#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 April 21, 2026; 8:53 GMT TreeBASE (cc) 1994-2008 Study reference: Vitek N.S., Danilov I.G., Nakajima Y., & Hirayama R. 2017. Redescription of the skull of “Trionyx” kyrgyzensis and improved phylogenetic taxon sampling of Cretaceous and Paleogene soft-shelled turtles (Trionychidae) of Asia, including the oldest crown trionychids. Journal of Systematic Palaeontology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19738] [ The following blocks are input data for analysis step 20047 ] BEGIN TAXA; TITLE TaxaForAnalysisStep20047; DIMENSIONS NTAX=38; TAXLABELS Amyda_cartilaginea Apalone_ferox Apalone_mutica Apalone_spinifera Aspideretoides_foveatus Axestemys_byssina Axestemys_cerevisia Axestemys_montinsana Axestemys_quinni Axestemys_splendida Chitra_indica Cyclanorbis_elegans Cyclanorbis_senegalensis Cycloderma_aubryi Cycloderma_frenatum Dogania_subplana Gilmoremys_lancensis Hutchemys_arctochelys Hutchemys_rememdium Hutchemys_sterea Hutchemys_tetraneton Lissemys_punctata Nilssonia_formosa Nilssonia_gangetica Nilssonia_hurum Nilssonia_leithii Nilssonia_nigricans Palea_steindachneri Pelochelys_bibroni Pelodiscus_sinensis Petrochelys_kyrgyzensis Plastomenus_thomasii Rafetus_euphraticus Rafetus_swinhoei Trionyx_allani Trionyx_triunguis Trionyx_uintaensis outgroup_to_trionychids ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M39923] TITLE Kyrgyzensis_38; LINK TAXA = TaxaForAnalysisStep20047; DIMENSIONS NCHAR=89; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4 5 6 7 8 9" MISSING=? GAP= -; CHARSTATELABELS 1 'Width/length of nuchal bone' / less_than_2 greater_than_2 greater_than_3 greater_than_4, 2 Anterior_and_posterior_costiform_processes_of_nuchal_bone_united / no yes, 3 Position_of_anterior_edge_of_first_body_vertebra_relative_to_nuchal_bone / posterior_edge_of_nuchal middle_of_nuchal anterior_edge_of_nuchal, 4 First_and_second_neurals_fused / no yes, 5 Total_number_of_peripherals / 22 20 '14-18' 0, 6 Prenuchal_bone / absent present, 7 Size_of_eighth_pleurals / large reduced_or_absent, 8 'Number of plastral callosities:' / five four two none nine, 9 Hyoplastra_and_hypoplastra_fuse_just_after_hatching / no yes, 10 Xiphiplastra_fuse / absent present, 11 'Hypo-xiphiplastral union' / xiphiplastra_lateral_to_hypoplastra hypoplastra_lateral_to_xiphiplastra, 12 'Revised Character 12: Number of neurals (not including preneural)' / eight seven six fewer_than_six, 13 Variability_in_position_of_neural_reversal / always_at_the_same_neural always_at_adjacent_neurals highly_variable, 14 'Revised Character 14: costals that meet at the midline' / none 'eighth,' 'seventh and eighth,' 'sixth, seventh, and eighth,' 'more than sixth, seventh, and eighth', 15 Suprascapular_fontanelles / closed_at_hatching closed_in_large_adults_only open_throughout_life, 16 Epiplastron_shape / 'J-shaped' 'I-shaped', 17 Length_of_epiplastra_anterior_to_entoplastron_contact / 'short (.165-.29)' 'intermediate (.31-.36)' 'long (.42 or longer)', 18 Depression_on_eight_costal_for_contact_of_ilia / present absent, 19 Bridge_length / 'long (well over one half hypoplastron width)' 'short (less than one half hypoplastron width)', 20 'Carapace, straight line length' / less_than_200_mm. '200-600 mm.' greater_than_600_mm., 21 'Carapace margin straight to concave posterolaterally. 