#NEXUS BEGIN TAXA; DIMENSIONS NTAX=46; TAXLABELS outgroup_to_trionychids Cycloderma_aubryi Pelochelys_bibroni Amyda_cartilaginea Cyclanorbis_elegans Nilssonia_formosa Cycloderma_frenatum Nilssonia_gangetica Nilssonia_hurum Chitra_indica Nilssonia_leithii Nilssonia_nigricans Lissemys_punctata Cyclanorbis_senegalensis Pelodiscus_sinensis Palea_steindachneri Dogania_subplana Trionyx_triunguis Plastomenus_thomasii Hutchemys_rememdium Hutchemys_arctochelys Hutchemys_tetraneton Hutchemys_sterea Gilmoremys_lancensis Axestemys_quinni Axestemys_cerevisia Axestemys_byssina Axestemys_montinsana Axestemys_splendida Aspideretoides_foveatus Trionyx_allani Trionyx_uintaensis Apalone_ferox Apalone_mutica Apalone_spinifera Rafetus_swinhoei Rafetus_euphraticus Petrochelys_kyrgyzensis Amyda_gregaria Ulutrionyx_ninae Trionyx_kansaiensis Khunnuchelys_kizylkumensis Gobiapalone_breviplastra Gobiapalone_orlovi Perochelys_lamadongensis Kuhnemys_maortuensis ; END; BEGIN CHARACTERS; Title Kyrgyzensis_46; DIMENSIONS NCHAR=89; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9"; 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 outgroup_to_trionychids 000000010000010000010000000000000000000000001000110100000000000000000000010?0000000000000 Cycloderma_aubryi 10103001111{0 1}0{1 2}010001100211011103110200000111-01011010100010110100000000001000000000000000 Pelochelys_bibroni 21113003000{0 1}01100111000200010011000100020020010111011111100001011000000000010000000{0 1}000?0 Amyda_cartilaginea 211130020000011021110000010111010001001000100102111110100010010010000000000100000001000?0 Cyclanorbis_elegans 11103004101{0 1}0{1 2}000111000200111102110200000001-01111120000010101110000000001000000000000000 Nilssonia_formosa 1111300300000100011100120101110100020020000010021101--10001101---00000000???0000000100000 Cycloderma_frenatum 10003001101{0 1}0{1 2}010001100210011103110200011021-01111110100010110100000000001000000000100000 Nilssonia_gangetica 21103002000{0 1}1{1 2}00111100000101110100020020000010011111002000100101000000000001000000{0 1}100000 Nilssonia_hurum 21103002000{0 1}1{1 2}00111100010201110100020020000011021101000000100101100000000001000000{0 1}100000 Chitra_indica 2121300300000100011201021001000100010001002002020001111110010101100000000001000000{0 1}100000 Nilssonia_leithii 21103002000{0 1}01001111001101011101000200200000000211010010001001010?????????????????{0 1}1000?0 Nilssonia_nigricans 2110300200000{1 2}-01111001001011101000100200020100211020010001001010?????????????????