#NEXUS BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=31; TAXLABELS Coptis_quinquefolia Aconitum_anthora Aconitum_lycoctonum Aconitum_napellus Actaea_cordifolia Actaea_racemosa Anemone_blanda Anemone_bracteata Anemone_nemorosa Anemone_pulsatilla Anemonella_thalictroides Aquilegia_atrata Aquilegia_chrysantha Aquilegia_ecalcarata Callianthemum_anemonoides Clematis_apiifolia Clematis_terniflora Clematis_vitalba Consolida_regalis Delphinium_cheilanthum Delphinium_pictum Dichocarpum_stoloniferum Ficaria_verna Isopyrum_thalictroides Nigella_damascena Ranunculus_repens Semiaquilegia_adoxoides Thalictrum_aquilegiifolium Thalictrum_minus Trollius_chinensis Trollius_europaeus ; END; BEGIN CHARACTERS; TITLE Ranunculaceae_CYC2; DIMENSIONS NCHAR=348; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Coptis_quinquefolia -------------------------------------------------------------------------------------------------------------------cAtGAcaTTGtgGaA----cgATGTaCTGGcGATACCaAgAgTGta------TCTTGtAgTACTGAATGTGATGTGGTTTCtGAAATTGAT---GAGGGACAG-AACGTC--ATCTTTAAA--GCGAAA-TCT-------TTAGACCGTGCTGTTTCG---AGAGAgAAAACaaaGAACAAATCCTCATGTCgGACTACATTGtATCCTGTTGCaAGAGATTCAAGGGCGAAg Aconitum_anthora GAGACTTCCCCTTGAAATCGCCCGCAGGTTTTTCGATCTTCAAGATAAGCTTGGCTTCGATAAGGCTAGTAA---AACTGTTGAGTGGCTGATGAATAAATCGGGAGAAGCGATTGATGAAGTCTATAAAGA-C-GGCCGGACCGGAGATAACAAGAGCTCA------ACTTCGACTTCTGAGTGTGATGCGGTGTCTGAAAATAAGGATCTGGGGCAA-AAGAATTTCTCTGAA----GCTGAGAAA------ACCAAA----------------------------------------ACTGTTAGAACTGCGCCATATCAGCTTGATAGGGATTCGAGGGAGAAG Aconitum_lycoctonum GAGACTTCCCCTTGAAATCGCCCGCAGGTTTTTCGATCTTCAAGATAAGCTTGGCTTCGATAAGGCTAGTAA---AACTGTTGAGTGGCTGATGAATAAATCGGGAGAAGCGATTGATGAAGTCTATAAAGA-C-GGCCGGACCGGAGATAACAAGAGCTCA------ACTTCTACTTCTGAGTGTGATGCGGTGTCTGAAAATAAGGATCTGGGGCAA-AAGGATTTCTCTGAA----GCTGACAAA------GCCAAA----------------------------------------ACTGTTAGAACTGCGCCATATCAGCTTGATAGGGATTCGAGGGAGAAG Aconitum_napellus GAGACTTCCCCTTGAAATCGCTCGCAGGTTTTTCGATCTTCAGGATAAGCTTGGTTTCCACAAGGCTAGTAA---AACTGTTGACTGGTTAATGAATAAATCGGGAGAAGCGATTGATGAGGTCTATAAAGG-C-GGCAGCACCGGAGATAACAAGAGCCCA------TCTTCGGTTTCAGAGTGTGATGTGGTGTCTGAAAATAAGGATGAGGGGCAA-AAGAGTTTCTCTAAA----GCTGAGAAA------ATGAAA----------------------------------------ACCATTAGAACTACGCCAAATCAGCTTGATAGGAATTCGAGGGAGAAG