0, no 1, yes', 22 Sexual_dimorphism_in_disc_length / no yes, 23 Jugal_contacts_squamosal / no 'in one-half of sample', 24 Jugal_contacts_parietal_on_skull_surface / no 'in one-half of samples' yes, 25 Vomer_contacts_prefontal / no, 26 Dorsal_edge_of_apertura_narium_externum_laterally_emarginate / no weakly strongly, 27 Dorsal_edge_of_apertura_narium_externum_medially_emarginate / no yes, 28 Basisphenoid_contacts_palatines / no yes, 29 Vomer_divides_maxillae / yes no, 30 Vomer_reaches_intermaxillary_foramen / yes no, 31 Vomer_contacts_basisphenoid / no occasionally, 32 Size_of_foramen_palatinum_posterius / large small small_and_divided many_small_openings, 33 Foramen_palatinum_posterius_forms_in / 'palatine and pterygoid and/or maxilla' palatine_only, 34 Foramen_jugulare_posterius_excluded_from_fenestra_postotica_by_pterygoid_arching_to_contact_opisthotic / no yes, 35 Foramen_jugulare_posterius_excluded_from_fenestra_postotica_by_descending_proces_of_opisthotic_which_reaches_pterygoid / no yes, 36 Foramen_posterius_canalis_carotici_interni_relative_to_lateral_crest_of_basioccipital_tubercle / above_it in_it below_it, 37 Maxilla_contacts_frontal_in_front_of_orbit / no yes, 38 '"Exoccipital contacts pterygoid' / no 'yes" NOTE: Scoring in Meylan 1987 is backwards. Temporary Solution: change the wording of the character instead of the scoring. So until it is written otherwise,' yes no., 39 Basisphenoid_shape / not_medially_constricted occasionally_medially_constricted medially_constricted, 40 Premaxilla_absent / no occasionally usually, 41 Vomer_lost / no yes, 42 Jugal_contacts_orbit / yes no, 43 'Epipterygoid, if present, contacts the palatine' / yes in_ca._50% no, 44 Contact_beteen_pterygoid_and_foramen_nervi_trigermini_occurs_when_epipterygoid_is_present / yes no, 45 When_epipterygoid_is_present_pterygoid_contacts_foramen_nervi_trigemini / between_epipterygoid_and_quadrate_or_not_at_all between_prootic_and_epipterygoid_or_not_at_all between_epipterygoid_and_parietal_or_not_at_all, 46 Epipterygoid_contacts_prootic_anterior_to_foramen_nervi_trigemini / no in_ca._50% yes, 47 Epipterygoid_contacts_prootic_posterior_to_foramen_nervi_trigemini / no yes, 48 Epipterygoid_fuses_to_pterygoid / in_subadults in_adults_only never, 49 Average_ratio_of_intermaxillary_foramen_length_to_length_primary_palate / 0.07 about_0.20_to_0.40 about_0.60, 50 Postorbital_bar_relative_to_orbit / about_2_times_orbit_diameter 'about equal to orbit to 1/3 of orbit' 'less than 1/5 of orbit', 51 Quadratojugal_participates_in_processus_trochlearis_oticum / no yes, 52 'Revised Character 52: parietal contribution to the processus trochlearis oticum' / 'none,' '16.6% or less, 2., 22.1% or more', 53 Ventral_keel_on_8th_cervical_present_and_limited_to_posterior_end / no yes, 54 Strong_dorsal_process_on_cervicals / no yes, 55 Number_of_ossifications_in_corpus_hyoidis / '1,' '6,' 8, 56 Number_of_ossifications_in_cornu_branchiale_II / 1_only '2-6' 7_or_more, 57 Ossifications_of_cornu_branchiale_II_broad_and_strongly_sutured / no yes, 58 Basihyals_in_close_contact_and_projecting_anteriorly / no yes, 59 Symphyseal_ridge_strong_and_present_in_a_depression / no yes, 60 'Foramen intermandibularis caudalis enclosed by prearticular:' / never, 61 Ilia_curve_medially / yes, 62 Ischia_extend_into_thyroid_fenestra / no, 63 Metiscial_processes_present_and_distinct / no, 64 