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#NEXUS
[I am a comment. Truncated data from: Ronquist et al. 2012. and Zhang et al. 2016. Sys Biol.]
Begin data;
Dimensions ntax = 20 nchar = 510;
Format datatype = mixed(standard:1-200, DNA:201-510) interleave = yes gap = - missing = ?;
Matrix
[Morphology, Vilhelmsen, 200 chars]
Raphidioptera 0000000000 000011?001 ?000?00000 01-210?100 000000-000 10000-0??1 011000???1 -2-00?100? 00--000000 -0-0?1-000 ?2?0000??? 0-00?0--00 001?010100 0000100031 01001010?0 ???0011100 000000???? 011--100?? ??01000000 010-02000-
Xyela 0010000100 0010000-00 0010111010 0001010000 0000010110 0001100010 0200000000 0100010000 0100011000 0000000100 0002100000 1000010000 00?0010000 0100100000 0000000100 0011100010 0000000000 1000000000 0000010200 001010000-
Runaria 0010000010 0100000-00 002-001000 00010?0010 1110020110 1100100020 0210100100 110001000? 0???0??0?3 2102110??? 000?1??110 101?11?010 0000000000 1100000021 110?1??210 100110?120 1-11001000 1100000100 0000010210 00????0010
Diprion 00100???0? ?010000-?0 ?100001??? ?00?00?010 110002?2?? ?100100030 0?102001?? 001000000? 010001?003 ?101?1100? ?0??1????? 10111121?? ?00?000000 ??00?0?000 ?1001012?? ?????11121 0-1101-000 1100000100 00000101?0 ?010?0100-
Phylacteophaga 0010000000 0000000-00 0000001000 000110?010 1200021211 10001111-0 0210200111 100000000? 00--1?0003 2102110001 221210011? 1211112111 00?1000010 120010103- 1110101210 0110111021 0-0101-000 4101010100 10000101?0 0010101010
Onycholyda 00110???0? ??110100?2 0000?22??? ?00101?100 010002?2?? ??01111011 021000?0?? 0100010000 0???0????3 ?100?10100 ?00?1????? 1?0??10000 ??0?01?000 ??00100000 ???0010??? ????100000 0001000000 1001000000 0000011200 0010111?1?
Cephus 0011010020 0110011000 1000?01000 0001020000 0000120210 1001111010 0210021100 1101110000 0100010113 1100000110 1001100000 101100--00 0001110100 0200100011 1100120100 1011100021 0001100000 1101000100 00001101?0 0010100010
Sirex 0111110020 0110010100 0000?01000 0003120111 00000202?1 1101110020 0200021100 110001101? 0???0??110 ?10001?120 0102100??? 1000010020 0001000100 0100110000 1000102100 0111100101 0101000000 1100010100 00000101?0 0021100011
Orussus 1111110001 1110110112 1000101000 0012101110 2100120210 10111101-0 0201021100 1101221220 1---1?2022 021201-121 1002110111 1000010001 0011010010 0201100101 1111101210 0111101121 0-11200011 3101101111 10000101?1 202110000-
Vespidae 00111100?1 011011?112 1000101102 ?011001110 2102121211 1011111011 0210221110 1101211221 0101132123 220011?121 2212110111 100000--01 0011011-10 120211013- 1111101211 1110112121 0101200000 4101010110 10012101?0 000-000011
Asioxyela ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????10??? ?????????? ?????????? ?????????? ????????00 0000000000 1????????? ?????????? ??????????
Nigrimonticola 0????????? ????0????? ??10?1???? ????????00 ?????????? ?????????? ?????????? ??????000? ????????0? ?????00??? ????10???? 1????????? ?????????0 ?????????? ?????????? ????????0? 00?0?00000 ?????????0 ????01?2?? ?010???00?
Xyelotoma 0????????? ????0????? ??10?0???? ????????10 ?????????? ?????????? ????2????? ??????000? ?????????? ?????01??? ?????????? ?2???1???? ?????????? ?????????? ?????????? ???????100 0-0?00???? 1?????0100 ??0?0????? ??????????
Undatoma ?????????? ?????????? ?????????? ????????10 ??100??2?? ?00?11001? ?????????? 01000?000? ??????0?0? ?????1-??? ?????????? 1????11??? ????????00 ?????????? ?????????? ????????21 1001001000 1?????01?0 0???0?0200 ?0???0????