{0 1}1000?0 Lissemys_punctata 10002101111{1 2}0{1 2}010001100100011001110200000010100011010000010100110000000001100000000100000 Cyclanorbis_senegalensis 211031001012-4000001000211010002110200000021-0101101000001011110000000000101000000--00000 Pelodiscus_sinensis 31113001000{1 2}2{1 2}102110001102011101101200200000200211110010000001010000000000010000001100000 Palea_steindachneri 11113003000{0 1}0{1 2}002110000202011101001200200001-2021201--100000-1--000000000???00000001000?0 Dogania_subplana 31113003000010202110000102011101001210100000-001121100100010010110000000000100000001000?0 Trionyx_triunguis 2111300300010{1 2}10011100000200110100020100000000011?12001000000101000000000001000010{0 1}100000 Plastomenus_thomasii 31?03001011{1 2}-{2 3}0??0010?00???01-011112100000??????-201??????0??????000000111011001?1--00000 Hutchemys_rememdium 31?0300101110{1 2}01?1010????????????????????????????????????????10??11110011200?????{0 1}010000? Hutchemys_arctochelys 31?0300101110{1 2}01?0010????????????????????????????????????????????10111111210?????1010000? Hutchemys_tetraneton 31?0300?0011010???000????????????????????????????????????????????1101001?20???????010000? Hutchemys_sterea 21?030010111020100000????????????????????????????????????????????1001001120??????1110000? Gilmoremys_lancensis 31?0300?0201020??1110?12120{0 1}11021112000?0001-2021100?????????????0000000?10111?1100{0 1}00000 Axestemys_quinni 2??0301????1?22????20????????????????????????????????????????????000000??????????000??1?? Axestemys_cerevisia 31?030130000?1200?120????????????????????????????????0?????????0?-0000000000?????0001-10? Axestemys_byssina 311?301{2 3}000??220?1120????????????????????????????????0??????0????-0?00000000?????0??1100? Axestemys_montinsana 311030?3000???{0 1}00?12???0?101??0??00?0?0?00???????1?2?1????0?01001-000??0000000?00???10010 Axestemys_splendida 3110300300011{1 2}1001120?0001011000000{1 2}000000?????21112?????????????000?000000{0 1}00?0?0{0 1}{0 1}00000 Aspideretoides_foveatus 3110300300011{1 2}1001110?00021110?1??010?0000??1?2?1212?????????????000?00000000??0?0{0 1}100000 Trionyx_allani 3110300{1 2 3}100{0 1}0{1 2}1001110??????????????????????????????2?????????????-00?0?00001?????00111000 Trionyx_uintaensis 311130130001?{2 3}{0 1}001110?0101010000000000?000{0 1}00{0 1}02110210????0?01000-000000000100?000{0 1}101000 Apalone_ferox 2111301300012{1 2}100111010002010001000200000000000221120020000001101000000{0 1}0{0 1}000000001100000 Apalone_mutica 31113011000{0 1}2{1 2}200111011102010101000200000001-0012212001000000101000000000{0 1}000000001100000 Apalone_spinifera 2111301100012{1 2}200111010002010001000200100001-0022212002000000101000000000{0 1}000000001100000 Rafetus_swinhoei ---13014000----0011200100101000110020000000000022112---00001-1--1?????????????????--00000 Rafetus_euphraticus 2111301400010{1 2}10011100000101000100020010000000022112102000010110100000000001000000{0 1}100000 Petrochelys_kyrgyzensis 311?30040000?10011110??????1?????002?00????????????1?0???????????00?00000001?????0110-000 Amyda_gregaria 211130030000?1?021110?100101??010?0?000?0000000{1 2}1{1 2}0?01??????011110000000000100000001010?0 Ulutrionyx_ninae 311130130001?22??0110??0?