Actaea_cordifolia GAGACTCTCCCTTGAAGTCGCACGCAAGTTCTTTGATCTTCAAGATATGCTTGGTTTTGATAAAGCCAGTAA---GACCGTTGACTGGTTGTTGACGAAGTCGGAGGAAgCCATCAAGGAGCTCAGTAAA-----GGGTGCACTGGTGACGCCAAGAGTACTATA---TCTTCAACTTCTGAATGTGACGTGGTATCggatattgat---gtggGGaag-aaaGgctactccaaA----GGGAAATCT------TTAgATGGCTTTGTTTCG----AGAATGAAAATAATGAAgAAATCGTCGTGTTACACTACATCTCATCTTCTTGCAAGAGATTCGAGGCTGAAG Actaea_racemosa GAGACTCTCCCTTGAAGTCGCTCGCAAGTTCTTTGATCTTCAAGATATGcTTGGTTTTGATAAAGCCAGTAA---GACTGTTGACTGGTTGTTGAcGAAGTCGGAGGAACCCATCAAGGAGcTCAGTAAA-----GGGTGCACTGATGACACCAAGAGTACTATA---TCTTTAACTTCTGAATGTGACGTAGTATCGAAAATTGAT---GAGGGGAAG-AAAGACTACTCCAAG----GGGAAATCT------TTAGATGGCTTTGTTTCG----AGAAAGAAAATAATGAAGAAACCGTCGTGTTACACTACATCTCATCTGCTTGCAAGAGATTCGAGGCTGAAG Anemone_blanda GAGACTTTCCCTTGAAATTGCTCGCAAATTCTTTAATCTTCAAGATATGCTTGGTTTTGATATAGCAAGTAA---GACCGTTGAGTGGTTGCTAAAGCAGTCCGAGCAAGCAATTCAAGAGCTTAGTCCA----TCGTGTACTAGCAAAACCAACAATGAGGCTTCTTCTTCTATTTTTGAATTCGGTGACGCCTCTAAAATTGCC-------------------------------------------------------TTGAGTGTGCCA---AAGAGCATGATGGCGCGGTCA------------------------------AGTAGAGGTTTGAGGGTACAA Anemone_bracteata GAGACTGTCACTTGATATTGCTCGAAAGTTCTTTAATCTTCAAGATATGCTTGGATTTGATATAGCAAGTAA---GACTGTCGAGTGGCTGCTGAAGCAATCGGAGGAAGCTATTCATGCGCTTAGTAAA----TCGTGCACTGACAAAATCAAGAGTGCTGTTTCTTCTTCTACTTCTGAATGTGGTAAAGCTGAT------------TTGGGACAC-AATCGT------------------------------------------GTGTCA---AAGGGCATGATGGTGAATAAATCGCCATCAAGTAGAGAT------------GCACGGGATTTGAGGGTACAG Anemone_nemorosa GAGACTTTCCCTTGAAATTGCTCGCAAATTCTTTAATCTTCAAGATATGCTTGGTTTTGATATAGCAAGTAA---GACTGTTGAGTGGTTGCTGAAGCAGTCCGAGCAAGCAATTCAAGAGCTTATTACA----TCGTGTACTAGCAAAACCAaCAatGaGGCTTCTTcTTcTatttctgAatgCGGtGaGGCCTCTAAAATTGAC-------------------------------------------------------TTGAGTGTGCCA---AAGAGCATGATGGCGCGGTCA------------------------------AGTAGAGATTTGAGGGTACAA Anemone_pulsatilla TAGACTGTCACTTGATATTGCTCGCAGGTTTTTTAATCTTCAAGATATGCTTGGATTTGATATAGCAAGTAG---GACTGTTGAGTGGTTGCTGAAGCAGTCGGAGGAAGCCATTGATGAGCTTCGTAAA----TCGTGCATTGGCAAAACCAGGACTGGT------------------GAAGGTGGTGAAGCCTCTAAAACTGGT---TTGGGACAC-AATGGT------------------------------------------GTGTCG---AAGGGCATGACAGTAAATAAATCGCTCTCA---------------------AGTAGAGATTTGAGGGTACAA Anemonella_thalictroides