Dahuratoma 0?1??????? ????0????? ??10?????? ????????00 ?????????? ?????????? ?????????? ??????000? ??????0??? ?????????? ?????????? ?0???11??? ?????????? ?????????? ?????????? ????????00 1-01001000 1?010?0100 000?0??100 ?0????????
Cleistogaster 0????????? ????0????? ??000????? ????????10 ?????????? ?????1???? ?????????? 1101??022? ??????2??? ?????01??? ?????????? 1????0--?? ???????011 ???2????3? ?????????? ????????21 0101200000 3?????1101 100?2?02-1 ?02?10?0??
Ghilarella 0????????? ?????????? ?????0???? ????????00 ?????????? ?????????? ?????????? ??????100? ?????????? ?????01??? ?????????? ?????1???? ????????00 ?????????? ?????????? ????????21 000100-100 1????????? 000?(0,1)?0??? ?0????????
Mesorussus 11???????? ?????1???? ??020(0,1)???? ?????????? 21???????? ?????1???? ?????????? ?????????? ?????????? ?????????? ?????????? 1????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
Prosyntexis 00???????? ?????????? ??00?????? ????????00 ???00????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? 1????????? ????????00 ?????????? ?????????? ????????21 000110-100 1?????11?? ?00?1??2-0 ?0??1?????
Pseudoxyelocerus ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ????????10 1001001000 1????????? ?????????? ??????????
[16S, 100 sites]
Raphidioptera ATAATCATTTGTTTCTTAATTAGGGACTAGTATGAAGGATTGGACGAGATATTTTCTGTCTCAAATTTTATTTTTTAGTAAAAAAGCT-AAAATTTATTT
Xyela ATAATCATTAGTCTTTTAATTGAGGGCTGGAATGAATGATTGAACGAAGTATTAACTGTCTCGAATTTAATTTTTGAGTTAAAAAGCT-TAAATTTTATT
Runaria ATAATCATTAGTCTTTTAATTGAAGACTTGTATGAAGGATTGAATGAAATATATACTGTCTCGAATTTAATTTTTGAGTTAAAAAGCT-TAAATATTATT
Diprion ATAATAATTTGTCCTCTAATTAAGGACTAGAATGAATGATTTGACGAAGTTAAAACTTTCTCGAAATTAATTTTTAAGTTAAAAAGCT-TAAATAATATT
Phylacteophaga ATAATAATTAGTCTATTAATTGTAGGCTGGTATGAAAGATTGAACGAGGTAAATACTGTCTCGAATTTAATTTTTGAGTTAAAAAGCT-TAAATTTTATT
Onycholyda ATAATCATTAGTCTTTTAATTAAGGTCTAGAATGAAGGATTGAACGAAGTAAAATCTGTCTCAAATTTAATATTTAAGTCAAAAAGCT-TAAATAAATTT
Cephus ATAATCATTAGTTTTTTAATTGAAAGCTTGTATGAATGATTGAATAAAATATTTATTGTCTCAAATTTAATTTTTAAATTAAAAAGTT-TAAATTTTATT
Sirex ATAATCAATTGTTTTTTAATTTAAATCTAGAATGAATGGTTTAACGAAATATTAACTGTCTCGAATTTAAATTTTTAGTAAAAATGCTGAAAATATATTT
Orussus ATAATCAATAGTTCTTTAATTGGGAACTTGTATGAAGGATTGAACGAGATAGTAACTTTCTAGAATTTAATTTTTAGATTAAAAAGTC-TAAATTTAATT
Vespidae ATAATCAATAGTTTTTTAATTGGAAACTGGAATGAAGGAGTGGATGAAATATAGATTGTCTCGAATTTAAATTAAAAGTAAAAATGCT-TTTATATAGTT
Asioxyela ????????????????????????????????????????????????????????????????????????????????????????????????????
Nigrimonticola ????????????????????????????????????????????????????????????????????????????????????????????????????
Xyelotoma ????????????????????????????????????????????????????????????????????????????????????????????????????
Undatoma ????????????????????????????????????????????????????????????????????????????????????????????????????
Dahuratoma ????????????????????????????????????????????????????????????????????????????????????????????????????
Cleistogaster ????????????????????????????????????????????????????????????????????????????????????????????????????
Ghilarella ????????????????????????????????????????????????????????????????????????????????????????????????????
Mesorussus ????????????????????????????????????????????????????????????????????????????????????????????????????