{0 1}0??????????????0???????1?{1 2}?????0?0???0?0000000000100?000110??00 Trionyx_kansaiensis 3121300{1 2 3}000011{0 1}??1120????????????????????????????????????????????0100000?001?????0110?01? Khunnuchelys_kizylkumensis ????????????????????????0??11101000200{0 1}?01000{0 1}02???0????????????????????????00??0???????1 Gobiapalone_breviplastra 31113012000{0 1}0{1 2}1001110????????????????????????????????0??????010??00000000001?????0110000? Gobiapalone_orlovi 31113012000{0 1}0{1 2}1011110?00?100000100{0 1}20?0?0???????110200????0?0100?000000000010000001100000 Perochelys_lamadongensis 310130120000?0?01?1?0?12?????????????????0???????1?0?01000??010??00000000001?????0010000? Kuhnemys_maortuensis ???130120000?1{1 2}0??110????????????????????????????????????????????0?000?0000??????0010?0?? END; BEGIN TREES; Title 'Bayesian: Petrochelys kyrgyzensis only'; ID 0156a409730e18; LINK Taxa = Taxa; TRANSLATE [0] 1 outgroup_to_trionychids, [1] 2 Cycloderma_aubryi, [2] 3 Pelochelys_bibroni, [3] 4 Amyda_cartilaginea, [4] 5 Cyclanorbis_elegans, [5] 6 Nilssonia_formosa, [6] 7 Cycloderma_frenatum, [7] 8 Nilssonia_gangetica, [8] 9 Nilssonia_hurum, [9] 10 Chitra_indica, [10] 11 Nilssonia_leithii, [11] 12 Nilssonia_nigricans, [12] 13 Lissemys_punctata, [13] 14 Cyclanorbis_senegalensis, [14] 15 Pelodiscus_sinensis, [15] 16 Palea_steindachneri, [16] 17 Dogania_subplana, [17] 18 Trionyx_triunguis, [18] 19 Plastomenus_thomasii, [19] 20 Hutchemys_rememdium, [20] 21 Hutchemys_arctochelys, [21] 22 Hutchemys_tetraneton, [22] 23 Hutchemys_sterea, [23] 24 Gilmoremys_lancensis, [24] 25 Axestemys_quinni, [25] 26 Axestemys_cerevisia, [26] 27 Axestemys_byssina, [27] 28 Axestemys_montinsana, [28] 29 Axestemys_splendida, [29] 30 Aspideretoides_foveatus, [30] 31 Trionyx_allani, [31] 32 Trionyx_uintaensis, [32] 33 Apalone_ferox, [33] 34 Apalone_mutica, [34] 35 Apalone_spinifera, [35] 36 Rafetus_swinhoei, [36] 37 Rafetus_euphraticus, [37] 38 Petrochelys_kyrgyzensis, [38] 39 Amyda_gregaria, [39] 40 Ulutrionyx_ninae, [40] 41 Trionyx_kansaiensis, [41] 42 Khunnuchelys_kizylkumensis, [42] 43 Gobiapalone_breviplastra, [43] 44 Gobiapalone_orlovi, [44] 45 Perochelys_lamadongensis, [45] 46 Kuhnemys_maortuensis; TREE 'con all compat+' = (1:0.06465995,(((5:0.1115445,14:0.1215301):0.08379779,(13:0.1116766,(2:0.08247048,7:0.09170591):0.0868445):0.1021857):0.1533716,((24:0.1333524,(22:0.1029378,((19:0.1120263,23:0.1050084):0.09812109,(20:0.09314591,21:0.09325621):0.08884739):0.1411248):0.187525):0.1797067,(((16:0.09436362,(15:0.09963249,17:0.1076417):0.07608157):0.0804676,((6:0.07922912,38:0.08771433):0.06741189,((8:0.07586905,9:0.08015058):0.05412381,(11:0.07117771,12:0.08245172):0.05080417):0.05719249):0.05996234):0.07730217,((4:0.09786809,(3:0.08283452,10:0.120424):0.1346943):0.