GAGACTCTCCCTTGAAATCGCTCGCAAGTTCTTTGATCTGCAAGACATGCTTGGTTTTGACAAGGCAAGTAA---AACTgtTgaAtgGTTGCTGGgGAaGTCGGAagAAGCAATtAATGAGgTTAGTAAA----GGGTGCACTGGTGACACCAAAAGCACAGTATCTTCTTCTACTTCTGAATGTGAGGTAGTGTCAGAAATTGAT---GAGGGGCAG-AAAGGC-TTAACTAAA---GGGAAATCT--------GTAGATGGCATTGTTGTG---AGAGAGAAAAGGATAAATAAAATGTTGTGCAGAACTTCATGTCATATTCTCGCGAAAGACTCAAGGGTGAAG Aquilegia_atrata GAGACTCTCCCTTGAAATCGCTCGCAAGTTCTTTGATCTGCAAGACATGCTTGGTTTTGATAAGGCAAGTAA---AaCtGttGAATGGTTGCTGGGGAAGTCAGAAGAAGCAATTAATGAGCTCCATAAA----GGGTGCACTGGTGAAACCAAAAGCACAGTA---TCTTCTACTTCTGAATGTGATGTAGTGTCAGAAATTGAT---GAGGGGCAG-AAAGGC-TTAACTAAAATTGATGAGAAGCAATCT--ATAGATGGCATTGTTTTG---AGAGAGAAAACGACAACTAAAATGTTGAGCAGAACTACATGTCATATCCTTGCAAAAGACTCAAGGGTGAAG Aquilegia_chrysantha -AGACTCTCCCTTGAAATCGCTCGCAAGTTCTTTGATCTGCAAGACATGCTTGGTTTTGATAAGGCAAGTAA---AACTGTTGAATGGTTGCTGGGGAAGTCAGAAGAAGCAATtAATGAGCTCCAtaaa----GGGTGCACTGGtGAAACCAAAAGCaCAGTA---TCTTCTACTTCtgaAtgTGATGTAGtGTCAgaaATTGAT---GAGGGGCAG-AAAGgC-TTAACtAAAAttgatgaGAAGCAaTct--aTagatGGCATTGTtttg---AGAGAGAaaacgaCAACtaaaAtgTTGAGCAGAACTACATGTCATATCCTTGCAAAAGACTCAAGGGTGAAG Aquilegia_ecalcarata -------------------------------------------------CTTGGTTTTGATAAGGCAAGTAA---AactgttGAATGGTTGCTGGGGAAGTCAGAAGAAGCAATTAATGAGCTCCGTAAA----GGGTGCACTGGTGAAACCAAAAGCACAGTA---TCTTCTACTTCTGAATGTGATGTAGTGTCAGAAATTGAT---GAGGGGAAG-AAAGGC-TTAACTAAAATTGATGAGAAGCAATCT--ATAGATGGCATTGTTTTG---AGAGAGAAAACGACAACTAAAATGTTGAGCAGAACTACATGTCATATCCTTGCAAAAGACTCAAGGGTGAAG Callianthemum_anemonoides GAGACTtTCAATTGAAATCgCCCGCAAGTTCTTTGATCTTCAAGACATTcTTGGTTTCGATCAGGCTAGTAA---AACTGTTGGGTGGTTGCTGATGAAGTCGGAGGAGGCAATCAAGGGGCTCACTAAA----GGGTTCACTGCTGACACCAAGAGCAAtGTA---TgTTcTACTTCTGAATGTGGTTATGTGTCGGAAATTGAT---GAGGggcgt-aaa----------------cgcgcaAGA--------GAGGAACTTCTTCtAGCT---GAGAaTacaATGATGAACAAAACGACaTGTAGGACT---------------ACAAgAgATTTGAgGGTGAAG Clematis_apiifolia GAGACTGTCTCTTGAAATTGCTCGCAAGTTCTTTAATCTTCAAGATATGCTTGGTTTTGGCATAGCAAGCAA---GACTGTTGAGTGGTTGTTGAAGCAGTCGGAGGAAGCGATTGATGAGCTCAAACAA----GCTTGTGCTATCGAAACCAAGATTCCTTTTTCTTCTCCTACTCCTGAATGTGGTCAGGTTTCAGGACACAAG------GGTGTG-AAA----------------GGTAAGGAT--------TTGGATGGCAATGTGTCA---AAATGGATGCCGGTGAATAAGGCTCCGTCAGGTAGAGAT------------GCAAGAGATTTGAGGGTAAAG Clematis_terniflora