#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on July 17, 2025; 9:29 GMT TreeBASE (cc) 1994-2008 Study reference: O'leary M., Allard M., Novacek M., Meng J., & Gatesy J. 2004. "Building the mammalian sector of the tree of life: Combining different data and a discussion of divergence times for placental mammals." In: Cracraft J., & Donoghue M.J., eds. Assembling the Tree of Life. pp. 490-516. Oxford, United Kingdom, Oxford University Press. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1302] [ The following blocks are input data for analysis step 2420 ] BEGIN TAXA; TITLE TaxaForAnalysisStep2420; DIMENSIONS NTAX=33; TAXLABELS Anagalida Artiodactyla Asioryctes Carnivora Cetacea Chiroptera Dermoptera Desmostylia Hyracoidea Insectivora Kennalestes Lagomorpha Leptictidae Macroscelidea Marsupialia Metacheiromys Microsyopidae Monotremata Palaeanodon Palaeoryctoidea Perissodactyla Pholidota Plesiadapidae Primates Proboscidea Rodentia Scandentia Sirenia Tubulidentata Ukhaatherium Vincelestes Xenarthra Zalambdalestes ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2613] TITLE MAM_96_Feb.03; LINK TAXA = TaxaForAnalysisStep2420; DIMENSIONS NCHAR=96; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4 5" MISSING=? GAP= -; CHARSTATELABELS 1 Anal_and_Urogenital_Openings / combined separate, 2 Eggshell / present absent, 3 Unilaminar_blastocyst_stage / absent present, 4 Microlecithel_Egg / absent present, 5 Cochlea / straight spiral, 6 Supraspinous_fossa / absent present, 7 Mammary_glands / teats_absent teats_present, 8 Chorioallantoic_membrane / present suppressed, 9 Pseudovaginal_canal / absent present, 10 Alisphenoid_in_auditory_bulla / 'small, absent' 'present, large', 11 Cheek_tooth_replacement / all_premolars last_premolar_only, 12 Dental_enamel / 'no distinct "tubercles"' 'distinct "tubercles"', 13 Sphenorbital_Fissure / not_confluent confluent, 14 Modified_trophoblast / absent 'present, inner cell mas', 15 Chorioallantoic_Placenta / absent 'present, definitive', 16 Intrauterine_Gestation / short prolonged, 17 Ureter_pathway / not_lateral lateral_to_Mullerian_ducts, 18 Corpus_Callosum / absent present, 19 Epipubic_Bones / present absent, 20 Upper_molar_stylar_shelves / broad narrow, 21 Mullerian_Ducts / unfused fused_into_median_vagina, 22 Shell_membrane / present absent, 23 Seminal_Vesicle / absent present, 24 Retinal_Cones / complex 'simple,lacking oil droplets', 25 Optic_Foramen / absent_or_indistinct separated_from_sphen._fiss., 26 Ventral_expansion_of_frontal / absent 'present, contacts palatine', 27 Alisphenoid_orbital_exposure / 'broad, contacts parietal' 'reduced, no parietal contact', 28 Interparietal_Ossification / present absent, 29 Tooth_development / elaborate_with_enamel 'suppresed teeth, enamel', 30 Rectus_thoracis_muscle / absent present, 31 Subarcuate_Fossa / well_excavated shallow_or_absent, 32 Mastoid_basicranium_exposure / present reduced_or_absent, 33 Penis / not_suspended 'pendulous, suspended', 34 Sustentacular_facet / no_contact contacts_distal_astr._facet, 35 Ribs / not_markedly_flattened flattened_near_vert._ends, 36 Forelimb_elongation / not_markedly_elongated elongated_into_wing_strut, 37 Patagium / absent 'present, interdigital', 38 'Occipitopollicalis, humeropatag' / absent present, 39 Ulnar_ends / not_reduced 'reduced prox., distally', 40 Fenestra_rotundum / faces_posterolaterally faces_directly_posteriorly, 41 'Subarc. fos., dor. sem. canal' / 'moderate, canal fused' 'expanded, canal separate', 42 Embryonic_disk_orientation / not_mesometrial oriented_mesometrially, 