Supplementary Information for v410, 081 -------------------------------------------------------------------------------------------------------------I. List of 158 characters used for phylogenetic analysis. -------------------------------------------------------------------------------------------------------------1. Large dermal plates: absent (0); present (1). 2. Skull shape: lateral orbits, interorbital skull roof wide and arched (0); dorsal orbits, interorbital skull roof narrow and flat or concave (1). 3. Premaxilla: absent (0); present (1). 4. Premaxilla forming part of orbit: absent (0); present (1). 5. Posterodorsal process on posterior portion of premaxilla: absent (0); present (1). 6. Postrostral: absent (0); postrostral mosaic of small variable bones (1); large median postrostral, with or without accessory bones (2); paired E bones (3). 7. Paired frontals: absent (0); present (1). 8. C-bone: absent (0); present (1). 9. Tectal (sensu Cloutier & Ahlberg, 1996): absent (0); present (1). 10. Number of tectals: one (0); two or more (1). 11. Supraorbital (sensu Cloutier & Ahlberg, 1996): absent (0); present (1). 12. Number of supraorbitals: one (0); two (1); more than two (2). 13. B-bone: absent (0); present (1). 14. Anterior margin of parietal: between or in front of orbits (0); slightly posterior to orbits (1); much posterior to orbits (2). 15. Pineal opening: open (0); closed (1). 16. Parietal-supraorbital contact: absent (0); present (1). 17. Extratemporal: absent (0); present (1). 18. Intertemporal: present (0); absent (1). 19. Number of marginal bones alongside postparietal: single (0); two or more (1). 20. Dermal joint between parietal and postparietal: absent (0); present (1). 21. Number of extrascapulars: two (0); three (1); four (2); five (3). 22. Median extrascapular overlap: median extrascapular overlapped by lateral extrascapulars (0); median extrascapular overlapping lateral extrascapulars (1); median extrascapular abutting lateral extrascapulars (2). 23. Position of anterior nostril: facial (0); marginal (1); palatal (2). 24. Processus dermintermedius: absent (0); present (1). 25. Posterior nostril: present (0); absent (1). 26. Position of posterior nostril: external, far from jaw margin (0); external, close to jaw margin (1); palatal (2). 27. Posterior nostril: associated with orbit (0); not associated with orbit (1). 28. Lacrimal posteriorly enclosing posterior nostril: absent (0); present (1). 29. Number of sclerotic plates: four or less (0); more than four (1). 30. Ethmoid commissure: present (0); absent (1). 31. Course of ethmoid commissure: middle portion through median rostral (0); sutural course (1); through bone center of premaxilla (2). 32. Course of supraorbital canal: between anterior and posterior nostrils (0); anterior to both nostrils (1). 33. Course of supraorbital canal: straight (0); lyre-shaped (1). 34. Contact of supraorbital and infraorbital canals: in contact rostrally (0); not in contact rostrally (1). 35. Relationship of infraorbital canal to premaxilla: infraorbital canal entering premaxilla (0); infraorbital canal following dorsal margin of premaxilla (1). 36. Posterior end of supraorbital canal: in postparietal (0); in parietal (1); in intertemporal 37. 38. 39. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54. 55. 56. 57. 58. 59. 60. 61. 62. 63. 64. 65. 66. 67. 68. 69. 70. 71. 72. 73. 74. 75. 76. 77. 78. (2). Contact of otic and supraorbital canals: not in contact (0); in contact (1). Position of anterior pit line: on postparietal (0); on parietal (1). Middle and posterior pit-lines on postparietal: posteriorly situated (0), mesially situated(1). Course of infraorbital canal in relation to anterior portion of postparietal: through marginal bones alongside postparietal (0); along the margin of postparietal (1); through postparietal (2). Maxilla: absent (0); present (1). Posterior expansion of maxilla: present (0); absent (1). Posteriorly deep maxilla: present (0); absent (1). Preopercular extending forward, close to orbit: absent (0); present (1). Dermohyal: absent (0); present (1). Squamosal, quadratojugal and preopercular bones: separated (0); fused (1). Squamosal: absent (0); present (1). Subsquamosals: absent (0); present (1). Quadratojugal: absent (0); present, small (1); present, large (2). Preopercular-maxillary contact: present (0); absent (1). Jugal-quadratojugal contact: absent (0); present (1). Preoperculosubmandibular: absent (0); present (1). Foramina on dermal cheek bones: absent (0); present (1). Vertical bar-like preopercular: absent (0); present (1). Anterior portion of preopercular canal: present (0); absent (1). Jugal canal: present (0); absent (1). Dentary: absent (0); present (1). Relative length of dentary: long (0); short (1). Marginal teeth on dentary: present (0); absent (1). Teeth of dentary: reaching anterior end of dentary (0); not reaching anterior end (1). Parasymphysial tooth whorl: absent (0); present (1). Axis of parasymphysial tooth whorl: parallel to dentary (0); perpendicular to dentary (1). Meckelian bone exposed immediately anterior to first coronoid: yes (0); no (1). Splenial: absent (0); present (1). Postsplenial: absent (0); present (1). Surangular: absent (0); present (1). Raised crest on angular: absent (0); present (1). Coronoids (sensu stricto, excluding parasymphysial dental plate or anterior coronoid): present (0); absent (1). Tusks of coronoids (sensu stricto): absent (0); present (1). Dentition on coronoid: broad marginal "tooth field" (0); narrow marginal tooth row (1); single tooth row (2). Anterior end of prearticular: far from jaw symphysis (0); near jaw symphysis (1). Prearticular - dentary contact: present (0); absent (1). Teeth radial rows on prearticular: absent (0); present (1). Anterior mandibular (precoronoid) fossa: absent (0); present (1). Labial pit: absent (0); present(1). Foramina on external surface of lower jaw: absent (0); present (1). Middle pit line of lower jaw: not developed into enclosed canal (0); developed into enclosed oral canal or intermediate morphology (1). Anterior pit line of lower jaw: not developed into enclosed canal (0); developed into 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. 91. 92. 93. 94. 95. 96. 97. 98. 99. 100. 101. 102. 103. 104. 105. 106. 107. 108. 109. 110. 111. enclosed canal linking oral and mandibular canals (1). Course of mandibular canal: passing through dentary (0); not passing through dentary (1). Course of mandibular canal: not passing through most posterior infradentary (0); passing through most posterior infradentary (1). Branchiostegal rays: present (0); absent (1). Number of branchiostegal rays per side: ten or more (0); two to seven (1); one (2). Submandibulars: absent (0); present (1). Width of submandibulars: narrow (0); broad (1). Median gular: present (0); absent (1). Size of lateral gular: lateral gular and brachiostegal rays of similar size (0); lateral gular covering approximately half the intermandibular space. Palatal opening surrounded by premaxilla, maxilla, dermopalatine, and vomer: absent (0); present (1). Posterior process of vomer: absent (0); present (1). Articulation of vomers: vomers not articulating with each other (0); vomers articulating with each other (1). Vomerine tusks: absent (0); present (1). Articulation of pterygoids: pterygoids not articulating with each other (0); pterygoids articulating with each other (1). Position of parasphenoid: beneath sphenethmoid part of endocranium (0); beneath sphenethmoid and otico-occipital part (1). Parasphenoid: protruding forward in ethmoid region of endocranium (0); behind ethmoid region (1). Denticulated field of parasphenoid: without spiracular groove (0); with spiracular groove (1). Dental plate: denticles on entopterygoid or naked bone (0); tooth plate on entopterygoid (1); dentine plate on entopterygoid (2). Form of head of hyomandibular: single headed (0); double headed (1). Posterior margin of palatoquadrate: sloping forward (0); erect or sloping backward (1). Dorsal endoskeletal articulation between otico-occipital and ethmosphenoid blocks of braincase: absent (0); present (1). Ventral endoskeletal articulation between otico-occipital and ethmosphenoid blocks of braincase: absent (0); present (1). Orientation of intracranial joint or fissure: vertical or anteroventrally slanting (0); posteroventrally slanting (1). Position of intracranial joint or fissure relative to cranial nerves: joint through