AAGACTGTCTCTTGAAATTGCTCGCAAGTTCTTTAATCTTCAAGATATGCTTGGTTTCGGCATAGCAAGCAA---GACTGTTGAGTGGTTGTTGAAGCAGTCGGAGGCAGCGATTGATGAGCTCAAACAT----GCTTGTACTAGCGAAACCAAGACTGCTTTTTCTTCTTTTACTCCTGAATGTTGCCAGGTTTCAGGGCACAAG------GGTGTG-AAA----------------GGTAAGGAT--------TTGGATGGCAATGTGTCA---AAATGGATACCGGTGAATAAGGCTCCGTCAGGTAGAGAT------------GCAAGAAATTTGAGAGTCCAG Clematis_vitalba GAGACTGTCTCTTGAAATTGCTCGCGAGTTCTTTAATCTTCAAGATATGCTTGGTTTTGGCATAGCAAGCAA---GACTGTTGAGTGGTTGTTGAAGCAGTCGGAGGCAGCGATTGATGAGCTCAAACAA----GCTTGTGCTATTGAAACCAAGACTCCTTTTTCTTTACCAACTCCTGAATGTGGTCAGGTTTCAGGACACAAG------GGTGTG-AAA----------------GGTAAGGAC--------TTGGATGGCAATGTGTCA---AAATGGATGCCGGTGAATAAGGCTCCGTCAGGTAGAGAT------------GCAAGAGATTTGAGGGTACAG Consolida_regalis GAGACTGTCTCTTGAAATCGCTCGAAGATTTTTCGGTCTTCAAGATAAACTCGGTTTCAGCAAGGCTAGTAA---AACTGTTGAGTGGTTGCTGAACAAATCGGAAGAAGCCATCAATGAGATCAATAAAGGA-AGCAGTTCAATTGATAACAAGAGCCCT------TCTTCTGTTTCCGAGTGTGATGTAGTGTCTGAC---------GAAGGGCAA-AAGGGT--ttgTCTCGA--GTTGAGAAC--------AtgAAA---------------------------------------ATGCTTACAACTATGTCAAATCTGCGTGCTAAGGAAGCTAGGGAGGAG Delphinium_cheilanthum GAGACTGTCCCTTGGAATCGCTCGCAGGTTTTTCAATCTTCAAGATAAGCTTGGTTTCGACAAGGCTAGTAA---AACTGTTGAGTGGTTGCTGAATAAATCGGAAGGAGCGATTGATGAGATCAACAAAGGT----------------------------------------GTTTCTGAGTGTGATGTAGTGTCTGAAAATAAG---GAGGGGCAA-AAGGGT--TTCTCTAGA--GTTGAGAAG--------ATGAAA---------------------------------------ACAGCTACACCAACATCATATATGCGTGTTAGGGAAGCAAGGGAGAAG Delphinium_pictum GAGACTTCCCCTAGAAATTGCACGCAAGTTTTTCGATCTTCAAGACATGCTTGGCTTTGATAAGGTTAGTAA---AACTGTTGAGTGGTTGCTGCATAAGTCAGAAGATGCGATAGGGAAGATCAGTAAGGGT-GTTAGTACTGGTGATAACAAGAGCAAA------TCTTCTATGGCCGAAAGTGATGTAGTATCTGAAAAT------GAGGGGCAA-AAACGT--TTCTCTAAA--GTTGAGAAA--------GTGAAA---------------------------------------ACATTCAGGACTATGTCATATCCACTTGATAGGGATTCAAGAAAGAAG Dichocarpum_stoloniferum GAGACTCTCCCTTGGAATCGCTCGCAAGTTCTTTgaTctgCAAGACATGCTTGGTTTTGATAAGGCAAGTAA---AACTGTTGATTGGTTGCTGGGGAAGTCGGAACAAGCAATTACTGAGCTCAGTAAA----GGGTACACTGGTGACGCCAAAAGCACAGTA---TCTTCAACTTCTGAATGTGATGTAGTGTCGGAAATTGAT---GAGGGGCAG-AAACAc--TTAACTAAA--GGGAAA-TCt-------GTAGATGGcATTGTTTTG---AGAGAGAAAtCGATAAATAAAATGTTGTGTACAACTACcTGTCATACCCTTGCtAAAGACTCAagGGTGAAG Ficaria_verna