Angle_of_acromion_process_to_scapula_approaches_that_of_coracoid / yes, 65 Coracoid_longest_of_three_pectoral_processes / yes, 66 Development_of_surface_sculpturing_of_carapace_&_plastron / all_metaplastic_portions_of_carapace_and_plastron_have_sculpturing trionychid_pattern_grades_towards_the_center_of_carapacial_and_plastral_disk_to_smooth_pattern, 67 Nuchal_notch / anterior_rim_of_nuchal_convex_or_slightly_notched ' anterior rim of carapace with deep nuchal notch, as developed in H. rememdium', 68 'Shape of neural 1 and 2 (neural 2 and 3 of Meylan 1987)' / neurals_1_and_2_hexagonal_with_short_posterior_sides 'neural 1 circular to rectangular and neural 2 octagonal, as developed in H. rememdium and H. arctochelys', 69 Splitting_of_costals_along_distal_margin / costal_rim_rounded_or_graded 'dorsal rims split into separately protruding dorsal and visceral portions, as developed in H. rememdium and H. arctochelys', 70 Lateral_notch_in_carapace_at_the_level_of_costal_5 / 'absent, lateral carapacial margin rounded' 'present, lateral carapacial margin shows a waist, as developed in H. arctochelys', 71 Skin_callosity_developed_on_the_visceral_side_of_costals_6_and_7 / 'absent, visceral side smooth' 'present, visceral side sometimes develops a callosity, as seen in H. arctochelys', 72 'Mid-line contact of hyoplastra, hypoplastra, xiphiplastra' / 'hyo-, hypo- and xiphiplastra do not contact another fully, even in adults' 'hyo-, hypo- and xiphiplastra contact another fully along the entire mid-line in adults', 73 Shape_of_deep_portion_of_entoplastron / lateral_branches_of_entoplastron_more_or_less_straight_and_merge_anterior_at_a_clear_angle 'entoplastron wide and rounded, as seen in P. aff. thomasii', 74 Hyoplastron / 'entoplastron abuts loosely against hyoplastron, no anterior flap' 'entoplastron abuts loosely against hyoplastron, hyoplastron develops anterior flap' entoplastron_tightly_integrated_via_development_of_anterior_flap, 75 Peripheral_ossification / 'lateral bridge does not extend beyond lateral processes of hyo-hypoplastron' 'lateral bridge extends laterally beyond bridge processes of hyo-hypoplastron, ossifies peripheral aspects of the shell', 76 Number_of_lateral_hyoplastral_processes / one two three_or_more, 77 Extensive_secondary_palate_consisting_of_infolded_maxillae / absent present_as_developed_in_Plastomenus_thomasii, 78 Accessory_ridges_of_upper_triturating_surfaces / absent present, 79 Posterior_portion_of_narial_canal_defined_by_bone / absent 'present, as developed in Gilmoremys lancensis', 80 Dentary_symphysis / 'short,' 'extremely long, mandible extremely elongate and pincer-like, as developed in Plastomenus thomasii', 81 Parietal_contribution_to_orbits / parietals_neither_contribute_to_orbit_margins_or_orbit_walls 'parietals either contribute to orbit walls, as developed in Gilmoremys lancensis, or orbit margin', 82 Proportions_of_costals_VIII / wider_than_long_to_nearly_square significantly_taller_than_wide, 83 'Posterior edge of neural 5 in relation to posterior edge of costal 5 (not counting preneural)' / posterior anterior, 84 'Posterior edge of neural 6 in relation to posterior edge of costal 6 (not counting preneural)' / posterior anterior, 85 'Hyo-hypoplastral callosity entirely lacks sculpturing on metaplastic portion' / yes, 86 Xiphiplastral_callosity_entirely_lacks_sculpturing_on_metaplastic_portion / no yes, 87 'Nuchal sutures to preneurals, neurals, or costal 1 medial to postnuchal fontanelles before it sutures to costal lateral to fontanelles' / no yes, 88 Length_of_lateral_lobe_of_hyoplastron_in_comparison_to_medial_lobe_of_hyoplastron / 'shorter,' longer, 89 Triturating_surface_of_maxilla / 'flat, about perpendicular to closest external surface of maxilla' 'vaulted, forming an acute angle less than 45 degrees with closest external surface of maxilla', ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 ] [ . . . . . . . . . . ] Amyda_cartilaginea 211130020000011021110000010111010001001000100102111110100010010010000000000100000001000?0 Apalone_ferox 2111301300012{12}100111010002010001000200000000000221120020000001101000000{01}0{01}000000001100000 Apalone_mutica 31113011000{01}2{12}200111011102010101000200000001-0012212001000000101000000000{01}000000001100000 Apalone_spinifera 2111301100012{12}200111010002010001000200100001-0022212002000000101000000000{01}000000001100000 Aspideretoides_foveatus 3110300300011{12}1001110?00021110?1??010?0000??1?2?1212?????????????000?00000000??0?0{01}100000 Axestemys_byssina 311?301{23}000??220?1120????????????????????????????????0??????0????-0?00000000?????0??1100? Axestemys_cerevisia 31?030130000?1200?120????????????????????????????????0?????????0?-0000000000?????0001-10? Axestemys_montinsana 311030?3000???{01}00?12???0?101??0??00?0?0?00???????1?2?1????0?01001-000??0000000?00???10010 Axestemys_quinni 2??0301????1?22????20????????????????????????????????????????????000000??????????000??1?? Axestemys_splendida 3110300300011{12}1001120?0001011000000{12}000000?????21112?????????????000?000000{01}00?0?0{01}{01}00000 Chitra_indica 2121300300000100011201021001000100010001002002020001111110010101100000000001000000{01}100000 Cyclanorbis_elegans 11103004101{01}0{12}000111000200111102110200000001-01111120000010101110000000001000000000000000 Cyclanorbis_senegalensis 211031001012-4000001000211010002110200000021-0101101000001011110000000000101000000--00000 Cycloderma_aubryi 10103001111{01}0{12}010001100211011103110200000111-01011010100010110100000000001000000000000000 Cycloderma_frenatum 10003001101{01}0{12}010001100210011103110200011021-01111110100010110100000000001000000000100000 Dogania_subplana 31113003000010202110000102011101001210100000-001121100100010010110000000000100000001000?0 Gilmoremys_lancensis 31?0300?0201020??1110?12120{01}11021112000?0001-2021100?????????????0000000?10111?1100{01}00000 Hutchemys_arctochelys 31?0300101110{12}01?0010????????????????????????????????????????????10111111210?????1010000? Hutchemys_rememdium 31?0300101110{12}01?1010????????????????????????????????????????10??11110011200?????{01}010000? Hutchemys_sterea 21?030010111020100000????????????????????????????????????????????1001001120??????1110000? Hutchemys_tetraneton 31?0300?0011010???000????????????????????????????????????????????1101001?20???????010000? Lissemys_punctata 10002101111{12}0{12}010001100100011001110200000010100011010000010100110000000001100000000100000 Nilssonia_formosa 1111300300000100011100120101110100020020000010021101--10001101---00000000???0000000100000 Nilssonia_gangetica 21103002000{01}1{12}00111100000101110100020020000010011111002000100101000000000001000000{01}100000 Nilssonia_hurum 21103002000{01}1{12}00111100010201110100020020000011021101000000100101100000000001000000{01}100000 Nilssonia_leithii 21103002000{01}01001111001101011101000200200000000211010010001001010?????????????????