Trees identified using limited taxon sample in Dias et al. (2003) Contents: 1. Nexus file containing aligned sequences 2. Weighted neighbor joining tree 3. Weighted neighbor joining bootstrap tree 4. Majority rule consensus of trees sampled by MrBayes 2.01 (modified to use the WAG model) 5. References -------- 1. Nexus file (cut and paste material from #NEXUS to End; in order to execute. #NEXUS [ Unless otherwise noted, all sequences are from Arabidopsis. ] [ Sequences from other taxa begin with: ] [ Chre=Chlamydomonas reinhardtii; Os=rice; Pehy=petunia; ] [ Phpa=Physcomitrella patens; Zm=maize. ] [ PCMYB designates 3 repeat mybs (Braun and Grotewold 1999) ] Begin data; Dimensions ntax=46 nchar=105; Format datatype=protein gap=-; Matrix PCMYB1 KGPWSKEEDNTIIDLVEKYGPK---KWSTISQHLP-GRIGKQCRERWHNHLNPGINKNAWTQEEELTLIRAHQIYGNKWAELMKFLPGRSDNSIKNHWNSSVKKK PCMYB2 KGAWKKEEDELLSELVKDYMENDRPPWSKISKELP-GRIGKQCRERWHNHLNPTIIKSPWTREEELILVQAQRGNGNKWAEIAKLLPGRTENNIKNHWNCSVKKR PCMYB3 KGPWTHEEDEKIVELVEKYGPA---KWSIIAQSLP-GRIGKQCRERWHNHLNPDINKDAWTTEEEVALMNAHRSHGNKWAEIAKVLPGRTDNAIKNHWNSSLKKK PCMYB4 KGPWTKEEDEMIVQLIEKYGPK---KWSTIARFLP-GRIGKQCRERWHNHLNPAINKEAWTQEEELLLIRAHQIYGNRWAELTKFLPGRSDNGIKNHWHSSVKKK PCMYB5 KGPWTQEEDDKIVELVKKYGPA---KWSVIAKSLP-GRIGKQCRERWHNHLNPGIRKDAWTVEEESALMNSHRMYGNKWAEIAKVLPGRTDNAIKNHWNSSLKKK PhpaPCMYB KGAWTKEEDDRIMELVNKYGAK---KWSVIAQNLP-GRIGKQCRERWHNHLNPSIKREAWTQQEDLALIRAHQLYGNKWAEIAKFLPGRTDNSIKNHWNSTMKKK ChreMYB RGPWTPEEDKQLTDLVLSCGAQ---RWSTIAESIP-GRSGKSCRLRWWNHLSPQVKKGPFSDFEDAVIVRSHEKYGNKWSVIAKLLPGRTDNAVKNRWNSTLKRK PhpaMYB2 RGPWTSEEDQKLVSHITNNGLS---CWRAIPKLAGLLRCGKSCRLRWTNYLRPDLKRGIFSEAEENLILDLHATLGNRWSRIAAQLPGRTDNEIKNYWNTRLKKR AtMYB1 KGPWSKEEDDVLSELVKRLGAR---NWSFIARSIP-GRSGKSCRLRWCNQLNPNLIRNSFTEVEDQAIIAAHAIHGNKWAVIAKLLPGRTDNAIKNHWNSALRRR AtMYB22 KKRWTESEDIKLKEMVALEP-K---KWTKVAKHFE-GRTPKQCRERWHNHARPNVKKTTWSEEEDQILIEVHKVIGAKWIQISEQLPGRSYNNVKNHWNTTKRRV AtMYB44 KGPWSPEEDEQLRRLVVKYGPR---NWTVISKSIP-GRSGKSCRLRWCNQLSPQVEHRPFSAEEDETIARAHAQFGNKWATIARLLNGRTDNAVKNHWNSTLKRK AtMYB52 RGHWRPAEDEKLRELVEQFGPH---NWNAIAQKLS-GRSGKSCRLRWFNQLDPRINRNPFTEEEEERLLASHRIHGNRWSVIARFFPGRTDNAVKNHWHVIMARR AtMYB20 KGPWTAEEDRKLINFILTNGQC---CWRAVPKLSGLLRCGKSCRLRWTNYLRPDLKRGLLSDYEEKMVIDLHSQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKK AtMYB3 KGAWTKEEDQLLVDYIRKHGEG---CWRSLPRAAGLQRCGKSCRLRWMNYLRPDLKRGNFTEEEDELIIKLHSLLGNKWSLIAGRLPGRTDNEIKNYWNTHIKRK AtGL1 KGLWTVEEDNILMDYVLNHGTG---QWNRIVRKTGLKRCGKSCRLRWMNYLSPNVNKGNFTEQEEDLIIRLHKLLGNRWSLIAKRVPGRTDNQVKNYWNTHLSKK AtMYB118 