GAGACTTTCCCTAGAAATCGCTCGTAAGTTTTTTGATCTTCAAGATATGCTTGGTTTTGATAAAGCAAGTAA---AACTGTTGAGTGGTTGTTGAGACATTCGGAGGAAGCCATTAATGAGCTTAGTAAG----GGGTGCACAGGCGACACAAAGAGTACTCTG---TCTTCTATTATGGAATGTGAGCTAGGGTCGGAAATTGCC---AGAGGAAAG-AAA----------------CGGAAA-TCC-------CTTGATGCTAATGTATCA---ATTGAGAAAAAGATGAGTAAATCGCCATCAAGTGGTGCT------------ACAAGAGATTCAAGAGTAAAG Isopyrum_thalictroides GAGACTCTCCCTTGAAATTGCTCGCAAGTTCTTTGATcTGCAAGACATGCTTGGGTTCGACAAGGCAAGTAA---AACTGTTGAATGGTTGCTGGGGAAGTCGGAACAAGCAATTAATGAGCTCAGGAAA----GGGTGCACTGGTGACACCAAAAGCACAGTA---TCTTCTACTTCTGATTGTGAtGTAGTGTCGGAAATTGAC---GAGGGGaAg-AAAGGC--TTAACTAAA--GGGAAA-TCT-------aTagAtggcatTGTTTTG---AGAGAGAAAACGACAAATAAAATGTtGtgCAGAACTACATGCCATATCCTTGCAAAAGACTCAAGGGTGAAG Nigella_damascena GAGGCTCTCCCTTGAAATTGCTCGCGAGTTCTTTAATCTTCAAGATTTGCTTGGTTACGACAAAGCAAGCAA---AACTGTTGACTGGTTATTGAGGTTATCTGAAGAAGCCATCAACCAGATTAGTAAA----GCTTGCCCTGCTGAGACCAAGAGTGCTAAA---TCTTCTACTTCTGAATGTAATGTAGTGTCCCATATTAAT---GAGACGAAG-CAAAAA-CTCCCAT-----GGGAAGAAG--------CCTCTAGATGTGGTTGCCTCCAGAGAAAAA---------------------------------------------AATGATTCCAGACTGAAA Ranunculus_repens ----------------------------------------------------------GATAAAGCAAGTAA---AactgttGATTGGTTGTTGAGGCAGTCAGAGGAAGCGATTAATGAGCTTACGAAA----GGGTTTGTG------------------------TCTTCTATTTCTGAATGTGAACTAGTGTCAGAAATTAAA---GACATGAAA-CGG----------------AAGATG-TCT-------ATTGATGGAAATGTTGCA---AGCCAGAAAAAGATGAATAAATTGGAAGCAAGTGGAACT------------ACAAGGGATTCCAGGATGAAG Semiaquilegia_adoxoides GAGACTCTCCCTTGAAATCGCTCGCAAGTTCTTTGATCTGCAAGACATGCTTGGTTTTGATAAGGCAAGTAA---AACTGTTGAATGGTTGCTGGGGAAGTCAGAAGAAGCAATTAATGAGCTCCGTAAA----GGGTGCACTGGTGAAACCAAAAGCACAGTA---TCTTCTACTTCTGAATGTGATGTAGTGTCAGAAATTGAT---GAGGGGCAG-AAAGGC--TTAACTAAAATTGATGAGAAGCAATCT-ATAGATGGCATTGTTTTG---AGAGAGAAAACGACAACTAAAATGTTGAGCAGAACTACAtGTCATATCCTTGCAAAAGACTCAAGGGTGAAG Thalictrum_aquilegiifolium -------------------------AAGTTctTTgATttgcaagaCatgcttgGtttcgatAAGGCAAgtaa---aacTATTGAAtGGTTgCTGGGGAAGTCGGAaGaAGCAaTTAATGaGcTCaGtAAA----GGgtGCactGgtgaCAACAAAAGTgCAGtA---TcTTcTAcTTcTgAATGTGATGTAGTGTCGGAAATtGaC---AaGGgGgag-aaaggc--ttaactaaA--GGgaAa-tcT-------GTAGATGGCATTGTTGTT---AGAGAAAAAAGGACAAATCAAATGTTGTGCAAAACTACATGCCtTATTCTTGCAAAAGACTCAAGGGTGAAG Thalictrum_minus -------------------CGCTCGCAGtTCTTTGAtCTGcaaGACATGCTTGGTTTCgATAAGGCAAGTAA---aaCtattGAATGGTTGCTGGGGAAGTCGGAAgAAGCAATTAATGAGCTCAGTAAA----GGCTGCACTGGTGACaCCAAAAGTACAgTA---TCTTCTACTTCTGAATGTGATGTAgtGTCGGAAATTGAT---GAGGGGCAg-AAAGGC--TTAACTAAA--GGGAaA-TCT-------GTAGATGGCATTGTTGTT---gGAGAGAAAAGGATAAATgAAATGtTGTGCAgAACTACaTGTCATATTCTTGCAAAAgACTCaagGGtGAAG