08184844,((18:0.08074858,30:0.09641142):0.06492944,(((28:0.08149735,29:0.07790524):0.06673468,(25:0.1079688,(26:0.1044503,27:0.09225495):0.09734028):0.1031828):0.05259967,((31:0.09273339,32:0.09733641):0.07259941,((36:0.08827597,37:0.0795753):0.06862867,(33:0.07396362,(34:0.08944498,35:0.07825593):0.09001733):0.07058393):0.08006278):0.0486888):0.0688023):0.06351337):0.06314971):0.1559732):0.1605384):0.06465995); END; BEGIN TREES; Title 'Bayesian: All Fossils'; ID 0156a407b25914; LINK Taxa = Taxa; TRANSLATE [0] 1 outgroup_to_trionychids, [1] 2 Cycloderma_aubryi, [2] 3 Pelochelys_bibroni, [3] 4 Amyda_cartilaginea, [4] 5 Cyclanorbis_elegans, [5] 6 Nilssonia_formosa, [6] 7 Cycloderma_frenatum, [7] 8 Nilssonia_gangetica, [8] 9 Nilssonia_hurum, [9] 10 Chitra_indica, [10] 11 Nilssonia_leithii, [11] 12 Nilssonia_nigricans, [12] 13 Lissemys_punctata, [13] 14 Cyclanorbis_senegalensis, [14] 15 Pelodiscus_sinensis, [15] 16 Palea_steindachneri, [16] 17 Dogania_subplana, [17] 18 Trionyx_triunguis, [18] 19 Plastomenus_thomasii, [19] 20 Hutchemys_rememdium, [20] 21 Hutchemys_arctochelys, [21] 22 Hutchemys_tetraneton, [22] 23 Hutchemys_sterea, [23] 24 Gilmoremys_lancensis, [24] 25 Axestemys_quinni, [25] 26 Axestemys_cerevisia, [26] 27 Axestemys_byssina, [27] 28 Axestemys_montinsana, [28] 29 Axestemys_splendida, [29] 30 Aspideretoides_foveatus, [30] 31 Trionyx_allani, [31] 32 Trionyx_uintaensis, [32] 33 Apalone_ferox, [33] 34 Apalone_mutica, [34] 35 Apalone_spinifera, [35] 36 Rafetus_swinhoei, [36] 37 Rafetus_euphraticus, [37] 38 Petrochelys_kyrgyzensis, [38] 39 Amyda_gregaria, [39] 40 Ulutrionyx_ninae, [40] 41 Trionyx_kansaiensis, [41] 42 Khunnuchelys_kizylkumensis, [42] 43 Gobiapalone_breviplastra, [43] 44 Gobiapalone_orlovi, [44] 45 Perochelys_lamadongensis, [45] 46 Kuhnemys_maortuensis; TREE 'con all compat+' = (1:0.0546866,(((5:0.08367859,14:0.09367722):0.0712428,(13:0.08459544,(2:0.06435567,7:0.06988264):0.07058449):0.0843907):0.1276779,((24:0.1104378,(19:0.08988237,((20:0.07736174,21:0.07739142):0.07886837,(22:0.08723469,23:0.08655618):0.0670156):0.1086758):0.173489):0.1656824,(((16:0.07834141,(15:0.0791283,17:0.08746603):0.06358834):0.07555743,((38:0.06936843,(41:0.07262945,42:0.06805047):0.07202358):0.06152341,((45:0.07889012,46:0.06572464):0.06077572,((11:0.05743225,12:0.06754579):0.04685738,((4:0.07919445,6:0.06643926):0.06047351,(8:0.06121876,9:0.06639375):0.05434436):0.05889724):0.05411621):0.04897627):0.03844887):0.06955033,((31:0.07799591,(39:0.07466615,(18:0.07081496,(3:0.06108989,10:0.09254689):0.1110603):0.05286028):0.04878467):0.04306712,(((25:0.0896658,(26:0.08710858,27:0.07682087):0.09240203):0.09767033,(28:0.07340979,(29:0.06833702,30:0.08308668):0.06943785):0.07613849):0.0845775,(((32:0.07581466,40:0.07029276):0.05389654,(43:0.06211457,44:0.06627342):0.05040874):0.0370045,((36:0.07304764,37:0.06833482):0.06204984,(33:0.05558535,(34:0.06876781,35:0.05497233):0.07176785):0.06542973):0.05793662):0.06353068):0.06662083):0.04155144):0.1599702):0.1343866):0.0546866); END; BEGIN