{01}1000?0 Nilssonia_nigricans 2110300200000{12}-01111001001011101000100200020100211020010001001010?????????????????{01}1000?0 Palea_steindachneri 11113003000{01}0{12}002110000202011101001200200001-2021201--100000-1--000000000???00000001000?0 Pelochelys_bibroni 21113003000{01}01100111000200010011000100020020010111011111100001011000000000010000000{01}000?0 Pelodiscus_sinensis 31113001000{12}2{12}102110001102011101101200200000200211110010000001010000000000010000001100000 Petrochelys_kyrgyzensis 311?30040000?10011110??????1?????002?00????????????1?0???????????00?00000001?????0110-000 Plastomenus_thomasii 31?03001011{12}-{23}0??0010?00???01-011112100000??????-201??????0??????000000111011001?1--00000 Rafetus_euphraticus 2111301400010{12}10011100000101000100020010000000022112102000010110100000000001000000{01}100000 Rafetus_swinhoei ---13014000----0011200100101000110020000000000022112---00001-1--1?????????????????--00000 Trionyx_allani 3110300{123}100{01}0{12}1001110??????????????????????????????2?????????????-00?0?00001?????00111000 Trionyx_triunguis 2111300300010{12}10011100000200110100020100000000011?12001000000101000000000001000010{01}100000 Trionyx_uintaensis 311130130001?{23}{01}001110?0101010000000000?000{01}00{01}02110210????0?01000-000000000100?000{01}101000 outgroup_to_trionychids 000000010000010000010000000000000000000000001000110100000000000000000000010?0000000000000 ; END; [ The following blocks are output data for analysis step 20047 ] BEGIN TREES; TITLE 'Bayesian: Petrochelys kyrgyzensis only 38'; LINK TAXA = TaxaForAnalysisStep20047; TREE 'con all compat+' = [&R] (outgroup_to_trionychids:0.06465995,(((Cyclanorbis_elegans:0.1115445,Cyclanorbis_senegalensis:0.1215301):0.08379779,(Lissemys_punctata:0.1116766,(Cycloderma_aubryi:0.08247048,Cycloderma_frenatum:0.09170591):0.0868445):0.1021857):0.1533716,((Gilmoremys_lancensis:0.1333524,(Hutchemys_tetraneton:0.1029378,((Plastomenus_thomasii:0.1120263,Hutchemys_sterea:0.1050084):0.09812109,(Hutchemys_rememdium:0.09314591,Hutchemys_arctochelys:0.09325621):0.08884739):0.1411248):0.187525):0.1797067,(((Palea_steindachneri:0.09436362,(Pelodiscus_sinensis:0.09963249,Dogania_subplana:0.1076417):0.07608157):0.0804676,((Nilssonia_formosa:0.07922912,Petrochelys_kyrgyzensis:0.08771433):0.06741189,((Nilssonia_gangetica:0.07586905,Nilssonia_hurum:0.08015058):0.05412381,(Nilssonia_leithii:0.07117771,Nilssonia_nigricans:0.08245172):0.05080417):0.05719249):0.05996234):0.07730217,((Amyda_cartilaginea:0.09786809,(Pelochelys_bibroni:0.08283452,Chitra_indica:0.120424):0.1346943):0.08184844,((Trionyx_triunguis:0.08074858,Aspideretoides_foveatus:0.09641142):0.06492944,(((Axestemys_montinsana:0.08149735,Axestemys_splendida:0.07790524):0.06673468,(Axestemys_quinni:0.1079688,(Axestemys_cerevisia:0.1044503,Axestemys_byssina:0.09225495):0.09734028):0.1031828):0.05259967,((Trionyx_allani:0.09273339,Trionyx_uintaensis:0.09733641):0.07259941,((Rafetus_swinhoei:0.08827597,Rafetus_euphraticus:0.0795753):0.06862867,(Apalone_ferox:0.07396362,(Apalone_mutica:0.08944498,Apalone_spinifera:0.07825593):0.09001733):0.07058393):0.08006278):0.0486888):0.0688023):0.06351337):0.06314971):0.1559732):0.1605384):0.06465995); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr101830] END;