Trollius_chinensis GAGACTGTCCGTTGAAATTTCCCGCAAGTTCTTTGATCTTCAAGATATGCTTGGTTTTGATAAAGCAAGTAA---GACTGTTGAGTGGTTGATGAAGCAGTCAGAGCAAGCTATCGGTGAGCTAAGAAAAGAT-AGCAGCACTGGTGAT---------------------------------------GTAGTTTCAGAAATTGAT---GAGGGGAAA-AAGGGA--TTCTCCTCA--AGGAAA-TCC-------TTAGAC------------------------GTTTCAAAAAAAACGTCGTGCAAAACT---------ATTCTTGCAGGGGATTTGAGGGTAAAG Trollius_europaeus GAGACTGTCCGTTGAAATTTCCCGCAAGTTCTTTGATCTTCAGGATATGCTTGGTTTTGATAGAGCAAGTAA---GACTGTTGAGTGGTTGATGAAGCAGTCGGAGCAAGCTATCGGTGAGCTAAGAAAAGAT-GGCAGCACTGGTGACACCAAGACA------------------------------ACAGTTTCAGAAATTGAC---GATGGGAAA-AAAGGA--TGCTCCTCA--AGGAAA-TCC-------TTGGAC------------------------GTTTCAAAAAAAACGTCGTGCAAAACT---------TTTCTTGCAAGGGATTTGAGGGTAAAG ; END; BEGIN mrbayes; Outgroup Coptis_quinquefolia; Lset Nst = 6 Rates = gamma; showmodel; mcmc ngen = 2000000 samplefreq = 100 printfreq = 1000; sump burnin = 5000; sumt burnin = 5000; END; BEGIN TREES; Title Ranunculaceae_CYC2; LINK Taxa = Taxa; TRANSLATE [0] 1 Coptis_quinquefolia, [1] 2 Aconitum_anthora, [2] 3 Aconitum_lycoctonum, [3] 4 Aconitum_napellus, [4] 5 Actaea_cordifolia, [5] 6 Actaea_racemosa, [6] 7 Anemone_blanda, [7] 8 Anemone_bracteata, [8] 9 Anemone_nemorosa, [9] 10 Anemone_pulsatilla, [10] 11 Anemonella_thalictroides, [11] 12 Aquilegia_atrata, [12] 13 Aquilegia_chrysantha, [13] 14 Aquilegia_ecalcarata, [14] 15 Callianthemum_anemonoides, [15] 16 Clematis_apiifolia, [16] 17 Clematis_terniflora, [17] 18 Clematis_vitalba, [18] 19 Consolida_regalis, [19] 20 Delphinium_cheilanthum, [20] 21 Delphinium_pictum, [21] 22 Dichocarpum_stoloniferum, [22] 23 Ficaria_verna, [23] 24 Isopyrum_thalictroides, [24] 25 Nigella_damascena, [25] 26 Ranunculus_repens, [26] 27 Semiaquilegia_adoxoides, [27] 28 Thalictrum_aquilegiifolium, [28] 29 Thalictrum_minus, [29] 30 Trollius_chinensis, [30] 31 Trollius_europaeus; TREE con_50_majrule = (1:8,(((30:1,31:1):5,(23:5,25:5,26:5,((17:2,(16:1,18:1):1):2,(8:3,(10:2,(7:1,9:1):1):1):1):1):1):1,((15:5,((21:2,(19:1,20:1):1):2,((5:1,6:1):2,(4:2,(2:1,3:1):1):1):1):1):1,(22:4,24:4,(11:2,(28:1,29:1):1):2,(27:3,(14:2,(12:1,13:1):1):1):1):2):1):1); END;