43 'masseteric, buccinator canals' / absent present, 44 Paired_incisive_foramina / small 'elongated, open posteriorly', 45 Posterodorsal_pr._premaxilla / small_or_absent 'large, contacts frontal', 46 Maxilla_and_frontal_contact / broad confined_by_premaxilla_above, 47 Infraorbital_canal / 'present, moderately long' reduced_to_a_foramen, 48 Premax._palatal_exposure / exposure_small exposure_large, 49 'Glenoid fossa form, position' / even_with_basicranium well_dorsal_to_basicranium, 50 Postglenoid_foramen / opens_ventrally opens_in_lateral_sq., 51 Hypoglossal_foramina / single two_or_three_foramina, 52 Incisor_number / 'at least 1-3 present' '1 lost, 2 large, growing', 53 Hemochorial_Placenta / not_opposite_blastocyst opposite_blastocyst, 54 Allantoic_diverticulum / 'present, well - developed' 'small, rudimentary', 55 Clavicle / 'present, well-developed' greatly_reduced_or_absent, 56 Molar_crowns / sectorial_or_connate 'bunodont, large hypocones', 57 Tegman_tympani / 'plate-like' 'inflated, pneumatized', 58 Mastoid_exposure_on_occipital / exposed amastoidy, 59 Jugal_development / extends_nearly_to_glenoid 'reduced, forward of glenoid' 'extending, ventral crest', 60 Carpals / alternating 'compressed, serial', 61 'Yolk Sac, allantois' / 'sac large,asacculate allan.' 'sac small, sacculate allan.', 62 Bilophodonty / not_present present, 63 Forward_displacement_of_orbits / not_present present, 64 Infraorbital_canal_length / moderately_long 'very short, ventral,', 65 Zygomatic_proc._squamosal / narrow robust_dorsally_and_laterall, 66 Premaxilla_extension / not_extensive strong_posterodorsal_process, 67 'Sacro-innominate fusion' / not_extensive 'extensive, sac-ischiatic f.', 68 Inferior_ramus_of_stapedial / ventral_to_tegmen_tympani dorsal_to_tegmen_tymapni, 69 Pancreas / not_diffuse diffuse, 70 M._Styloglossus / simple bifurcate, 71 Cochlear_canaliculus / present absent, 72 Pes / pentadactyl tridactyl, 73 Eustachian_sac / not_present 'large,covers ear cavity', 74 Tuber_maxillaris / absent present, 75 Lacrimal_lateral_process / absent present_and_large, 76 Penial_glandular_fossa / absent present, 77 Postorbital_bar / 'incomplete, absent' complete, 78 Tympanic_arterial_canals / not_present present, 79 Anterior_carotid_foramen / simple modified_into_tube, 80 Lateral_tegmen_tympani / not_expansive expands_to_cover_epitympanic, 81 'Maxillary-frontal contact' / narrrow broad_in_facial_region, 82 Lacrimal / with_extensive_facial_proces confined_to_orbit, 83 Sphenopalat._dorsalpalat._F. / separate in_common_recess, 84 Glaserian_fissure / weak_or_absent_in_adult 'distinct, elongate', 85 'Mastoid tubercle(tympanohyal)' / small_or_absent 'large, reaches prom.', 86 Upper_incisor_number / five less_than_five, 87 Posterior_nasals / dorsally_expansive dorsally_constricted, 88 Exit_for_ext._jugular_vein / Postglenoid_foramen 'intraglenoid sinus, foramen', 89 Intrafenestral_ridge_promon. / 'absent, indistinct' 'distinct,', 90 Piriform_fenestra / 'small, absent' large, 91 Stapes_shape / rectangular columnar 'concave-sided' triangular slightly_convex convex, 92 Stapedial_foramen / large small absent, 93 Foramen_ovale / posterior_to_alisphenoid within_alisphenoid betwn_alis._and_squamosal, 94 Internal_carotid_artery_course / extrabullar perbullar transpromontorial, 95 Stapedial_artery / present absent, 96 Septomaxilla / present absent, ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 ] [ . . . . . . . . . . ] Anagalida ????1????0000??????1????1???0?00?0?????00?1?00000010???0001??00000?0?????00?011010?0011000?01201 