#NEXUS BEGIN DATA; DIMENSIONS NTAX=86 NCHAR=219; FORMAT SYMBOLS=" 0 1" MISSING=? INTERLEAVE; MATRIX [For the source trees encoded in our crocodylian supertree dataset, there was one case where the same characters were coded for two non-overlapping taxon sets. Identical allozyme loci were scored for Alligatoroidea and for non-alligatoroid crocodylians (Gatesy et al. Fig. 2). Densmore (1983) separately coded alleles in each of these two presumed groups. Therefore, even though the same loci were examined for both "groups," the character codings were incompatible between matrices. Analysis of our supertree dataset without the allozyme data supported these two monophyletic groups. Thus, it was acceptable to concatenate the alligatoroid and non-alligatoroid allozyme datasets, end to end, in our supertree analysis (Gatesy et al. Fig. 4). This procedure yielded no duplications of character evidence.] [morphology = 64] [ 111111111122222222223333333333444444444455555555556666] [ 123456789012345678901234567890123456789012345678901234567890123] Paleognathae 000000000000000000000000000000000000000000000000000000000000000 Neognathae ??????????????????????????????????????????????????????????????? Testudines ??????????????????????????????????????????????????????????????? Caiman_yacare 001000110000000000110100011100000000000000000000110001000000101 Caiman_latirostris 011000110000000000110100011100000000000000000000110001000000101 Melanosuchus_niger 111000110000000000110100011100000000000000000000110001000000101 Paleosuchus_palpebrosus 000001010000000000110100011100000000000000000000110001000000101 Paleosuchus_trigonatus 000001010000000000110100011100000000000000000000110001000000101 Alligator_mississippiensis 000000001111111011010100011100000000000000000000110001000000101 Alligator_sinensis 000000000111111011010100011100000000000000000000110001000000101 Crocodylus_rhombifer 000000000000000000000000000000011001010000011111010001000000101 Crocodylus_acutus 000000000000000000000000000000011001010000011111010001000000101 Crocodylus_intermedius 000000000000000000000000000000011001010000011111010001000000101 Crocodylus_moreletii 000000000000000000000000000000011001010000011111010001000000101 Crocodylus_siamensis 000000000000000000000000000001101001010000011111010001000000101 Crocodylus_johnstoni 000000000000000000000000000011101001010000011111010001000000101 Crocodylus_mindorensis 000000000000000000000000000011101001010000011111010001000000101 Crocodylus_novaeguineae 000000000000000000000000000011101001010000011111010001000000101 Crocodylus_porosus 000000000000000000000000000011101001010000011111010001000000101 Crocodylus_palustris 000000000000000000000000000000101001010000011111010001000000101 Crocodylus_niloticus 000000000000000000000000000000001001010000011111010001000000101 Crocodylus_cataphractus 000000000000000000000000000000000001010000011111010001000000101 Osteolaemus_tetraspis 000000000000000000000000000000000110010000011111010001000000101 Tomistoma_schlegelii 000000000000000000000000000000000000001111101111010001000000101 Gavialis_gangeticus 000000000000000000000000000000000000000000000000000000011111001 Glen_Rose_Form 000000000000000000000000000000000000000000000000000000000000010 Bernissartia_fagesii 000000000000000000000000000000000000000000000000000000000000010 Hylaeochampsa_vectiana 000000000000000000000000000000000000000000000000000000000000000 