KGPWTMEEDLILINYIANHGDG---VWNSLAKSAGLKRTGKSCRLRWLNYLRPDVRRGNITPEEQLIIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKY AtMYB53 KGPWLPEEDDKLINYIHKHGHS---SWSALPKLAGLNRCGKSCRLRWTNYLRPDIKRGKFSAEEEETILNLHAVLGNKWSMIASHLPGRTDNEIKNFWNTHLKKK AtMYB29 KGAWTAEEDKKLISYIHEHGEG---GWRDIPQKAGLKRCGKSCRLRWANYLKPDIKRGEFSYEEEQIIIMLHASRGNKWSVIARHLPKRTDNEIKNYWNTHLKKL AtMYB36 KGPWSPEEDVKLKDYIDKYGTGG--NWIALPQKIGLKRCGKSCRLRWLNYLRPNIKHGGFSEEEDRIILSLYISIGSRWSIIAAQLPGRTDNDIKNYWNTKLKKK AtMYB30 KGPWTPEEDIILVTYIQEHGPG---NWRAVPTNTGLLRCSKSCRLRWTNYLRPGIKRGNFTEHEEKMIVHLQALLGNRWAAIASYLPQRTDNDIKNYWNTHLKKK AtMYB61 KGLWSPEEDEKLLTHITNHGHG---CWSSVPKLAGLQRCGKSCRLRWINYLRPDLKRGAFSPEEENLIVELHAVLGNRWSQIASRLPGRTDNEIKNLWNSSIKKK AtMYB18 KGLWSPEEDEKLRSFILSYGHS---CWTTVPIKAGLQRNGKSCRLRWINYLRPGLKRDMISAEEEETILTFHSSLGNKWSQIAKFLPGRTDNEIKNYWHSHLKKK AtMYB13 KGPWSAEEDRILINYISLHGHP---NWRALPKLAGLLRCGKSCRLRWINYLRPDIKRGNFTPHEEDTIISLHQLLGNRWSAIAAKLPGRTDNEIKNVWHTHLKKR AtMYB101 KGPWTTTEDAILTEYVRKHGEG---NWNAVQKNSGLLRCGKSCRLRWANHLRPNLKKGSFTPDEEKIIIDLHAKLGNKWARMASQLPGRTDNEIKNYWNTRMKRR AtMYB2 KGPWTEEEDAILVNFVSIHGDA---RWNHIARSSGLKRTGKSCRLRWLNYLRPDVRRGNITLEEQFMILKLHSLWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKQ AtMYB102 KGPWTSEEDQKLVDYIQKHGYG---NWRTLPKNAGLQRCGKSCRLRWTNYLRPDIKRGRFSFEEEETIIQLHSFLGNKWSAIAARLPGRTDNEIKNFWNTHIRKK AtMYB39 KGPWLPEEDDKLTAYINENGYG---NWRSLPKLAGLNRCGKSCRLRWMNYLRPDIRRGKFSDGEESTIVRLHALLGNKWSKIAGHLPGRTDNEIKNYWNTHMRKK AtMYB58 RGPWSHDEDLKLISFIHKNGHE---NWRSLPKQAGLLRCGKSCRLRWINYLRPDVKRGNFSAEEEDTIIKLHQSFGNKWSKIASKLPGRTDNEIKNVWHTHLKKR AtMYB75 KGAWTTEEDSLLRQCINKYGEG---KWHQVPVRAGLNRCRKSCRLRWLNYLKPSIKRGKLSSDEVDLLLRLHRLLGNRWSLIAGRLPGRTANDVKNYWNTHLSKK AtMYB90 KGAWTAEEDSLLRLCIDKYGEG---KWHQVPLRAGLNRCRKSCRLRWLNYLKPSIKRGRLSNDEVDLLLRLHKLLGNRWSLIAGRLPGRTANDVKNYWNTHLSKK PehyAN2 KGAWTEEEDLLLRECIDKYGEG---KWHLVPVRAGLNRCRKSCRLRWLNYLRPHIKRGDFSLDEVDLILRLHKLLGNRWSLIAGRLPGRTANDVKNYWNTHLRKK AtMYB123 RGAWTDHEDKILRDYITTHGEG---KWSTLPNQAGLKRCGKSCRLRWKNYLRPGIKRGNISSDEEELIIRLHNLLGNRWSLIAGRLPGRTDNEIKNHWNSNLRKR ZmC1 RGAWTSKEDDALAAYVKAHGEG---KWREVPQKAGLRRCGKSCRLRWLNYLRPNIRRGNISYDEEDLIIRLHRLLGNRWSLIAGRLPGRTDNEIKNYWNSTLGRR ZmPL1 RGAWTAKEDDTLAAYVKAHGEG---KWREVPQKAGLRRCGKSCRLRWLNYLRPNIKRGNISYDEEDLIVRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSTLGRR AtMYB16 KGPWTPEEDQKLLAYIEEHGHG---SWRSLPEKAGLHRCGKSCRLRWTNYLRPDIKRGKFNLQEEQTIIQLHALLGNRWSAIATHLPKRTDNEIKNYWNTHLKKR AtMYB106 KGPWTPEEDQKLLAYIEEHGHG---SWRSLPEKAGLQRCGKSCRLRWTNYLRPDIKRGKFTVQEEQTIIQLHALLGNRWSAIATHLPKRTDNEIKNYWNTHLKKR AmMIXTA KGPWTVDEDQKLLAYIEEHGHG---SWRSLPLKAGLQRCGKSCRLRWANYLRPDIKRGPFSLQEEQTIIQLHALLGNRWSAIASHLPKRTDNEIKNYWNTHLKKR