profundus foramen (0); joint through trigeminal foramen (1). Processus descendens of sphenoid or otico-sphenoid bridge: absent (0); present (1). Autopalatine articulates with postnasal wall: absent (0); present (1). Anterior palatal fenestra (fossa apicalis): absent (0); present (1). Paired internasal cavity: absent (0); present (1). Vomeral area with grooves and raised areas: absent (0); present (1). Fenestra ventralis: absent (0); present (1); common ventral fenestra for anterior and posterior nostrils (2). Large median opening and several small dorsolateral openings in postnasal wall: absent (0); present (1). Eye stalk or unfinished area for similar structure: absent (0); present (1). Postorbital process on braincase: present (0); absent (1). Basipterygoid articulation: absent (0); present (1). 112. Basipterygoid (postorbital) pilla: absent (0); present (1). 113. Position of exit of pituitary vein: in front of basipterygoid process (0); dorsal to vertical portion of basipterygoid process (1); posterior to basipterygoid process (2). 114. Basicranial fenestra with arcual plates: absent (0); present (1). 115. Unconstricted cranial notochord: absent (0); present (1). 116. Supraotic cavity: absent (0); present (1). 117. Posttemporal fossae: absent (0); present (1). 118. Anocleithrum: element developed as postcleithrum (0); element developed as anocleithrum sensu stricto (1); element absent (2). 119. Presupracleithrum: absent (0); present (1). 120. Dorsal cleithrum (AL of the Placodermi), ventral cleithrum (AVL of the Placodermi) and pectoral spine (SP of the Placodermi): not fused (0); fused (1). 121. Cleithrum: absent (0); present (1). 122. Dorsal end of cleithrum: pointed (0); broad and rounded (1). 123. Paired pectoral spines: absent (0); present (1). 124. Clavicle (IL of the Placodermi): absent (0); present (1). 125. Relationship of clavicle to cleithrum: ascending process of clavicle overlapping cleithrum laterally (0); ascending process of clavicle wrapping round anterior edge of cleithrum, overlapping it both laterally and mesially (1). 126. Interclavicle: absent (0); present (1). 127. Triradiate scapulocoracoid: absent (0); present (1). 128. Subscapular foramen: absent (0); present (1). 129. Endoskeletal supports in pectoral fin: multiple elements articulating with girdle (0); single element ("humerus") articulating with girdle (1). 130. Pectoral propterygium: absent (0); present (1). 131. Deltoid and supinator processes: absent (0); present (1). 132. Axis of pectoral fin skeleton: no more than 5 axial elements (0); more than 5 axial elements (1). 133. Pectoral fin radials: not jointed (0); jointed (1). 134. Pectoral fin radials: most axial elements bearing only preaxial radials (0); symmetrical array of preaxial and postaxial radials (1). 135. Dorsal fin: double (0); single (1). 136. Dorsal and anal fins: present (0); absent (1). 137. Basal scutes on fins: absent (0); present (1). 138. Basal fulcra: absent (0); present (1). 139. Median fin spines: absent (0); present (1). 140. Epichordal lepidotrichia in tail: absent (0); present (1). 141. Relative size of epichordal and hypochordal lepidotrichia: epichordals less developed than hypochordals (0); epichordals and hypochordals equally developed (1); epichordals more developed than hypochordals (2). 142. Supraneural spines: present on thoracic and abdominal vertebrae (0); restricted to a few vertebrae at anterior end of column, or absent (1). 143. Well-ossified ribs: absent (0); present (1). 144. Scales: rhombic (0); rounded (1). 145. Peg on rhombic scale: narrow (0); broad (1). 146. Anterodorsal peg-like process on scale: absent (0); present (1). 147. Endochondral bone: absent (0); present (1). 148. Cosmine: absent (0); present (1). 149. Cosmine with large pore ornamentation: absent (0); present (1). 150. Enamel lining of pore canals: absent (0); present (1). 151. 152. 153. 154. 155. 156. 157. 