Borealosuchus_formidabilis 000000000000000000000000000000000000000000000000000110000000101 Borealosuchus_wilsoni 000000000000000000000000000000000000000000000000001110000000101 Borealosuchus_acutidentatus 000000000000000000000000000000000000000000000000001110000000101 Borealosuchus_sternbergii 000000000000000000000000000000000000000000000000000010000000101 Leidyosuchus_canadensis 000000000000000000000000000000000000000000000000110001000000101 Thoracosaurus_neocesariensis 000000000000000000000000000000000000000000000000000000000001001 Thoracosaurus_macrorhynchus 000000000000000000000000000000000000000000000000000000000001001 Thecachampsoides_minor 000000000000000000000000000000000000000000000000000000000011001 Eogavialis_africanus 000000000000000000000000000000000000000000000000000000000111001 Gryposuchus_colombianus 000000000000000000000000000000000000000000000000000000101111001 Ikanogavialis_gameroi 000000000000000000000000000000000000000000000000000000101111001 Gavialis_lewisi 000000000000000000000000000000000000000000000000000000011111001 Pristichampsus_vorax 000000000000000000000000000000000000000000000000000001000000101 Diplocynodon_hantoniensis 000000000000000000000011101100000000000000000000110001000000101 Diplocynodon_ratelii 000000000000000000000011101100000000000000000000110001000000101 Diplocynodon_darwini 000000000000000000000001101100000000000000000000110001000000101 Baryphracta_deponiae 000000000000000000000000101100000000000000000000110001000000101 Stangerochampsa_mccabei 000000000000000000000100011100000000000000000000110001000000101 Brachychampsa_montana 000000000000000000001000011100000000000000000000110001000000101 Brachychampsa_sealeyi 000000000000000000001000011100000000000000000000110001000000101 Alligator_mefferdi 000000001111111011010100011100000000000000000000110001000000101 Alligator_olseni 000000000011111011010100011100000000000000000000110001000000101 Alligator_mcgrewi 000000000001111011010100011100000000000000000000110001000000101 Alligator_prenasalis 000000000000111011010100011100000000000000000000110001000000101 Ceratosuchus_burdoshi 000000000000000001010100011100000000000000000000110001000000101 Hassiacosuchus_haupti 000000000000000001010100011100000000000000000000110001000000101 Allognathosuchus_polyodon 000000000000000111010100011100000000000000000000110001000000101 Allognathosuchus_wartheni 000000000000000111010100011100000000000000000000110001000000101 Wannaganosuchus_brachymanus 000000000000001011010100011100000000000000000000110001000000101 Procaimanoidea_kayi 000000000000000111010100011100000000000000000000110001000000101 Arambourgia_gaudryi 000000000000011011010100011100000000000000000000110001000000101 Eocaiman_cavernensis 000000000000000000110100011100000000000000000000110001000000101 Purussaurus_spp. 000010110000000000110100011100000000000000000000110001000000101 Orthogenysuchus_olseni 000110110000000000110100011100000000000000000000110001000000101 Mourasuchus_spp. 000110110000000000110100011100000000000000000000110001000000101 Caiman_lutescens 011000110000000000110100011100000000000000000000110001000000101 Melanosuchus_fisheri 111000110000000000110100011100000000000000000000110001000000101 Crocodylus_palaeindicus 000000000000000000000000000000001001010000011111010001000000101 Crocodylus_robustus 000000000000000000000000000000000110010000011111010001000000101 Crocodylus_lloidi 