Prosyntexis ????????????????????????????????????????????????????????????????????????????????????????????????????
Pseudoxyelocerus ????????????????????????????????????????????????????????????????????????????????????????????????????
[EF1aF2, 210 sites]
Raphidioptera GCTGAGCGTGAGCGTGGTATCACTATAGATATCGCACTGTGGAAATTTGAAACTGCAAAATACTATGTCACTATAATTGATGCTCCGGGCCATCGTGATTTCATTAAGAACATGATTACGGGTACGTCCCAGGCCGATTRTGCTGTCTTGATAGTTGCGGCCGGCACAGGAGAATTCGAAGCTGGTATTTCAAAGAACGGACAAACTCGT
Xyela GCTGAGCGYGARCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACCGCCAGGTACTACGTCACCATCATCGACGCCCCTGGCCACAGGGATTTCATCAAGAACATGATCACTGGTACCTCTCAGGCCGATTGCGCCGTACTTATCGTCGCTGCCGGTACTGGAGAATTTGAAGCCGGTATCTCCAAGAACGGACAGACCCGC
Runaria GCCGAGCGTGAGCGTGGTATCACCATCGATATCGCCCTGTGGAAATTCGAGACGGCCAAATACTACGTGACGATCATCGACGCCCCGGGGCACAGAGATTTCATCAAGAACATGATCACCGGAACTTCGCAGGCCGATTGCGCCGTACTGATCGTCGCCGCAGGTACCGGAGAGTTCGAGGCCGGTATCTCCAAGAACGGCCAGACCCGC
Diprion GCTGAGCGTGAACGTGGTATCACAATTGATATCGCACTTTGGAAATTTGAAACTGCCAAGTACTATGTGACTATCATCGATGCGCCGGGACACAGAGATTTCATTAAGAACATGATCACTGGTACGTCTCAGGCCGACTGTGCAGTGTTGATTGTGGCTGCTGGTACGGGAGAATTCGAAGCTGGTATTTCCAAGAACGGTCAGACCCGT
Phylacteophaga GCTGAGCGTGAACGTGGTATCACCATTGACATTGCTCTGTGGAAGTTTGAGACTGCCAAGTACTACGTTACCATCATTGACGCCCCTGGACACAGAGATTTCATTAAGAACATGATCACTGGAACGTCGCAAGCTGATTGTGCTGTGTTGATCGTCGCTGCTGGTACGGGAGAATTCGAGGCTGGTATCTCGAAAAATGGGCAGACTCGT
Onycholyda GCTGAGCGTGANCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACCGCCAAGTACTATGTCACCATCATCGACGCCCCCGGTCACAGGGATTTCATCAAGAACATGATCACTGGTACTTCGCAGGCTGATTGTGCTGTGCTGATCGTCGCTGCCGGTACGGGAGAGTTCGAGGCTGGTATCTCGAAGAACGGACAGACCCGC
Cephus GCCGAGCGTGAACGTGGTATCACCATTGACATTGCTCTCTGGAAATTCGAGACGGCCAAATATTACGTGACCATCATCGATGCTCCCGGACACAGAGATTTCATCAAGAACATGATCACGGGAACGAGTCAGGCCGATTGTGCTGTGCTAATTGTGGCAGCTGGTACTGGAGAGTTCGAGGCGGGTATCTCGAAGAACGGACAGACCCGT
Sirex GCTGAGCGCGAACGTGGTATCACCATTGACATTGCCCTGTGGAAATTCGAAACGGCAAAATATTACGTTACTATTATTGATGCTCCCGGACACAGAGATTTCATCAAGAACATGATCACTGGAACTTCGCAAGCCGATTGTGCAGTTCTGATTGTCGCGGCTGGTACCGGAGAATTTGAGGCCGGTATTTCGAAAAATGGACAGACTCGT
Orussus GCTGAGCGYGARCGTGGTATCACTATTGACATTGCCTTGTGGAAGTTTGAAACGGCTAAATACTATGTCACTATTATCGATGCGCCTGGACACAGAGACTTTATTAAAAACATGATTACTGGAACCTCGCAAGCTGACTGCGCTGTACTCATTGTCGCCGCAGGTACCGGCGAGTTTGAAGCCGGTATCTCCAAGAATGGACAGACTCGT
Vespidae GCTGAGCGCGAGCGTGGTATCACCATTGACATTGCTCTTTGGAAATTCGAAACTTCTAAATACTACGTCACAATTATTGACGCACCTGGACACAGAGATTTCATCAAGAACATGATCACTGGAACCTCGCAAGCAGATTGCGCTGTGCTGATCGTAGCTGCTGGTACAGGAGAATTTGAGGCTGGTATTTCTAAGAACGGACAAACGCGT
Asioxyela ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Nigrimonticola ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Xyelotoma ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Undatoma ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Dahuratoma ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Cleistogaster ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ghilarella ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Mesorussus ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Prosyntexis ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Pseudoxyelocerus ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