ZmB2 KGPWTQEEDEKLLHYIQKNGHG---SWRTLPRLAGLNRCGKSCRLRWTNYLRPDIKRGKFSQEEEQTILHLHSVLGNKWSAIATHLPGRTDNEIKNFWNTHLKKR AtMYB12 RGRWTAEEDQILSNYIQSNGEG---SWRSLPKNAGLKRCGKSCRLRWINYLRSDLKRGNITPEEEELVVKLHSTLGNRWSLIAGHLPGRTDNEIKNYWNSHLSRK AtMYB11 KGRWTAEEDRTLSDYIQSNGEG---SWRSLPKNAGLKRCGKSCRLRWINYLRSDIKRGNITPEEEDVIVKLHSTLGTRWSTIASNLPGRTDNEIKNYWNSHLSRK ZmP1 RGRWTAEEDQLLANYIAEHGEG---SWRSLPKNAGLLRCGKSCRLRWINYLRADVKRGNISKEEEDIIIKLHATLGNRWSLIASHLPGRTDNEIKNYWNSHLSRQ ZmP2 RGRWTAEEDQLLANYIAEHGEG---SWRSLPKNAGLLRCGKSCRLRWINYLRADVKRGNISKEEEDIIIKLHATLGNRWSLIASHLPGRTDNEIKNYWNSHLSRQ OsP RGRWTTEEDEKLAGYIAKHGEG---SWRSLPKNAGLLRCGKSCRLRWINYLRAGVKRGNISNQEEDVIIKLHATLGNRWSLIASHLPGRTDNEIKNYWNSHLSRQ ZmIF25 KGRWTREEDEILARYIEEHGEG---SWRSLPKNAGLLRCGKSCRLRWINYLRAGLKRGNITEEEEDVIVKLHATLGNRWSLIAGHLPGRTDNEIKNHWNSHLRRR ZmIF35 KGRWTKEEDEVLARYIKEHGEG---SWRSLPKNAGLLRCGKSCRLRWINYLRAGLKRGNISEEEEDMIIKLHATLGNRWSLIAGHLPGRTDNEIKNYWNSHLSRR OsIF RGRWTKEEDEKLARYIRENGEG---AWRSMPKNAGLLRCGKSCRLRWINYLRADLKRGNISPQEEDIILNLHATLGNRWSLIAGHLPGRTDNEIKNYWNSHLSRK ; End; 2. Tree identified by weighted neighbor joining (Bruno et al. 2000) of distances calculated assuming the WAG model of sequence evolution (Whelan and Goldman 2001) (((((AtMYB58:0.167742,AtMYB13:0.152638):0.109344,((AtMYB18:0.356060, AtMYB61:0.176854):0.060097,(AtMYB20:0.223631, PhpaMYB2:0.161309):0.062625):0.052605):0.011568,((((ZmB2:0.091652, AtMYB53:0.118499):0.038888,AtMYB39:0.203661):0.024543, AtMYB102:0.139289):0.015205,(AtMYB30:0.309906,(AtMYB29:0.233628, ((AtMYB106:0.010315,AtMYB16:0.020205):0.015431, AmMIXTA:0.059614):0.085638):0.032034):0.025479):0.026733):0.042301, ((AtMYB101:0.338383,(AtMYB2:0.215717,AtMYB118:0.128203):0.277201):0.045624, (AtMYB36:0.331879,(((AtMYB52:0.501663,AtMYB1:0.259610):0.038486, (AtMYB44:0.287173,ChreMYB:0.261787):0.083745):0.037636,(AtMYB22:1.146613, ((PCMYB5:0.066130,PCMYB3:0.070220):0.065419,(PhpaPCMYB:0.114778, (PCMYB2:0.449819,(PCMYB4:0.113242, PCMYB1:0.081188):0.092351):0.015304):0.072228):0.190361):0.171668):0.615001) :0.113999):0.020300):0.049150,(((OsIF:0.095498,(ZmIF35:0.029384, ZmIF25:0.057466):0.032866):0.011916,(OsP:0.057629,(ZmP2:0.000000, ZmP1:0.000000):0.040631):0.027606):0.048778,(AtMYB11:0.078702, AtMYB12:0.053228):0.064843):0.107831,(AtMYB3:0.159095,(AtGL1:0.357368, ((PehyAN2:0.065441,(AtMYB90:0.047642,AtMYB75:0.026698):0.062242):0.289716, ((ZmPL1:0.015454,ZmC1:0.036926):0.169895, AtMYB123:0.180187):0.012733):0.080260):0.057646):0.011016); 3. Bootstrap consensus of weighted neighbor joining trees