#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 September 20, 2025; 2:02 GMT TreeBASE (cc) 1994-2008 Study reference: Mort M., Crawford D., & Fairfield K. 2004. Phylogeny and character evolution in California Coreopsis: Insights from morphology and from sequences of the nuclear and plastid genomes. Systematic Botany, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1092] [ The following blocks are input data for analysis step 1949 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1949; DIMENSIONS NTAX=13; TAXLABELS Coreopsis_bigelovii Coreopsis_californica Coreopsis_calliopsidea Coreopsis_cyclocarpa Coreopsis_douglasii Coreopsis_gigantea Coreopsis_hamiltonii Coreopsis_maritima Coreopsis_mutica Coreopsis_petrophila Coreopsis_senaria Coreopsis_stillmanii Dahlia_coceinea ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M747] TITLE Coreopsis_ITS; LINK TAXA = TaxaForAnalysisStep1949; DIMENSIONS NCHAR=504; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Coreopsis_bigelovii TCGAACCCTGCAC-AGCAGAAC-AACCCGTGAACATGT-AAAACAACCGGCTTTACGAGGACCAATGATTTT--GTCTTGAGCCTTATGGAGCC--TTGTTGACTTGTATT-CC-TGGCTACCTC-TTTTGGTTGTCTTGGAT-GTCAAGTTGGCACAACTAACAACTC---GCACAACACGTGCCAAGGAAAA-CAAAACATAAA-GGGCT-GTTGTGATGACACCCCGTT--AGGGTGTGCTCGTTGCACGTAAATTCTTTGTTAAAC-CATCACGTCGCTCCCACCAACTGTCCT--TTAATGGGACTCGTT-TGATTGGGGCGGAGATTGGTCTCCCGTGCCCAT--GGCATGGTTGGTCTAAATCGAAGTCCCTTCATGTGTGACACACGACTAGTGGTGGTTGATAAGACTGTCGTCTCGTGTT-GTGTGTTCGGTTCATGAGGGGTAAGCTTTAT-AAAG-ACCCTG-ATGTGTTGTC-CTACGACAATGCTTCGAT Coreopsis_californica TCGAACCCTGCAC-AGCAGAAC-AACCCGTGAACATGT-AAAACAACTGGC-TTACGAGTCCCAATGCTTTT--GTCTTGTGCCTCGTAAATCC--TTGTTGACTTGTATT-CA-TGTCCACCAC-TTTTGGTTGTCATGGAT-GTCAAGTTGGCACAACTAACAAATC---GCACAACATGTGCCAAGGAAAAATAAAACTTAAA-GGGCTTGT-GCCATGATGCCCCGTTT-ACGGTGTGCGTTGTGCATGTTGCCTCTTTGT-AA-C-CATCACGTCGCCCC-ACCAACCATCCC--ATCATGGGACTTGTT-GGTTTGGGGCGGAGATTGGTCTCCTATGCCCTTCCGGCATGGCTGGCCTAAATGGAAGTCCCTACATGAGTGACGCACGACTAGTGGTGGTTGTTAAGACTGTCGTCTCTTGTTTGTGTGTTCGGTTCATGCGGGTTAAGCTCTAC--AAG-ACCCTA-ACGTGT-GTC-CAATGACGATGCTTCGAT Coreopsis_calliopsidea