TREES; Title 'Parsimony: All Fossils'; ID 0156470f4ab51; LINK Taxa = Taxa; TRANSLATE [0] 1 outgroup_to_trionychids, [1] 2 Cycloderma_aubryi, [2] 3 Pelochelys_bibroni, [3] 4 Amyda_cartilaginea, [4] 5 Cyclanorbis_elegans, [5] 6 Nilssonia_formosa, [6] 7 Cycloderma_frenatum, [7] 8 Nilssonia_gangetica, [8] 9 Nilssonia_hurum, [9] 10 Chitra_indica, [10] 11 Nilssonia_leithii, [11] 12 Nilssonia_nigricans, [12] 13 Lissemys_punctata, [13] 14 Cyclanorbis_senegalensis, [14] 15 Pelodiscus_sinensis, [15] 16 Palea_steindachneri, [16] 17 Dogania_subplana, [17] 18 Trionyx_triunguis, [18] 19 Plastomenus_thomasii, [19] 20 Hutchemys_rememdium, [20] 21 Hutchemys_arctochelys, [21] 22 Hutchemys_tetraneton, [22] 23 Hutchemys_sterea, [23] 24 Gilmoremys_lancensis, [24] 25 Axestemys_quinni, [25] 26 Axestemys_cerevisia, [26] 27 Axestemys_byssina, [27] 28 Axestemys_montinsana, [28] 29 Axestemys_splendida, [29] 30 Aspideretoides_foveatus, [30] 31 Trionyx_allani, [31] 32 Trionyx_uintaensis, [32] 33 Apalone_ferox, [33] 34 Apalone_mutica, [34] 35 Apalone_spinifera, [35] 36 Rafetus_swinhoei, [36] 37 Rafetus_euphraticus, [37] 40 Petrochelys_kyrgyzensis, [38] 42 Amyda_gregaria, [39] 43 Ulutrionyx_ninae, [40] 45 Trionyx_kansaiensis, [41] 46 Khunnuchelys_kizylkumensis, [42] 47 Gobiapalone_breviplastra, [43] 48 Gobiapalone_orlovi, [44] 49 Perochelys_lamadongensis, [45] 50 Kuhnemys_maortuensis; TREE 'Strict+' = (1,((((2,7),13),(5,14)),((19,((20,21),(22,23))),24)),(((((3,10),42),((4,6,8,9,11,12,49,50),(15,16,17)),18),(((((((25,26),27),28),29),30),31),(32,((33,(34,35)),(36,37)),43,(47,48)))),40,45,46)); TREE 'MajRule+' = (1,((((2,7),13),(5,14)),((19,((20,21),(22,23))),24)),(((((3,10),42),((4,(6,(8,9),11,12,(49,50))),(15,(16,17))),18),(((((((25,26),27),28),29),30),31),(32,((33,(34,35)),(36,37)),43,(47,48)))),40,45,46)); TREE 'Adams+' = (1,((((2,7),13),(5,14)),((19,((20,21),(22,23))),24)),(((((3,10),42),((4,6,(8,9,11,12,49),50),(15,16,17)),18),(((((((25,26),27),28),29),30),31),(32,((33,(34,35)),(36,37)),43,(47,48)))),40,45,46)); END; BEGIN TREES; Title Scaffold; ID 015a07f4145139; LINK Taxa = Taxa; TRANSLATE [0] 1 outgroup_to_trionychids, [1] 2 Cycloderma_aubryi, [2] 3 Pelochelys_bibroni, [3] 4 Amyda_cartilaginea, [4] 5 Cyclanorbis_elegans, [5] 6 Nilssonia_formosa, [6] 7 Cycloderma_frenatum, [7] 8 Nilssonia_gangetica, [8] 9 Nilssonia_hurum, [9] 10 Chitra_indica, [10] 11 Nilssonia_leithii, [11] 12 Nilssonia_nigricans, [12] 13 Lissemys_punctata, [13] 14 Cyclanorbis_senegalensis, [14] 15 Pelodiscus_sinensis, [15] 16 Palea_steindachneri, [16] 17 Dogania_subplana, [17] 18 Trionyx_triunguis, [18] 19 