000000000000000000000000000000000010010000011111010001000000101 Crocodylus_megarhinus 000000000000000000000000000000000000000000011111010001000000101 Euthecodon_arambourgii 000000000000000000000000000000000010010000011111010001000000101 Tomistoma_lusitanica 000000000000000000000000000000000000001111101111010001000000101 Paratomistoma_courtii 000000000000000000000000000000000000000111101111010001000000101 Gavialosuchus_americanus 000000000000000000000000000000000000000001101111010001000000101 Gavialosuchus_eggenbergensis 000000000000000000000000000000000000001111101111010001000000101 Tomistoma_cairense 000000000000000000000000000000000000000011101111010001000000101 Dollosuchus_spenceri 000000000000000000000000000000000000000000101111010001000000101 Brachyuranochampsa_eversolei 000000000000000000000000000000000000000000000111010001000000101 Dormaal_crocodyloid 000000000000000000000000000000000000000000000011010001000000101 Crocodylus_acer 000000000000000000000000000000000000000000000111010001000000101 Crocodylus_affinis 000000000000000000000000000000000000000000000011010001000000101 Asiatosuchus_grangeri 000000000000000000000000000000000000000000000011010001000000101 Asiatosuchus_germanicus 000000000000000000000000000000000000000000000001010001000000101 Prodiplocynodon_langi 000000000000000000000000000000000000000000000001010001000000101 Australosuchus_clarkae 000000000000000000000000000000000000100000011111010001000000101 Kembara_implexidens 000000000000000000000000000000000000100000011111010001000000101 Deinosuchus 000000000000000000000000000100000000000000000000110001000000101 [rag1 = 12] Paleognathae 000000000010 Neognathae 000000000010 Testudines 000000000000 Caiman_yacare 110101000001 Caiman_latirostris 110101000001 Melanosuchus_niger 010101000001 Paleosuchus_palpebrosus 001101000001 Paleosuchus_trigonatus 001101000001 Alligator_mississippiensis 000011000001 Alligator_sinensis 000011000001 Crocodylus_rhombifer 000000110101 Crocodylus_acutus 000000110101 Crocodylus_intermedius 000000110101 Crocodylus_moreletii 000000110101 Crocodylus_siamensis 000000010101 Crocodylus_johnstoni ???????????? Crocodylus_mindorensis ???????????? Crocodylus_novaeguineae ???????????? Crocodylus_porosus ???????????? Crocodylus_palustris ???????????? Crocodylus_niloticus 000000110101 Crocodylus_cataphractus 000000010101 Osteolaemus_tetraspis 000000010101 Tomistoma_schlegelii 000000001101 Gavialis_gangeticus 000000001101 fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? [cytb = 14] Paleognathae 00000000000001 Neognathae 00000000000001 Testudines 00000000000000 Caiman_yacare 10001000000010 Caiman_latirostris 00001000000010 Melanosuchus_niger 10001000000010 Paleosuchus_palpebrosus 01011000000010 Paleosuchus_trigonatus 01011000000010 Alligator_mississippiensis 00111000000010 Alligator_sinensis 00111000000010 Crocodylus_rhombifer 00000011010110 Crocodylus_acutus 00000111010110 Crocodylus_intermedius 00000111010110 Crocodylus_moreletii ?????????????? Crocodylus_siamensis 00000001010110 Crocodylus_johnstoni ?????????????? Crocodylus_mindorensis ?????????????? Crocodylus_novaeguineae ?????????????? Crocodylus_porosus ?????????????? Crocodylus_palustris ?????????????? Crocodylus_niloticus ?????????????? Crocodylus_cataphractus 00000000110110 Osteolaemus_tetraspis 00000000110110 Tomistoma_schlegelii 00000000001110 Gavialis_gangeticus 00000000001110 fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? [cmyc = 7] Paleognathae 0000000 Neognathae 0000000 Testudines ??????? Caiman_yacare 1110001 Caiman_latirostris ??????? Melanosuchus_niger 1110001 Paleosuchus_palpebrosus 0110001 Paleosuchus_trigonatus ??????? Alligator_mississippiensis 0010001 Alligator_sinensis ??????? Crocodylus_rhombifer ??????? Crocodylus_acutus ??????? Crocodylus_intermedius ??????? Crocodylus_moreletii ??????? Crocodylus_siamensis ??????? Crocodylus_johnstoni ??????? Crocodylus_mindorensis ??????? Crocodylus_novaeguineae ??????? Crocodylus_porosus ??????? Crocodylus_palustris ??????? Crocodylus_niloticus ??????? Crocodylus_cataphractus 0001011 Osteolaemus_tetraspis 0001011 Tomistoma_schlegelii 0000111 Gavialis_gangeticus 0000111 fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? [nd6glucytb = 14] Paleognathae 00000000000001 Neognathae 00000000000001 Testudines 00000000000000 Caiman_yacare 11010000000010 Caiman_latirostris 11010000000010 Melanosuchus_niger 11010000000010 Paleosuchus_palpebrosus 01010000000010 Paleosuchus_trigonatus ?????????????? Alligator_mississippiensis 00110000000010 Alligator_sinensis 00110000000010 Crocodylus_rhombifer 00000001010110 Crocodylus_acutus 00001011010110 Crocodylus_intermedius 00001011010110 Crocodylus_moreletii 00000111010110 Crocodylus_siamensis 00000000010110 Crocodylus_johnstoni 00000000010110 Crocodylus_mindorensis 00000000110110 Crocodylus_novaeguineae 00000000110110 Crocodylus_porosus 00000000010110 Crocodylus_palustris ?????????????? Crocodylus_niloticus 00000111010110 Crocodylus_cataphractus 00000000000110 Osteolaemus_tetraspis 00000000000110 Tomistoma_schlegelii 00000000001110 Gavialis_gangeticus 00000000001110 fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? fossil_taxon ?????????????? [bdnf = 9] Paleognathae 000000001 Neognathae 000000001 Testudines 000000000 Caiman_yacare 101100010 Caiman_latirostris 101100010 Melanosuchus_niger 101100010 Paleosuchus_palpebrosus 011100010 Paleosuchus_trigonatus 011100010 Alligator_mississippiensis 000100010 Alligator_sinensis 000100010 Crocodylus_rhombifer 000010110 Crocodylus_acutus ????????? Crocodylus_intermedius 000010110 Crocodylus_moreletii ????????? Crocodylus_siamensis ????????? Crocodylus_johnstoni ????????? Crocodylus_mindorensis ????????? Crocodylus_novaeguineae ????????? Crocodylus_porosus ????????? Crocodylus_palustris ????????? Crocodylus_niloticus ????????? Crocodylus_cataphractus 000001110 Osteolaemus_tetraspis 000001110 Tomistoma_schlegelii 000000010 Gavialis_gangeticus 000000010 fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? [allozymesA = 2] Paleognathae ?? Neognathae ?? Testudines 00 Caiman_yacare 11 Caiman_latirostris 11 Melanosuchus_niger 01 Paleosuchus_palpebrosus 00 Paleosuchus_trigonatus 00 Alligator_mississippiensis 00 Alligator_sinensis 00 Crocodylus_rhombifer ?? Crocodylus_acutus ?? Crocodylus_intermedius ?? Crocodylus_moreletii ?? Crocodylus_siamensis ?? Crocodylus_johnstoni ?? Crocodylus_mindorensis ?? Crocodylus_novaeguineae ?? Crocodylus_porosus ?? Crocodylus_palustris ?? Crocodylus_niloticus ?? Crocodylus_cataphractus ?? Osteolaemus_tetraspis ?? Tomistoma_schlegelii ?? Gavialis_gangeticus ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? [allozymesC = 2] Paleognathae ?? Neognathae ?? Testudines ?? Caiman_yacare ?? Caiman_latirostris ?? Melanosuchus_niger ?? Paleosuchus_palpebrosus ?? Paleosuchus_trigonatus ?? Alligator_mississippiensis ?? Alligator_sinensis ?? Crocodylus_rhombifer 11 Crocodylus_acutus 11 Crocodylus_intermedius 11 Crocodylus_moreletii 11 Crocodylus_siamensis 11 Crocodylus_johnstoni 11 Crocodylus_mindorensis 11 Crocodylus_novaeguineae 11 Crocodylus_porosus 11 Crocodylus_palustris 11 Crocodylus_niloticus 11 Crocodylus_cataphractus 10 Osteolaemus_tetraspis 10 Tomistoma_schlegelii 00 Gavialis_gangeticus 00 fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? [atp7a = 9] Paleognathae ????????? Neognathae ????????? Testudines 000000000 Caiman_yacare 110110000 Caiman_latirostris 110110000 Melanosuchus_niger 010110000 Paleosuchus_palpebrosus 001110000 Paleosuchus_trigonatus 001110000 Alligator_mississippiensis 000010000 Alligator_sinensis 000010000 Crocodylus_rhombifer 000001101 Crocodylus_acutus ????0???? Crocodylus_intermedius 000001101 Crocodylus_moreletii ????????? Crocodylus_siamensis ????????? Crocodylus_johnstoni ????????? Crocodylus_mindorensis ????????? Crocodylus_novaeguineae ????????? Crocodylus_porosus ????????? Crocodylus_palustris ????????? Crocodylus_niloticus ????????? Crocodylus_cataphractus 000000101 Osteolaemus_tetraspis 000000101 Tomistoma_schlegelii 000000011 Gavialis_gangeticus 000000011 fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? fossil_taxon ????????? [18Srflp = 5] Paleognathae ????? Neognathae ????? Testudines ????? Caiman_yacare 00000 Caiman_latirostris ????? Melanosuchus_niger ????? Paleosuchus_palpebrosus ????? Paleosuchus_trigonatus ????? Alligator_mississippiensis 00000 Alligator_sinensis ????? Crocodylus_rhombifer 01101 Crocodylus_acutus 01101 Crocodylus_intermedius 01101 Crocodylus_moreletii 01101 Crocodylus_siamensis 01101 Crocodylus_johnstoni 01101 Crocodylus_mindorensis 11101 Crocodylus_novaeguineae 11101 Crocodylus_porosus 01101 Crocodylus_palustris 01101 Crocodylus_niloticus 01101 Crocodylus_cataphractus 01101 Osteolaemus_tetraspis 00101 Tomistoma_schlegelii 00011 Gavialis_gangeticus 00011 fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? fossil_taxon ????? [28Srflp = 8] Paleognathae ???????? Neognathae ???????? Testudines ???????? Caiman_yacare 00000000 Caiman_latirostris ???????? Melanosuchus_niger ???????? Paleosuchus_palpebrosus ???????? Paleosuchus_trigonatus ???????? Alligator_mississippiensis 00000000 Alligator_sinensis ???????? Crocodylus_rhombifer 10001101 Crocodylus_acutus 01001101 Crocodylus_intermedius 01001101 Crocodylus_moreletii 10001101 Crocodylus_siamensis 00001101 Crocodylus_johnstoni 00001101 Crocodylus_mindorensis 00101101 Crocodylus_novaeguineae 00101101 Crocodylus_porosus 00011101 Crocodylus_palustris 00011101 Crocodylus_niloticus 00001101 Crocodylus_cataphractus 00001101 Osteolaemus_tetraspis 00000101 Tomistoma_schlegelii 00000011 Gavialis_gangeticus 00000011 fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? [12S = 15] Paleognathae 000000000000001 Neognathae 000000000000001 Testudines 000000000000000 Caiman_yacare 110111000000010 Caiman_latirostris 110111000000010 Melanosuchus_niger 010111000000010 Paleosuchus_palpebrosus 001111000000010 Paleosuchus_trigonatus 001111000000010 Alligator_mississippiensis 000001000000010 Alligator_sinensis 000011000000010 Crocodylus_rhombifer 000000011110110 Crocodylus_acutus 000000111110110 Crocodylus_intermedius 000000111110110 Crocodylus_moreletii ??????????????? Crocodylus_siamensis 