Artiodactyla 111111100000011111111111100000110000000000000000000000110010000000001000000000000000011000301201 Asioryctes ????1????0000??????1????100?0?00?0000?010?0000000010???00000?000000????0?00?00000000100111??2??1 Carnivora 111111100000011111111111100000000000000000000000000000000010000000000000000000000010011000301201 Cetacea 1111111000000111111111111000001100000000000000000000001?1010000000000000000000000000011000{234}11211 Chiroptera 111111100000011111111111100000001111111110000000000000000010000000010000000000000000011000{2345}{01}1201 Dermoptera 1111111000000111111111111000000?1111111110000000000000000120000000000000000000000000?11000{234}{02}1211 Desmostylia ????11???0000?????11????10??0????0000?0???0000000000??1?111??1111100???0?0??00000?00011000??1??1 Hyracoidea 1111111000000111111111111000000?0000000000000000000000111121100000000101111100000101011000301011 Insectivora 111111100000011111111111100000000000000000000000000000000010000000000000000000001111111000501201 Kennalestes ????1????0000??????1????1???0?00???????10?00??000010???0000??00000???????00?000000?0100111?0??01 Lagomorpha 111111100000011111111111100000000000000001111111111111000010000000011000000000000100011000{34}01111 Leptictidae ????11???0000?????11????100?0?00?0000?000?0000000000??000010?0000001???0?00?00001111111000?01201 Macroscelidea 111111100000011111111111100000000000000001100000000000000010000000010000000000000100011000501201 Marsupialia 111111111111100000000000000000000000000000000000000000000000000010000000000000000000000000{13}{02}{01}011 Metacheiromys ????11???0000??????1????110?1??0?0000?00??0?00000000??00?010?000000????0?00?000000?00?10?05011?1 Microsyopidae ????1????0000??????1????100?0??0??0????0??0000000000???0001??00000?0?????00?00000010011000?01201 Monotremata 0000000000?00000000000000000001000000000000000000000000000?000000000001000?0000000?01?00001200{01}0 Palaeanodon ????11???00???????????????0?1??0?0?00?00??0?????0000???000???0????00???0?????000???00?10?0?01201 Palaeoryctoidea ????1????0000??????1????1???0??0???00?00??0000000000???00010?00000?0???0?00?0{01}0000?101101140{12}201 Perissodactyla 111111100000011111111111100000110000000000100000000000111010000000000001101100000000011000{23}01011 Pholidota 11111110000001111111111111101111000000000000000000000000011000000010000000000000??00?11000121111 Plesiadapidae ????11???0000?????11????10??0??0?1000?00???01?000000???0001??0000000???0?00?00000000?11000??1??1 Primates 111111100000011111111111100000001100000000000000000000000010000000000000000011110000011000301201 Proboscidea 1111111000000111111111111001001?0000000000000000000000111121111111000110001100000000011000{234}01111 Rodentia 111111100000011111111111100000000000000001111111111111000010000000011000000000000100011000301201 Scandentia 111111100000011111111111100000001100000000000000000000000010000000000000000011110000011000{34}01201 Sirenia 1111111000000111111111111000001?0000000000000000000000111111111111000110001100000?00011000411211 Tubulidentata 111111100000011111111111100010000000000000000000000000000010100000000000000000000011111000{35}01201 Ukhaatherium ????11???0000?????01????100?0?00?0000?010?0000000010???00000?000000????0?00?00000000100111??2??1 Vincelestes ????01???00?1?????00????0?010?00?0000?010?0000000?10??000000?0001000??00?00?00000000110000?00200 Xenarthra 111111100000011111111111111111110000000000000000000001000010000000100000000000000000011000{13}01110 Zalambdalestes ????11???0000?????01????100?0?00?0000?010?0000000010???00000?000000????0?00?00000001110000??20?1 ; END; [ The following