Plastomenus_thomasii, [19] 20 Hutchemys_rememdium, [20] 21 Hutchemys_arctochelys, [21] 22 Hutchemys_tetraneton, [22] 23 Hutchemys_sterea, [23] 24 Gilmoremys_lancensis, [24] 25 Axestemys_quinni, [25] 26 Axestemys_cerevisia, [26] 27 Axestemys_byssina, [27] 28 Axestemys_montinsana, [28] 29 Axestemys_splendida, [29] 30 Aspideretoides_foveatus, [30] 31 Trionyx_allani, [31] 32 Trionyx_uintaensis, [32] 33 Apalone_ferox, [33] 34 Apalone_mutica, [34] 35 Apalone_spinifera, [35] 36 Rafetus_swinhoei, [36] 37 Rafetus_euphraticus, [37] 38 Petrochelys_kyrgyzensis, [38] 39 Amyda_gregaria, [39] 40 Ulutrionyx_ninae, [40] 41 Trionyx_kansaiensis, [41] 42 Khunnuchelys_kizylkumensis, [42] 43 Gobiapalone_breviplastra, [43] 44 Gobiapalone_orlovi, [44] 45 Perochelys_lamadongensis, [45] 46 Kuhnemys_maortuensis; TREE 'Scaffold Tree+' = (((2,7),(14,5),13),((6,4,9,8),(15,16,17),(33,34,35),37,(10,3,18)),(41,42)); END; BEGIN TREES; Title 'Parsimony: Petrochelys kyryzensis only'; ID 015a07f4b19d41; LINK Taxa = Taxa; TRANSLATE [0] 1 outgroup_to_trionychids, [1] 2 Cycloderma_aubryi, [2] 3 Pelochelys_bibroni, [3] 4 Amyda_cartilaginea, [4] 5 Cyclanorbis_elegans, [5] 6 Nilssonia_formosa, [6] 7 Cycloderma_frenatum, [7] 8 Nilssonia_gangetica, [8] 9 Nilssonia_hurum, [9] 10 Chitra_indica, [10] 11 Nilssonia_leithii, [11] 12 Nilssonia_nigricans, [12] 13 Lissemys_punctata, [13] 14 Cyclanorbis_senegalensis, [14] 15 Pelodiscus_sinensis, [15] 16 Palea_steindachneri, [16] 17 Dogania_subplana, [17] 18 Trionyx_triunguis, [18] 19 Plastomenus_thomasii, [19] 20 Hutchemys_rememdium, [20] 21 Hutchemys_arctochelys, [21] 22 Hutchemys_tetraneton, [22] 23 Hutchemys_sterea, [23] 24 Gilmoremys_lancensis, [24] 25 Axestemys_quinni, [25] 26 Axestemys_cerevisia, [26] 27 Axestemys_byssina, [27] 28 Axestemys_montinsana, [28] 29 Axestemys_splendida, [29] 30 Aspideretoides_foveatus, [30] 31 Trionyx_allani, [31] 32 Trionyx_uintaensis, [32] 33 Apalone_ferox, [33] 34 Apalone_mutica, [34] 35 Apalone_spinifera, [35] 36 Rafetus_swinhoei, [36] 37 Rafetus_euphraticus, [37] 38 Petrochelys_kyrgyzensis, [38] 39 Amyda_gregaria, [39] 40 Ulutrionyx_ninae, [40] 41 Trionyx_kansaiensis, [41] 42 Khunnuchelys_kizylkumensis, [42] 43 Gobiapalone_breviplastra, [43] 44 Gobiapalone_orlovi, [44] 45 Perochelys_lamadongensis, [45] 46 Kuhnemys_maortuensis; TREE 'Strict+' = (1,(((2,7),13),(5,14),((19,((20,21),(22,23))),24)),((3,10),4,6,8,9,11,12,(15,(16,17)),18,(25,26,27),28,29,30,31,32,(33,(34,35)),(36,37),38)); TREE 'MajRule+' = (1,((((5,14),(13,(2,7))),(24,(19,((20,21),(22,23))))),(31,(30,(29,(28,(27,(25,26))))),(((32,(36,37)),(33,(34,35))),(18,(3,10),((15,(16,17)),(4,(6,8,9,11,12,38)))))))); TREE 'Adams+' = (1,(((2,7),13),(5,14),((19,((20,21),(22,23))),24)),(((3,10),18,(32,(33,(34,35)),(36,37))),(4,6,8,9,(11,12)),(15,(16,17)),((25,26,27),28,29,30),31,38)); END;