TCGAACCCTGCGT-CGCATAAC-CACCGGTGAACATGT-AAAACATCTGGCTTTACGAGGACCAACGCTTCT--G-CTTTGCCCTTGTGGAGCC--TCGTCGACTTGTATTTCC--GGACACC-C-TTTGGGCTGTCTTGAAA-GTCAAACCGGCAAAACTAACAACTC---GCACAACACGTGCCAAGGAAAA-CCAAACTTAAA-GGGCATGT-GCCATGATGCCCCGTTTTACGGTG-GCTTGTAGCATGTTGCATCTTTAAAAAAC-TATCACGTCGCCCC-ACCAACCGTCCC--GTCAAAGGAATCGTT-GGATTGGGGCGTATATTGGCCTCTTGTGCCCAT--GGCATGGCTGGCTTAAATAGAAGTCCCTTCATGAGTGACGCACAACTAGTGGTGGTTGATAAAACTGTCGTCTCATGT--GTGCGTTTCGTTCATGCGGGTTAAGATTT-T-AAAG-ACCCTT-ATGTGTTGTC-CT{AG}TGACAACGCTTCGA{AT} Coreopsis_cyclocarpa TCGAAACCTG-AT-AGCAGAAC-AACCCGTGAACAAGTACGAACAATCGGCTTTGCGGGGACCAAAGCTTTT--GCTTTGAGCCTCGTAAAGCCCCTCGTCGACGCGTGTT-CA-TG-CCACC--TTTGGGG-TGTCCTGGAT-GTTAACTCGGCACAAC-AACAACCCCCGGCACAACACGTGCCAAGGAAAA-CAAAACTTAAA-GAGCTCGT-GCCAAGACGCCC?GTTT-ACGGTGCGCGCCTTGTACGTGGCCTCTTTGT-AAAC-CATCAAGTCGCCCCTACCTTCCTTCCCTTGTCA-GGGACGTGTT-GGATCGGGGCGGAGATTGGTCTCCTGTGTCCAT--GGCACGGTTGGCCTAAATGGTAGTCTCTTTGTGAGTGACGCACGACAAGTGGTGGTTGATAAGACTGTCTTCTCGTGTC-GTGTGTCTGGTTCACAAGGGTGAAGCTCTT-?AAA--ACCCTTGACGCATTGTC-TTTTGACGATCGTTCGAT Coreopsis_douglasii ?CGA-CCCTTCAC-AA?AGGAC-?ACCCGTGGAAAT-T-AAAAAAACTGGCCTTACGAATCTC{AC}ATTC{CT}TTT--{GT}TTTT-GCCCTCGTAAATCC--TTGTTGACTTGTATT-CA-TGTTTGCCAC-TTTCGGTTTTCATGGAT-ATCAAGTTGGCACAACTAACAACCC--GGCACAACACGTGCCAAGGAAAAACAA-ACTTTAA-GGGCTCGT-GCCATGAC?CCCCGTTT-ACGGTGTGTGTCGTGCATGTTCCC?C??TGT-AAACA-ATCACGTCGCCCC-GCCAACCATCCC--ATCATGGGACGTGTT-CGCTAGGGGCGGATATTGGTCTCCTATGCCCTT--GGCATGGTTGGCCTAAATGGAAGTCCCTTCATGAGTGACGCACGACTAGTGGTGGTTGTTAAGACTGTCGTATCTTGTT-GTGCGTTTGGTTCATGTGGGTTAGGCTCTAT-AAAG-ACCCTA-ACGTGTTGTC-CAATGACAATGCTTCGAT Coreopsis_gigantea TCGAACCCTGC---AGCAGAAC-GACCCGTGAACATGT-AAAACAACCGGTTTTACGAGGACCAATGCTTTT--GTCTTGA{GT}CCTCGTGGAGCC--TCGTCGACTTGTATT-CA-TGTCCACC-C-TTTGGGTTGGCCTGGAT-GTCAAGTCGGCAAAACTAACAACCC---GCACAACACGTGCCAAGGT{AT}AA-CCAAACTTAAA-GGGTCCGT-GCCATGATGCCCCGTTT-ACGGTGTGCATGTTGCATGTGGCCTCTTTGT-AAAC-CATCACGTCGCCCCAACCAACCGTCCC--ATCAAAGGACTCGTT-GGATTGGGGCGGAGATTGGCCTCCCATGCCCGT--GGCACGGTTGGCCTAAATAGAAGTCCCTTCATGAGTGACGCACGACTAGTGGTGGTTGATAAGACTGTCGTCTCGTGTC-GTGCGTTCGGATCATGCGGGTTAAGCTCTAT-AAAG-ACCCTT-ACGTGTTGTC-CTATG-CAATGCTTCGAT Coreopsis_hamiltonii TCGAACCCTGCAC-AGCAGA-C--ACC-GTGAACATGT-AAAACA-C-G-C-TTATGAG-ACCAATGATTT---GTCTTGAGCCTTATGGAGCC--TTGTTGACTTGTATT-CC-TAGCCACCTC-TTTTGGTTGTCTTGGAT-GTCAAGTTGGCACAACTAACAACTC--GGCACAACACGTGCCAAGGAAAA-CAAAACATAAA-GGGCT-GTTG{CT}GATGACACCCCGTT--AGGGTGTGCTCGTTGCACATGGCTTTTTTGT-AAAC-CATCACGTCGCTCCCACCAACTGTCAC--TTAACGGGACTTGTTTGGATTGGGGCGGAGATTGGTCTCCCGTGCCAAT--GGCATGGTTGGTCTAAATGGAAGTCCCTTCATGTGTGACACACGACTAGTGGTGGTTGATAAGACTGTCGTCTCGTGTT-GTGTGTTCGGTTCATGCGGGTTAAGCTTTAT--AAG-ACCCTG-ATGTGTTGTC-CAACAT-AATGCTTCGAT