blocks are output data for analysis step 2420 ] BEGIN TREES; TITLE Tb7195; LINK TAXA = TaxaForAnalysisStep2420; TREE MAM_96_PAUP_3 = [&R] (Monotremata,((Marsupialia,Vincelestes),((((((Xenarthra,Pholidota),Metacheiromys),Palaeanodon),(Artiodactyla,(Cetacea,(Perissodactyla,(Hyracoidea,(Sirenia,Proboscidea,Desmostylia)))))),(Carnivora,((Tubulidentata,(Insectivora,Leptictidae)),Palaeoryctoidea),Microsyopidae),(((Primates,Scandentia),Anagalida),(Dermoptera,Chiroptera),Plesiadapidae),(Macroscelidea,(Lagomorpha,Rodentia))),((Kennalestes,Asioryctes,Ukhaatherium),Zalambdalestes)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2047] END; BEGIN TREES; TITLE Tb7195; LINK TAXA = TaxaForAnalysisStep2420; TREE MAM_96_PAUP_1 = [&R] (Monotremata,((Marsupialia,Vincelestes),((((((Xenarthra,Pholidota),Metacheiromys),Palaeanodon),(Artiodactyla,(Cetacea,(Perissodactyla,(Hyracoidea,(Sirenia,Proboscidea,Desmostylia)))))),(Carnivora,((Tubulidentata,(Insectivora,Leptictidae)),Palaeoryctoidea),Microsyopidae),((Primates,Scandentia),(Dermoptera,Chiroptera),Plesiadapidae),((Macroscelidea,(Lagomorpha,Rodentia)),Anagalida)),((Kennalestes,Asioryctes,Ukhaatherium),Zalambdalestes)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2049] END; BEGIN TREES; TITLE Tb7195; LINK TAXA = TaxaForAnalysisStep2420; TREE MAM_96_Strict_Consensus = [&R] (Monotremata,(Marsupialia,(((((Xenarthra,Pholidota),Metacheiromys),Palaeanodon),(Carnivora,((Tubulidentata,(Insectivora,Leptictidae)),Palaeoryctoidea),Microsyopidae),(Primates,Scandentia),(Dermoptera,Chiroptera),(Macroscelidea,(Lagomorpha,Rodentia)),(Artiodactyla,(Cetacea,(Perissodactyla,(Hyracoidea,(Sirenia,Proboscidea,Desmostylia))))),Plesiadapidae,Anagalida),(Zalambdalestes,(Kennalestes,Asioryctes,Ukhaatherium))),Vincelestes)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2045] END; BEGIN TREES; TITLE Tb7195; LINK TAXA = TaxaForAnalysisStep2420; TREE MAM_96_included = [&R] (Monotremata,(Vincelestes,(Marsupialia,(((Asioryctes,Kennalestes,Ukhaatherium),Zalambdalestes),((((Xenarthra,Pholidota),Metacheiromys),Palaeanodon),((((Insectivora,Leptictidae),Tubulidentata),Palaeoryctoidea),Carnivora),((Primates,Scandentia),(Dermoptera,Chiroptera)),((Rodentia,Lagomorpha),Macroscelidea),(Artiodactyla,(Cetacea,(Perissodactyla,(Hyracoidea,(Sirenia,Proboscidea,Desmostylia)))))))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2050] END; BEGIN TREES; TITLE Tb7195; LINK TAXA = TaxaForAnalysisStep2420; TREE MAM_96_PAUP_4 = [&R] (Monotremata,((Marsupialia,((((((Xenarthra,Pholidota),Metacheiromys),Palaeanodon),(Artiodactyla,(Cetacea,(Perissodactyla,(Hyracoidea,(Sirenia,Proboscidea,Desmostylia)))))),(Carnivora,((Tubulidentata,(Insectivora,Leptictidae)),Palaeoryctoidea),Microsyopidae),((Primates,Scandentia),(Dermoptera,Chiroptera),Plesiadapidae),((Macroscelidea,(Lagomorpha,Rodentia)),Anagalida)),((Kennalestes,Asioryctes,Ukhaatherium),Zalambdalestes))),Vincelestes)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2046] END; BEGIN TREES; TITLE Tb7195; LINK TAXA = TaxaForAnalysisStep2420; TREE MAM_96_PAUP_2 = [&R] (Monotremata,((Marsupialia,Vincelestes),(((((Xenarthra,Pholidota),Metacheiromys),Palaeanodon),((Carnivora,((Tubulidentata,(Insectivora,Leptictidae)),Palaeoryctoidea),Microsyopidae),((Primates,Scandentia),(Dermoptera,Chiroptera),Plesiadapidae),((Macroscelidea,(Lagomorpha,Rodentia)),Anagalida),(Artiodactyla,(Cetacea,(Perissodactyla,(Hyracoidea,(Sirenia,Proboscidea,Desmostylia))))))),((Kennalestes,Asioryctes,Ukhaatherium),Zalambdalestes)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2048] END;