000000001110110 Crocodylus_johnstoni ??????????????? Crocodylus_mindorensis ??????????????? Crocodylus_novaeguineae ??????????????? Crocodylus_porosus ??????????????? Crocodylus_palustris ??????????????? Crocodylus_niloticus ??????????????? Crocodylus_cataphractus 000000000110110 Osteolaemus_tetraspis 000000000010110 Tomistoma_schlegelii 000000000001110 Gavialis_gangeticus 000000000001110 fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? fossil_taxon ??????????????? [16S = 13] Paleognathae 0000000000001 Neognathae 0000000000001 Testudines 0000000000000 Caiman_yacare 1100010000010 Caiman_latirostris 1100010000010 Melanosuchus_niger 0100010000010 Paleosuchus_palpebrosus 0010110000010 Paleosuchus_trigonatus 0010110000010 Alligator_mississippiensis 0001110000010 Alligator_sinensis 0001110000010 Crocodylus_rhombifer 0000001010110 Crocodylus_acutus ????????????? Crocodylus_intermedius 0000001010110 Crocodylus_moreletii ????????????? Crocodylus_siamensis ????????????? Crocodylus_johnstoni ????????????? Crocodylus_mindorensis ????????????? Crocodylus_novaeguineae ????????????? Crocodylus_porosus ????????????? Crocodylus_palustris ????????????? Crocodylus_niloticus ????????????? Crocodylus_cataphractus 0000000110110 Osteolaemus_tetraspis 0000000110110 Tomistoma_schlegelii 0000000001110 Gavialis_gangeticus 0000000001110 fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? fossil_taxon ????????????? [dloop = 8] Paleognathae ???????? Neognathae ???????? Testudines ???????? Caiman_yacare 00000001 Caiman_latirostris ???????? Melanosuchus_niger ???????? Paleosuchus_palpebrosus ???????? Paleosuchus_trigonatus ???????? Alligator_mississippiensis 00000001 Alligator_sinensis 00000000 Crocodylus_rhombifer 00100110 Crocodylus_acutus 01100110 Crocodylus_intermedius 11100110 Crocodylus_moreletii 11100110 Crocodylus_siamensis 00000110 Crocodylus_johnstoni 00010110 Crocodylus_mindorensis 00010110 Crocodylus_novaeguineae ???????? Crocodylus_porosus 00000110 Crocodylus_palustris 00000110 Crocodylus_niloticus 00000110 Crocodylus_cataphractus 00001110 Osteolaemus_tetraspis 00001110 Tomistoma_schlegelii 00000010 Gavialis_gangeticus 00000010 fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? [ldha = 7] Paleognathae ??????? Neognathae ??????? Testudines ??????? Caiman_yacare ??????? Caiman_latirostris 1011000 Melanosuchus_niger 1011000 Paleosuchus_palpebrosus 0111000 Paleosuchus_trigonatus 0111000 Alligator_mississippiensis ??????? Alligator_sinensis 0001000 Crocodylus_rhombifer 0000110 Crocodylus_acutus ??????? Crocodylus_intermedius 0000110 Crocodylus_moreletii ??????? Crocodylus_siamensis ??????? Crocodylus_johnstoni ??????? Crocodylus_mindorensis ??????? Crocodylus_novaeguineae ??????? Crocodylus_porosus ??????? Crocodylus_palustris ??????? Crocodylus_niloticus ??????? Crocodylus_cataphractus 0000010 Osteolaemus_tetraspis 0000010 Tomistoma_schlegelii 0000001 Gavialis_gangeticus 0000001 fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? fossil_taxon ??????? [chromosomes = 2] Paleognathae ?? Neognathae ?? Testudines ?? Caiman_yacare 00 Caiman_latirostris 10 Melanosuchus_niger 00 Paleosuchus_palpebrosus 00 Paleosuchus_trigonatus 00 Alligator_mississippiensis 10 Alligator_sinensis 10 Crocodylus_rhombifer 01 Crocodylus_acutus 01 Crocodylus_intermedius 01 Crocodylus_moreletii 01 Crocodylus_siamensis 01 Crocodylus_johnstoni 01 Crocodylus_mindorensis ?? Crocodylus_novaeguineae 00 Crocodylus_porosus 01 Crocodylus_palustris 01 Crocodylus_niloticus 01 Crocodylus_cataphractus 10 Osteolaemus_tetraspis 00 Tomistoma_schlegelii 00 Gavialis_gangeticus 10 fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? fossil_taxon ?? [digeneans = 12] OUTGROUP 000000000000 Neognathae ???????????? Testudines ???????????? Caiman_crocodilus 111100000000 Caiman_latirostris 111100000000 Melanosuchus_niger 011100000000 Paleosuchus_sp 001100000000 Paleosuchus_trigonatus ???????????? Alligator_sp 000100000000 Alligator_sinensis ???????????? Crocodylus_rhombifer 000010000011 Crocodylus_acutus 000010000011 Crocodylus_intermedius 000010000011 Crocodylus_moreletii ???????????? Crocodylus_siamensis 000001100111 Crocodylus_johnstoni 000001100111 Crocodylus_mindorensis ???????????? Crocodylus_novaeguineae ???????????? Crocodylus_porosus 000000100111 Crocodylus_palustris ???????????? Crocodylus_niloticus 000000011111 Crocodylus_cataphractus 000000011111 Osteolaemus_tetraspis 000000001111 Tomistoma_schlegelii ???????????? Gavialis_gangeticus 000000000001 fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? fossil_taxon ???????????? [ascaridoid nematodes = 8] OUTGROUP 00000000 Neognathae ???????? Testudines ???????? Caiman_crocodilus 11000000 Caiman_latirostris 11000000 Melanosuchus_niger 01000000 Paleosuchus_palpebrosus ???????? Paleosuchus_trigonatus ???????? Alligator_sp 01000000 Alligator_sinensis ???????? Crocodylus_rhombifer 00100011 Crocodylus_acutus 00100011 Crocodylus_intermedius ???????? Crocodylus_moreletii ???????? Crocodylus_siamensis ???????? Crocodylus_johnstoni 00001011 Crocodylus_mindorensis ???????? Crocodylus_novaeguineae 00011011 Crocodylus_porosus 00011011 Crocodylus_palustris 00000001 Crocodylus_niloticus 00000111 Crocodylus_cataphractus 00000111 Osteolaemus_tetraspis ???????? Tomistoma_schlegelii ???????? Gavialis_gangeticus 00000001 fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? fossil_taxon ???????? [globin_peptides = 3] Paleognathae ??? Neognathae ??? Testudines ??? Caiman_yacare 100 Caiman_latirostris ??? Melanosuchus_niger ??? Paleosuchus_palpebrosus ??? Paleosuchus_trigonatus ??? Alligator_mississippiensis 100 Alligator_sinensis ??? Crocodylus_rhombifer ??? Crocodylus_acutus ??? Crocodylus_intermedius ??? Crocodylus_moreletii ??? Crocodylus_siamensis ??? Crocodylus_johnstoni ??? Crocodylus_mindorensis ??? Crocodylus_novaeguineae ??? Crocodylus_porosus ??? Crocodylus_palustris ??? Crocodylus_niloticus 010 Crocodylus_cataphractus ??? Osteolaemus_tetraspis 010 Tomistoma_schlegelii 001 Gavialis_gangeticus 001 fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? fossil_taxon ??? [albumin_distances = 6] Paleognathae ?????? Neognathae ?????? Testudines ?????? Caiman_yacare 111000 Caiman_latirostris ?????? Melanosuchus_niger 111000 Paleosuchus_palpebrosus 011000 Paleosuchus_trigonatus ?????? Alligator_mississippiensis 001000 Alligator_sinensis ?????? Crocodylus_rhombifer ?????? Crocodylus_acutus ?????? Crocodylus_intermedius ?????? Crocodylus_moreletii 000110 Crocodylus_siamensis ?????? Crocodylus_johnstoni ?????? Crocodylus_mindorensis ?????? Crocodylus_novaeguineae ?????? Crocodylus_porosus ?????? Crocodylus_palustris 000110 Crocodylus_niloticus ?????? Crocodylus_cataphractus ?????? Osteolaemus_tetraspis 000010 Tomistoma_schlegelii 000001 Gavialis_gangeticus 000001 fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? fossil_taxon ?????? ; END; CONSTRAINTS outs=((1-3),4-86); CONSTRAINTS supermatrixstrict=(Paleognathae,Neognathae,(Testudines,((((((((((((((Caiman_yacare,Caiman_latirostris,(Melanosuchus_niger,Melanosuchus_fisheri),Caiman_lutescens),(Purussaurus_spp.,(Orthogenysuchus_olseni,Mourasuchus_spp.))),(Paleosuchus_palpebrosus,Paleosuchus_trigonatus)),Eocaiman_cavernensis),(((((((((Alligator_mississippiensis,Alligator_mefferdi),Alligator_sinensis),Alligator_olseni),Alligator_mcgrewi),Alligator_prenasalis),Arambourgia_gaudryi),Wannaganosuchus_brachymanus),(Allognathosuchus_polyodon,Allognathosuchus_wartheni,Procaimanoidea_kayi)),Ceratosuchus_burdoshi,Hassiacosuchus_haupti)),Stangerochampsa_mccabei),(Brachychampsa_montana,Brachychampsa_sealeyi)),(((Diplocynodon_hantoniensis,Diplocynodon_ratelii),Diplocynodon_darwini),Baryphracta_deponiae)),Deinosuchus),Leidyosuchus_canadensis),(((((((((Crocodylus_rhombifer,(Crocodylus_acutus,Crocodylus_intermedius),Crocodylus_moreletii),Crocodylus_niloticus),((Crocodylus_siamensis,(Crocodylus_porosus,Crocodylus_palustris)),(Crocodylus_johnstoni,(Crocodylus_mindorensis,Crocodylus_novaeguineae))),Crocodylus_palaeindicus),(Crocodylus_cataphractus,((Osteolaemus_tetraspis,Crocodylus_robustus),Crocodylus_lloidi,Euthecodon_arambourgii))),Crocodylus_megarhinus,(Australosuchus_clarkae,Kembara_implexidens)),((((Tomistoma_schlegelii,Tomistoma_lusitanica,Gavialosuchus_eggenbergensis),((((((Gavialis_gangeticus,Gavialis_lewisi),(Gryposuchus_colombianus,Ikanogavialis_gameroi)),Eogavialis_africanus),Thecachampsoides_minor),Thoracosaurus_neocesariensis,Thoracosaurus_macrorhynchus),Paratomistoma_courtii),Tomistoma_cairense),Gavialosuchus_americanus),Dollosuchus_spenceri)),Brachyuranochampsa_eversolei,Crocodylus_acer),Dormaal_crocodyloid,Crocodylus_affinis,Asiatosuchus_grangeri),Asiatosuchus_germanicus,Prodiplocynodon_langi)),Pristichampsus_vorax),(Borealosuchus_formidabilis,(Borealosuchus_wilsoni,Borealosuchus_acutidentatus)),Borealosuchus_sternbergii),Glen_Rose_Form,Bernissartia_fagesii,Hylaeochampsa_vectiana))); BEGIN ASSUMPTIONS; CHARSET morph = 1-63; CHARSET rag1 = 64-75; CHARSET cytb = 76-89; CHARSET cmyc = 90-96; CHARSET nd6glucytb = 97-110; CHARSET bdnf = 111-119; CHARSET allozymesA = 120-121; CHARSET allozymesC = 122-123; CHARSET atp7a = 124-132; CHARSET 18Srflp = 133-137; CHARSET 28Srflp = 138-145; CHARSET 12SrDNA = 146-160; CHARSET 16SrDNA = 161-173; CHARSET dloop = 174-181; CHARSET ldh_a = 182-188; CHARSET chromosomes = 189-190; CHARSET digeneans = 191-202; CHARSET ascaridoid_nematode = 203-210; CHARSET globin_peptides = 211-213; CHARSET albumin_distances = 214-219; CHARSET uncombinable = 191-219; TAXSET morph = 1 4-86; TAXSET rag1 = 1-15 21-25; TAXSET cytb = 1-13 15 22-25; TAXSET cmyc = 1-2 4 6-7 9 22-25; TAXSET nd6glucytb = 1-7 9-19 21-25; TAXSET bdnf = 1-11 13 22-25; TAXSET allozymesA = 4-10; TAXSET allozymesC = 11-25; TAXSET atp7a = 3-11 13 22-25; TAXSET 18Srflp = 4 9 11-25; TAXSET 28Srflp = 4 9 11-25; TAXSET 12SrDNA = 1-13 15 22-25; TAXSET 16SrDNA = 1-11 13 22-25; TAXSET dloop = 4 9-17 19-25; TAXSET ldh_a = 5-8 10-11 13 22-25; TAXSET chromosomes = 4-16 18-25; TAXSET digeneans = 1 4-7 9 11-13 15-16 19 21-23 25; TAXSET ascaridoid_nematode = 1 4-6 9 11-12 16 18-19 20-22 25; TAXSET globin_peptides = 4 9 21 23-25; TAXSET albumin_distances = 4 6 7 9 14 20 23-25; ; ENDBLOCK;