Coreopsis_maritima TCGAACCCTGCAC-AGCAGAAC-GACCCGTGAACATGT-AAAACAACCGG-TTTGCGAGGACCAATGCTTTT--GTGTTGAGCCTCGTGGAGCC--TCGTCGACTTGCATT-CA-TGTCCACC-C-TTTGGGTTGGCCTGGAT-GTCAAGTCGGCAAAACTAACAAC{CT}C---GCACAA{CT}ACGTGCCAAGGAAAA-CCAAACTTAAA-GGGTCCGT-GCCATGATGCCCCGTTT-ACGGTGTGCACGTTGCATGTGGCCTCTTTGT-AAAC-CATCACGTCGCCCCAACCAACCGTCCC--ATCAAAGGACTCGTT-GGATTGGGGCGGAGATTGGCCTCCTATGCCCGT--GGCACGGTTGGCCTAAATAGAAGTCCCTTCATGAGTGACGCACGACTAGTGGTGGTTGATAAGACTGTCGTCTCGTGTC-GTGCGTTCGGTTCATGCGGGTTAAGCTCTAT-AAAG-ACCCTT-ACGTGTTGTC-CTATG-CAATGCTTCGAT Coreopsis_mutica TCGAACCCTG-AT-AGCAGAAC-AACCCGTGAACAAGTAAGAACAATTGGCTTTGCGAGGACCGAAGCTTTG--GTTTTGATCCTCGTAAGGCCTCTCGTCGACGCGTGTT-CA-TG-CCACC-CATTAGGG-TGTCCTGGAT-GTCAAGTCGGCACAAC-AACAACCCCC-GCACAACACGTGCCAAGGAAAA-CTAAACTTAAAAGGGTCCGT-GCCATGACGCCCCGTTT-ACGGTGCGCGCGTTGTACGTGGCCTCTTTGT-AAAC-CATCAAGTCGCCCCCACCATCCATCCCTTGTC--GGGACGTGTT-GGATCGGGGCGGAGATTGGTCTCCCGTGTCCAT--GGCGCGGTTGGCCTAAATAGGAGTCCCTTTGTGAGTGACGCACGACAAGTGGTGGTTGATAAGACTGTCTTCTCGTGTC-GTGCGTTTGGTTCATTTGGGTGAAACTCTTAGAAA--ACCCTTGGCGCGTTGTC-TTGTGATGATGCTTCGAT Coreopsis_petrophila TCGAACCCTGCAT-AGCAGAAC-AACCCG{CG}GAACTTGTAAAAACATCTGGTTTTACGAGGACCAAAGCTTTT--GTTTTGAGTCTCGTAGAGCC--TCGCTGG-TTGCGCC-CA-TGGCCGTC-C-TATGGGCTGTCATGGATCTT?AGGCCGGCACAACTAACCAATC--GGCACAAGACGTGCCAAGGAAAAAAAATACTTAAA-GGGCCCGT-GTCATGTCGCCCCGTTT-ACGGTAAGCGTGCTGTGCGTGGCCTCTTTGT-AA-CCCATCACGTCGCCCC-ACTAACCATCC--------------TGTT-GGAGTGAGGCGGAGAATGGTCTCCTGTTCCTTT--GGTGCGGTTGGCCTAAATAAAAGTTCCTTCATGTGTGACGCACGACTAGTGGTGGTTGATAAGACTGTCGTATCATGTC-GTGCGTTCGGCTCATGCAGGTTAAACTTTTT-AAAG-ACCCTG-ACGTGTTGTCCTAGT---GATGCTTCGAT Coreopsis_senaria TCGAACCCTGCAA-AGCAGAAC-GACCCGTGAACATGTACAAACATCTGGCTTTATGAGGACCGAAGCTTTT--GTTTTGAGCCTTGTAAAGCC--TCGTCGACCTGTGTT-CA-TGGC-ATCCC-TTGGGG-TGTCATGGAT-GTCAGGTTGACACAACTAACTTTTC---GCACAACACGTGCCAAGGAAAA-CAATACTTAAA-CGACTCGT-GCCATGCCGCCCCGTTT-ACGGTAAGCGCGTTGCACGTGGCCTCTTTGT-AA-CACATCACGTCGCCCCCACCAACCGTCCCC-TTCTCGGGACTTGTT-GGATCGGGGCGGAGATTGGTCTCCCGTTCCCAT--GGCGCGGTTGGCCTAAATAGAAGACCCTTCATGAGTGACGCACGACTAGTGGTGGTTGATAAGACTGTCGTATCGTGTC-GTGTGTTCGGTTCATGCGGGTAGAACTCC{CT}TAAAAG-ACCCTC-ACGTGTTGTC-CTGTGACAATGCTTCGAT