identified as in part 1 above. A total of 500 bootstrap replicates were performed. +----AtMYB1 +230.0 ! +----AtMYB52 +-----------------------------------242.0 ! ! +----ChreMYB ! +338.0 ! +----AtMYB44 ! ! +----AtMYB75 ! +485.0 ! +500.0 +----AtMYB90 ! ! ! ! ! +---------PehyAN2 ! +305.0 ! ! ! +----ZmPL1 ! ! ! +500.0 ! +209.0 +250.0 +----ZmC1 ! ! ! ! ! ! ! +---------AtMYB123 ! +117.0 ! ! ! ! +-------------------AtGL1 ! ! ! ! ! +------------------------AtMYB3 ! ! ! ! +---------OsIF ! +124.0 +227.0 ! ! ! ! ! +----ZmIF25 ! ! ! ! +437.0 ! ! ! +378.0 +----ZmIF35 ! ! ! ! ! ! ! ! ! ! +---------OsP ! ! ! ! +343.0 +364.0 ! +-----466.0 ! +----ZmP1 ! ! +-31.0 ! +500.0 ! ! ! ! ! +----ZmP2 ! ! ! ! ! ! ! ! ! ! +----AtMYB12 ! ! ! ! +----------482.0 ! ! ! ! +----AtMYB11 ! ! ! ! ! ! ! ! +---------AtMYB101 ! ! ! +--------------------137.0 ! ! ! ! +----AtMYB118 ! ! ! +498.0 ! ! ! +----AtMYB2 ! ! ! ! ! ! +----AtMYB106 ! ! +168.0 +366.0 ! ! ! ! +476.0 +----AtMYB16 ! ! ! ! ! ! ! ! ! ! +254.0 +---------AmMIXTA ! ! ! ! ! ! ! ! ! ! +113.0 +--------------AtMYB29 ! ! ! ! ! ! ! ! ! ! ! +-------------------AtMYB30 +254.0 ! ! ! +-24.0 ! ! ! ! ! ! ! +---------AtMYB39 ! ! ! ! ! ! ! +168.0 ! ! ! ! ! ! ! ! ! +----AtMYB53 ! ! ! ! ! ! +------61.0 +191.0 ! ! ! ! ! ! ! +----ZmB2 ! ! +466.0 +------36.0 ! ! ! ! ! +--------------AtMYB102 ! ! ! ! ! ! ! ! +----AtMYB13 ! ! ! ! +-----388.0 ! ! ! ! ! +----AtMYB58 ! ! ! ! ! ! ! ! +-----------37.0 +----AtMYB20 ! ! ! ! +362.0 ! ! ! ! ! +----PhpaMYB2 ! ! ! +151.0 ! ! ! ! +----AtMYB18 ! ! ! +247.0 ! ! ! +----AtMYB61 ! ! ! ! ! +--------------------------------------------AtMYB36 ! ! ! +------------------------------------------------------AtMYB22 ! ! +----PCMYB5 ! +----------473.0 ! ! +----PCMYB3 ! ! +-----------------------------------254.0 +--------------PhpaPCMYB ! ! ! ! +----PCMYB4 +195.0 +463.0 ! ! +----PCMYB1 +194.0 +---------PCMYB2 4. Majority-rule consensus of 8000 trees from Bayesian analysis (Huelsenbeck and Ronquist 2001) using the WAG model of proein evolution (Whelan and Goldman 2001) and gamma distributed rates across sites. The complete set of trees sampled by the Markov chain are availble upon request from E.L. Braun /------ PCMYB1(1) /-95--+ | \------ PCMYB4(4) /-30-+ | | /------ PCMYB2(2) | \-34--+ /---------------------------33----------------------------+ \------ AtMYB22(10) | | | \----------------- PhpaPCMYB(6) | | /------ PCMYB3(3) +---------------------------------93---------------------------------+ | \------ PCMYB5(5) | | /--------------------------------------------------------------- ChreMYB(7) | | | | /------ PhpaMYB2(8) | | /-93--+ | | | \------ AtMYB20(13) | | /-69-+ | | | | /------ AtMYB61(21) | | | \-99--+ | | | \------ AtMYB18(22) | | /-18--+ | | | | /------ AtMYB53(17) | | | | /-98--+ | | | | | \------ AtMYB39(27) | | /-28--+ \-84-+ | | | | \------------ ZmB2(38) | | | | | | | | /------ AtMYB13(23) | | | \------100-------+ | | | \------ AtMYB58(28) | | | | | | /------ AtMYB29(18) | | /-43--+ /-41--+ | | | | | \------ AmMIXTA(37) | | | | /-39-+ | | | | | | /------ AtMYB16(35) | | | | | \-59--+ | | | | /-86--+ \------ AtMYB106(36) | | /----36----+ | | | | | | | \-14--+ \----------------- AtMYB30(20) | | | | | | | | | \----------------------- AtMYB102(26) | /-27--+ | | | | | | \----------------------------------- AtMYB101(24) | | | | | | | /-19--+ /---------------------------------------- AtMYB3(14) | | | | | | | | | | | | /----------------- AtGL1(15) | | | | | | | | | | | | | | /------ AtMYB75(29) | | | | | | /-------47--------+ /-99--+ | | | | \-68--+ | | | \------ AtMYB90(30) | | | | | | \100-+ | | | | | | \------------ PehyAN2(31) | | | | | | | | | | | | /------------ AtMYB123(32) | | | | \-45-+ | | | | | | /-------83-------+ /------ ZmC1(33) | | | | | | \-100-+ | | | | | | \------ ZmPL1(34) | | | | | | | | | | | | /------ AtMYB12(39) | | | /-49--+ \-73--+ /-------87-------+ | | | | | | | \------ AtMYB11(40) \-100-+ | | | | | | | | | | | /------ ZmP1(41) | | | | | | /-78--+ | | | | \-99--+ | \------ ZmP2(42) | | | | | /-92-+ | | | | | | \------------ OsP(43) | | | | | | | | | | \-100-+ /------ ZmIF25(44) | \100-+ | | /-99--+ | | | | | \------ ZmIF35(45) | | | \-85-+ | | | \------------ OsIF(46) | | | | | | /------ AtMYB118(16) | | \---------------------100---------------------+ | | \------ AtMYB2(25) | | | \---------------------------------------------------------- AtMYB36(19) | | /------ AtMYB1(9) | /-60--+ | | \------ AtMYB44(11) \---------------------------47---------------------------+ \------------ AtMYB52(12) 5. References Braun EL, Grotewold E (1999a) Newly discovered plant c-myb-like genes rewrite the evolution of the plant myb gene family. Plant Physiol 121: 21-24 Bruno WJ, Socci ND, Halpern AL (2000) Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17: 189-197 Dias AP, Braun, EL, McMullen, MD, Grotewold E (2003) Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiol 131: 610-620 Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755 Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699