Begin MrBayes; set autoclose=yes nowarnings=yes user=devel; exe data.nex; [partition] charset Dental = 1-473; charset Cranial = 474-674; charset Postcranial = 675-983; charset Soft_tissue = 984-1186; charset Molecular = 1187-1844; partition four = 4: Dental, Cranial, Postcranial, Soft_tissue Molecular; set partition = four; [substitution model] ctype ordered: 1 2 5-7 9 10 13 14 20-22 29 30 32-35 44 45 47 50 53 56-58 61 62 70 71 76 77 79 80 82 85-91 105 108 117 124-137 141 142 151 154 159 162 164 165 167 168 170 171 174 177 179 181 183 184 186 187 189 192 194-196 198 201 203-208 216-218 221 225 227 231 232 234-236 242 246-253 272 273 275-277 282 283 288 293-296 305-308 313-315 320 321 324 325 327 328 331 332 334 338 339 351-353 357 358 361-363 369-371 375-377 379 380 392 394 396-398 400 403 405 407 409 417-419 421 424 429 430 436 437 443 449 450 457 458 461 463 469 470 517 518 528-530 532 538-540 546-549 552 553 557 559 570 577 578 582 589 593 598 602 609 611 621-623 633 635 641-646 658-660 663 665 671 672 681 690 693 697 698 702 707 710 713 724-726 728 729 731 736 738 741 744 749 751-753 755 762 770 771 785 792 796 805 807 809 810 817 822 823 825-830 833 837-839 846 847 851 855 856 859 870 874 879 881 882 893-895 897 898 902 903 905 907-909 911 914-916 928 948 952 963 972 986 1021-1148 1150-1181 1183-1186 1187-1844; lset applyto = (all) coding = variable rates = gamma; [Mkv+G] [unlink shape = (all);] prset applyto = (all) ratepr = variable; [relaxed clock model] prset clockratepr = gamma(2, 200); prset clockvarpr = igr; prset igrvarpr = exp(10); [constraint backbone tree] constraint aa1 partial =Cacajao_calvus Chiropotes_chiropotes : Pithecia_pithecia Callicebus_donacophilus Alouatta_seniculus Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Saimiri_sciureus Cebus_apella Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Aotus_azarae Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa2 partial =Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia : Callicebus_donacophilus Alouatta_seniculus Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Saimiri_sciureus Cebus_apella Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Aotus_azarae Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa3 partial =Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus : Alouatta_seniculus Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Saimiri_sciureus Cebus_apella Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Aotus_azarae Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa4 partial =Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth : Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Saimiri_sciureus Cebus_apella Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Aotus_azarae Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa5 partial =Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus : Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Saimiri_sciureus Cebus_apella Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Aotus_azarae Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa6 partial =Saimiri_sciureus Cebus_apella : Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa7 partial =Saimiri_sciureus Cebus_apella Aotus_azarae : Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Callithrix_jacchus Cebuella_pygmaea Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa8 partial =Callithrix_jacchus Cebuella_pygmaea : Saguinus_oedipus Leontopithecus_rosalia Callimico_goeldii Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa9 partial =Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii : Saguinus_oedipus Leontopithecus_rosalia Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa10 partial =Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia : Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa11 partial =Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus : Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa12 partial =Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae : Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa13 partial =Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus : Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa14 partial =Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus : Hoolock_hoolock Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Tarsius_syrichta; constraint aa15 partial =Cercocebus_agilis Cercopithecus_neglectus : Hoolock_hoolock Presbytis_melalophos Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Tarsius_syrichta; constraint aa16 partial =Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos : Hoolock_hoolock Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Tarsius_syrichta; constraint aa17 partial =Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Hoolock_hoolock : Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus Tarsius_syrichta; constraint aa18 partial =Cercocebus_agilis Cercopithecus_neglectus Presbytis_melalophos Hoolock_hoolock Callithrix_jacchus Cebuella_pygmaea Callimico_goeldii Leontopithecus_rosalia Saguinus_oedipus Saimiri_sciureus Cebus_apella Aotus_azarae Brachyteles_arachnoides Lagothrix_lagotricha Ateles_belzebuth Alouatta_seniculus Cacajao_calvus Chiropotes_chiropotes Pithecia_pithecia Callicebus_donacophilus : Tarsius_syrichta; constraint aa19 hard = 2-.; [fossil ages in million years ago] calibrate Afrotarsius_chatrathi = uniform(29.5, 30.2) Afrotarsius_libycus = uniform(38.426, 39.552) Apidium_phiomense = uniform(29.5, 30.2) Arsinoea_kallimos = uniform(33.9, 34.8) Bahinia_pondaungensis = uniform(36.618, 37.473) Biretia_fayumensis = uniform(36.618, 37.473) Biretia_megalopsis = uniform(36.618, 37.473) Bugtipithecus_inexpectans = uniform(28.1, 33.9) Eosimias_centennicus = uniform(40, 45) Eosimias_sinensis = uniform(40, 45) Myanmarpithecus_yarshensis = uniform(36.618, 37.473) Parapithecus_fraasi = uniform(29.5, 30.2) Parapithecus_grangeri = uniform(29.5, 30.2) Phenacopithecus_spp = uniform(40, 45) Phileosimias_kamali = uniform(28.1, 33.9) Pondaungia_cotteri = uniform(36.618, 37.473) Proteopithecus_sylviae = uniform(33.9, 34.8) Serapia_eocaena = uniform(33.9, 34.8) Siamopithecus_eocaenus = uniform(33.9, 37.2) Aegyptopithecus_zeuxis = uniform(29.5, 30.2) Catopithecus_browni = uniform(33.9, 34.8) Epipliopithecus_vindobonensis = uniform(12.75, 13.65) Laccopithecus_robustus = uniform(7, 8) Oligopithecus_rogeri = uniform(31.1, 31.5) Oligopithecus_savagei = uniform(32.4, 33.2) Saadanius_hijazensis = uniform(28, 29) Victoriapithecus_macinnesi = uniform(12.1, 19.5) Branisella_boliviana = uniform(25.82, 27.02) Dolichocebus_gaimanensis = uniform(19.1, 20.5) Homunculus_patagonicus = uniform(16.1, 16.5) Soriacebus_ameghinorum = uniform(16.5, 17.5) Mohanamico_hershkovitzi = uniform(12, 13) Stirtonia_tatacoensis = uniform(12, 13) Neosaimiri_fieldsi = uniform(12, 13) Laventiana_annectens = uniform(12, 13) Killikaike_blacki = uniform(16.1, 16.5) Aotus_dindensis = uniform(12, 13) Chilecebus_carrascoensis = uniform(19.82, 20.36); prset nodeagepr = calibrated; prset brlenspr = clock:uniform; prset treeagepr = uniform(56.67, 66); prset topologypr = constraints(1-19); mcmcp nruns = 2 nchains = 8 ngen = 30000000 samplefreq=1000 printfreq = 10000 diagnfr = 50000; mcmcp filename = run1 relburnin=yes burninfrac=0.3 temp=0.05; mcmc; sumt; sump; End;