Coreopsis_stillmanii TCGAATCCTG-AT-AGCAGA-C--ACCCGTGGACATGT-AAAACAACCGGTTTTACGAG-ACCAATGCTTTTGTGTGTTGGCCCTTGTAAATCC--TTGTTGACTTGTGTT-CG-TGTCTACCAC-TTTTGGTTTACATGGAT-GTCAAGTTGGCACAACTAACAACCC--GGCACAACACGTGCCAAGGAAAA-ACAAACTTAAA-GGGCTCGT-GCCACGACGCCCCGTTT-ACGGTGCGCGACGTGCATGTGGCCTCTTTGT-AAAC-CATCACGTCGCCTCCACCAACC-TCTC--TTCTAGGGACTTGTT-GG-TTGGGGCGGAGATTGGTCTCCTATGCCCAT--GGCATGGTTGGCCTAAATTGGAGTCCCTT-ATGAGTGACGCACGACTAGTGGTGGTTGATAAGACTGTCGTCTCTTGTT-GTGCGTTCGGTTCATATGGGTTAAGCTCTAT--AAG-ACC-TG-ATGTGTTG-C-TATGGACGATGCTTCGAT Dahlia_coceinea TCGAAACCTGCAT-GGCAGAAC-AACCCGTGAACAAGTAAAAACATCCGGCTTGACACGAACCGGAACTTAT--GTTTTGGGTCGTGTGAAGTC--TTGTCGGCATGCGT--CAGTGGCTGCC-C-T-TGGGC-GTCTTGGAT-GTCATGTTGGCATAAC-AACAACCC---GCACAACACGTGCCAAGGACAA-CTAAACTTTAA-G-GCTCGT-GCCACGACGCCCCGTTA-TCGGTGTGCG?GTTGTATGTTGCTTCTTTGT-AAAC-CATCACGTCGCCCC-ACCAATCATCCT--GTCTTGGGAGGTGTT-GGGTCGGGGCGGAGATTGGCCTCCCGTTCCCAC-TGGCGCGGTTGGCCTAAATAGGAGTCCCTTCGTGAGCGACGCACGACTAGTGGTGGTTGTTAAGACTGTCGGCTCGTGTC-GTGCGTCTTGTTCATGCGGGTGATACTCT-T-AAAGTACCCGG-ACGCGTTGTC-TTGTTATGATGCTTCGAT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Coreopsis_ITS) = N: 1-504; CODONPOSSET CodonPositions (CHARACTERS = Coreopsis_ITS) = N: 1-504; END; [ The following blocks are output data for analysis step 1949 ] BEGIN TREES; TITLE Tb6724; LINK TAXA = TaxaForAnalysisStep1949; TREE Fig._1A.2 = [&R] (Dahlia_coceinea,(((Coreopsis_petrophila,Coreopsis_senaria),(((Coreopsis_douglasii,Coreopsis_californica),Coreopsis_stillmanii),((Coreopsis_bigelovii,Coreopsis_hamiltonii),(Coreopsis_calliopsidea,(Coreopsis_gigantea,Coreopsis_maritima))))),(Coreopsis_mutica,Coreopsis_cyclocarpa))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1282] END; BEGIN TREES; TITLE Tb6724; LINK TAXA = TaxaForAnalysisStep1949; TREE Fig._1A.1 = [&R] (Dahlia_coceinea,(((Coreopsis_petrophila,Coreopsis_senaria),((((Coreopsis_douglasii,Coreopsis_californica),Coreopsis_stillmanii),(Coreopsis_bigelovii,Coreopsis_hamiltonii)),(Coreopsis_calliopsidea,(Coreopsis_gigantea,Coreopsis_maritima)))),(Coreopsis_mutica,Coreopsis_cyclocarpa))Coreopsis); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1283] END;