;
End;
Begin mrbayes;
[partition]
charset MV = 1-200;
charset 16S = 201-300;
charset Ef1a = 301-510;
charset Ef1a12 = 301-510\3 302-510\3;
charset Ef1a3 = 303-510\3;
partition four = 4: MV, 16S, Ef1a12, Ef1a3;
set partition = four;
[substitution model]
exclude 7 31 61 83 107 121 122 133 182 183 198; [constant]
ctype ordered: 20 23 27 30 36 41 42 44 46 48 59 65 75 78 79 89 99 112 117 134 146 157 159 171 185 191 193 196;
lset applyto = (1) coding = variable rates = gamma; [morphology]
lset applyto = (2,3,4) nst = 6 rates = gamma; [GTR+G]
unlink statefreq = (all) revmat = (all) shape = (all);
prset applyto = (all) ratepr = variable;
[relaxed clock model]
prset clockratepr = lognorm(-7,0.6);
prset clockvarpr = igr [tk02];
prset igrvarpr = exp(10) [tk02varpr = exp(1)];
outgroup Raphidioptera;
taxset fossils = Asioxyela Nigrimonticola Xyelotoma Undatoma Dahuratoma Cleistogaster Ghilarella Mesorussus Prosyntexis Pseudoxyelocerus;
[constraints]
constraint HymenFossil = 2-.;
constraint Hymenoptera = 2-10;
constraint Holometabola = 1-10;
constraint Tenthredinidae = 3-5;
constraint CepSirOruApo = 7-10;
[ [Total-evidence Dating]
calibrate Asioxyela = unif(228,242) Nigrimonticola = unif(152,163) Xyelotoma = unif(152,163) Undatoma = unif(145,152) Dahuratoma = fixed(134) Cleistogaster = unif(168,191) Ghilarella = unif(113,125) Mesorussus = unif(94,100) Prosyntexis = unif(80,86) Pseudoxyelocerus = fixed(182);
prset nodeagepr = calibrated;
prset brlenspr = clock:fossilization [clock:uniform];
prset samplestrat = diversity [random];
prset sampleprob = 0.0001;
prset speciationpr = exp(10);
prset extinctionpr = beta(1,1);
prset fossilizationpr = beta(1,1);
prset treeagepr = offsetexp(300,390);
prset topologypr = constraint(HymenFossil);
mcmcp nrun = 2 nchain = 4 ngen = 500000 samplefr = 100;
mcmcp filename = hym.te printfr = 1000 diagnfr = 5000;
mcmc;
sump;
sumt;
delete fossils;
sumt output = hym.rf;
]
[ [Node dating]
delete fossils;
exclude 24 130 168; [constant]
calibrate Tenthredinidae = offsetgamma(100,150,25) CepSirOruApo = truncatednormal(140,175,25);
prset nodeagepr = calibrated;
prset brlenspr = clock:birthdeath [clock:uniform];
prset samplestrat = diversity [random];
prset sampleprob = 0.0001;
prset speciationpr = exp(10);
prset extinctionpr = beta(1,1);
prset treeagepr = offsetexp(300,390);
prset topologypr = constraint(Hymenoptera,Tenthredinidae,CepSirOruApo);
mcmcp nrun = 2 nchain = 4 ngen = 500000 samplefr = 100;
mcmcp filename = hym.nd printfr = 1000 diagnfr = 5000;
mcmcp startp = reset startt = random;
mcmc;
sump;
sumt;
]
[ [Non-clock, clockrate&calibrate ignored]
delete fossils;
prset brlenspr = uncons:gammadir(1,1,1,1);
prset topologypr = uniform;
mcmcp nrun = 2 nchain = 4 ngen = 500000 samplefr = 100;
mcmcp filename = hym.un printfr = 1000 diagnfr = 5000;
mcmc;
sump;
sumt;
]
End;
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