTCAAACTTAACCTCGAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTTTTTATAGTAATC------------------ATTAAATTA-CATATTAGTTAAACAGATG--TTATCTT-CTTTTGTCGGTTAACTG--CCCAGAAACAACAGGATTAGG--GTTATTGCATCTGATTTCCATGG Navarretia_sinistra_97146 CCATCACTGGTTAGTGATTCTTCAGGTTTCATTACATTGATGTCTTGGCTA--GCTGATTGGTCTTAAAATTTTGTATGAATTGCCCTGCAGCCACACAGAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATTATTCCCAGCAGCACCGGTGCTGCAAAGGTAGTTGCTTCACCTCTTGCACAC------------------AGTTTTCTTGCCAAAGCAGTT-GAACTATAATAGCTAC--TGTTTGAATCTTCACCATCATGTTGTGTTTTAGCTATGGTTGTGTCTAATAAGGTTCACTGTGTT-CTGAG-TTGTCTGATTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGTAAGCTGACCGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTGGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTGTGCAGGCTTCTTTCAAATTTGAATCTATGGCTAGACTACGTGATCTCGTCTTCTGACATTTGCAACATTGCAGGGAGGAATCTGAAGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAACAT----------------------------------------ATCATCCTTTAATGTA---------------CATG-------GCTTCAAACTTAACCTCGAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTTTTTATAGTAATC------------------ATTAAATTA-CAAATTAGTTAAACAGATG--TTATCTT-CTTTTGTCGGTTAACTG--CCCAGAAACAACAGGATTAGG--GTTATTGCATCTGATTTCCATGG Navarretia_sinistra_98004 CCATAACTGGTTAGTGATTCTTCAGGTTTCATTACATTGATGTCTTGGCTA--GCTGATTGGTCTTAAAATTTTGTATGAATTGCCCTGCAGCCACACAGAAGACTGTTGATGGACCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATTATTCCCAGCAGCACCGGTGCTGCAAAGGTAGTTGCTTCACCTCTTGCACAC------------------AGTTTTCTTGCCAAAGCAGTT-GAACTATAATAGCTAC--TGTTTGAATCTTCACCATCATGTTGTGTTTTAGCTGTGGTTGTGTCTAATAAGGTTCACTGTGTT-CTGAG-TTGTCTGATTGATTAGGGTGTGGCTTTTACAGGCTGTGGGAAAAGTGTTGCCATCTTTGAATGGTAAGCTGACCGGCATGTCTTTCCGTGTGCCTACCGTGGATGTCTCTGTTGTGGACCTTACTGTTAGACTTGCAAAGGCAGCTACTTACCAGCAGATCAAGGATGCCATTAAGTGAGTGTGTGCAGGCTTCTTTCAAATTTGAATCTATGGCTAGACTACGTGATCTCGTCTTCTGACATTTGCAACATTGCAGGGAGGAATCTGAAGGCAATCTCAAGGGGATTTTAGGATACACTGAAGATGATGTGGTCTCCACTGATTTTGTTGGTGATAGCAGGTAACAT----------------------------------------ATCATCCTTTAATGTA---------------CATG-------GCTTCAAACTTAACCTCGAACTAATGAAGACACTAAGATGTGAATACTGTTCCTTTTTTATAGTAATC------------------ATTAAATTA-CATATTAGTTAAACAGATG--TTATCTT-CTTTTGTCGGTTAACTG--CCCAGAAACAACAGGATTAGG--GTTATTGCATCTGATTTCCATGG ; END; BEGIN CODONS; CODONPOSSET CodonPositions (CHARACTERS = Navarretia_g3pdh) = N: 1-964; CODONPOSSET * CodonPositions (CHARACTERS = Navarretia_g3pdh) = N: 1-964; END;