158. Westoll-lines: absent (0); present (1). Pore clusters: absent (0); present (1). Rostral tubuli: absent (0); present (1). Acrodin: absent (0); present (1). Ganoine: absent (0); present (1). True enamel on teeth: absent (0); present (1). Plicidentine: absent (0); simple (1); labyrinthodont (2); dendrodont (3). Syndentine: absent (0); present (1). II. Data matrix with 158 morphological characters and 26 taxa. 0 = plesiomorphic state; 1,2,3 = apomorphic states; ? = unavailable character or logical impossibility. ---------------------------------------------------------------------------------------------------------------------character 00000000000000000000000000000000000000000000000000000 number: 00000000011111111112222222222333333333344444444445555 12345678901234567890123456789012345678901234567890123 ---------------------------------------------------------------------------------------------------------------------Acanthodes 000??0?00?0?0???????????????0???????????0???0?000??0? Achoania 10100??0????0?0????1??010011???10??1????????????????? AMF101607 10?????0????0??????0????????????????????????????????? Cheirolepis 101??1000?1?001?0?000?0?000000?001000??010011?00?0000 Ctenacanthus 000??0?00?0?0???????????????????????????0???0?000??0? Diabolepis 10100?00??1?1210?010??1?0111?01110110100????????????? Dicksonosteus 100??0?0????0?1????0????????0???0???0???0???0?000??00 Diplocercides 101001001?1200110101100000111??10???10120??0001000?00 Dipnorhynchus 100??101111?120000103?2?021??1?111?101000???????????? Dipterus 100??3011?11121000103?2?021??1?111?211000??0001021110 Eusthenopteron 1010020010110001001110011???1021100211001100001021000 Glyptolepis 1010010011100110110111000011?0?1100211121110001121010 Ichthyostega 11100010101100010110??1?1????0?10002??001110001021100 Kenichthys 1010020010110?01101110010111?01110121100110001102?001 Miguashaia 1010?100??12001100011?0?????10????02??120??0?010?0?00 Mimia 101110000?00000?00000?00000000000100000010011?0010000 Moythomasia 101110000?0?000?00002?00000000000100000010011?0010000 Onychodus 10100100111200111111120?0011?0?1?00?11001000101000000 Osteolepis 10100200101100011011100?1???1021100211001100001021000 Panderichthys 1110011010110001001010011????0?1?0021?001110001021100 Porolepis 1010010011100110110111000011?001100111121110001121010 Powichthys 1010010011100100101011010011?0?1101211001110?01121?1? Psarolepis 10111?00????010??001??010010?001010001011001??00?0?01 Speonesydrion 100??101????12000010??2??????1?111?10?00????????????? Uranolophus 100??10111??121000103?2?021??1??11?101000???????????? Youngolepis 10100?00????011?1010??010111?01110110100110001102?001 ---------------------------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------------------------character 00000000000000000000000000000000000000000000001111111 number: 55555566666666667777777777888888888899999999990000000 45678901234567890123456789012345678901234567890123456 ---------------------------------------------------------------------------------------------------------------------Acanthodes 0000??????????1????????1???0??????????????0000??00??? Achoania ?????????????????????????????????000?0010???11011?010 AMF101607 ?????????????????????????????????00??0????0?00??1???? Cheirolepis 00110000??00000000000000?01000?000??0000?000????????? Ctenacanthus 0000??????????1??????????????????0????????0000??0000? Diabolepis ???11000??11101??101010001????????00000011??????01001 Dicksonosteus 0?10??????????1??????????????????0????0???0000??0100? Diplocercides 01011000??100100011000000111?0?110???0000011111101??? Dipnorhynchus ???111?0??11101??1010101110??????0???111?2?100???100? Dipterus 010111?0??11101??101?1011100211010???111?1?100???100? Eusthenopteron 11010000?01110012110100001102100111110000010111001100 Glyptolepis 01010011001110012110100001101101100010011010111001010 Ichthyostega 11010000?111100021100000?111?0?1?101110100?000??01100 Kenichthys ?1010000?011100101101000011021001??0?0000??0111?01010 Miguashaia 01011000??100100011000000111?0?11????00??0?1????????? Mimia 00110000?100000000000000001000?000000000100000??11000 Moythomasia 00110000?100100000000000000000?000000000100000??11000 Onychodus 010100111?1110000110?00??101?1011????00100?01110?101? Osteolepis 11010000?01110011?1010000110210011??10000010111001??0 Panderichthys 11010000?0111001211010000110210011111000001011??01100 Porolepis 010100110011100121101000011011001?0010011010111001010 Powichthys ???1001100111001011000100110?1001?00?00110?0110111010 Psarolepis 000100111011100111100010011????0?000?0010?001101?1010 Speonesydrion ???111?0??11101??10101011100?110?????111?1??00???100? Uranolophus ?1?111?0??11101??100010111?0211010000111?0??00???100? Youngolepis ?10100110011100101100010011??100100010001010000111011 ---------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------character 1111111111111111111111111111111111111111111111111111 number: 0001111111111222222222233333333334444444444555555555 7890123456789012345678901234567890123456789012345678 -------------------------------------------------------------------------------------------------------------------Acanthodes 0??01020??0?0?0?10?000??????10001???0???00?????00000 Achoania 0?1?111?1????????????????????????????????11?0??????? AMF101607 ??10102??0???????????????????????????????0?????????? Cheirolepis ???????????011100101??01????1001000??0?010?????01000 Ctenacanthus 0?1000?00?0?0?0?00?0????????00001???0???00?????00000 Diabolepis 100??0???????11??1??????????????0???????110110100101 Dicksonosteus 0?1000?0000?000?11??000???????000???0???00???0000000 Diplocercides 0?0110?11?1?0?110100?????????000011?01?010????000100 Dipnorhynchus 200?1??001??011??1??????????????0????010110?101?0101 Dipterus 200?1??00??10111011???10?1110000010011?0110110?00101 Eusthenopteron 10011001111101110111111010000010011111?010????000110 Glyptolepis 110010111?110111011?101001110000010001?010????000130 Ichthyostega 10??10?0???201110111?1101000?10001211???10?????00120 Kenichthys 100?101?????011101????????????1?0????010110001?00110 Miguashaia ????1??????10?100111????????0000010?01?0?0??????0?00 Mimia 0000102000001110010100010?0010010000000110????011000 Moythomasia 0000102000001110010100010???10010000000110????011000 Onychodus ??0??0??1??101100100??100???00?0011?01?010????000100 Osteolepis 100?10?11??101110111????????0010010100101100010001?0 Panderichthys 100110?11?1101110111?1101000?1000121101010????000120 Porolepis 110110111??10111011?????????000001???01011010??00130 Powichthys 110?10111?010111011?1??????????00????010110101100110 Psarolepis 001?111?110??01011110001????????1???????11100??00110 Speonesydrion 200?1???0???011??1??????????????0????0?0110?10100101 Uranolophus 200?1??0???10111011111??????00000?0?0010?101101?0101 Youngolepis 10001?10110??111011?111?????????0????010110101100110 -------------------------------------------------------------------------------------------------------------------- III. Characters and character states defining major clades shown in Fig.3a. Based on a selected most-parsimonious tree (tree #1), which is the closest to the 50% majority rule consensus tree. Tree length = 317; Consistency index (CI) = 0.568; Homoplasy index (HI) = 0.432; Retention index (RI) = 0.765; Rescaled consistency index (RC) = 0.434. Asterisks indicate ambiguous character states resolved using DELTRAN. Character state is (1), unless marked otherwise. Osteichthyes: 3, 41, 57, 68(0), 111*, 121, 126*, 147 Sarcopterygii: 20, 24*, 27*, 32*, 38*, 64*, 65*, 66*, 71*, 72*, 79* , 93*, 98, 99, 105, 113, 115, 116, 148, 156 Achoania + Crown-group Sarcopterygii: 4(0), 5(0), 28 Crown-group Sarcopterygii: 6*, 9*, 11*, 21*, 29*, 34(0)*, 36(2)*, 37*, 44(0)* , 47*, 55*, 86*, 96*, 100, 109(0), 114*, 117*, 118*, 120*, 129*, 130(0)*, 140* Actinistia + Onychodontida: 12(2), 15*, 81, 85, 144, 148(0) Actinistia: 39, 40(2), 41(0), 58, 65(0), 66(0), 67, 97 Tetrapodomorpha + Dipnomorpha: 17*, 33, 42, 49(2), 50, 69*, 82(2)*, 83*, 90*, 107, 122, 125* , 127*, 145*, 149(0)*, 152*, 157* Dipnomorpha: 14, 16(0), 22, 52, 60*, 61*, 62(0)*, 94, 132*, 133, 134, 150 Porolepiformes: 15*, 18, 24(0), 39, 40(2), 43*, 48*, 70(2), 74*, 82, 101(0)*, 108*, 157(3) Dipnoiformes: 19*, 20(0), 35, 100(0), 117(0), 153 Dipnoiformes above Powichthys: 15*, 26, 31*, 36, 37(0), 98(0), 99(0),106,114(0), 128* Dipnoiformes above Youngolepis (or Dipnoi + Diabolepis): 13, 14(2), 58, 61(0), 68, 72(0), 75, 90(0), 105(0), 151, 152(0), 157(0), 158 Dipnoi: 3(0), 8, 17(0)*, 21(3)*, 23(2)*, 26(2), 30, 34, 41(0)*, 59, 77, 78, 84*, 91, 92, 107(2) Dipnoi above Uranolophus: 73*, 80(0)*, 95*, 97*, 115(0)* Dipnoi above Dipterus (or Dipnorhynchus + Speonesydrion): 15(0) Tetrapodomorpha: 6(2), 10(0), 12, 19*, 74*, 93(0), 137 Tetrapodomorpha above Kenichthys: 25, 31(2)*, 54*, 87*, 101(0)*, 142* Tetrapodomorpha above Osteolepis: 17(0), 70(2)*, 89*, 104*, 105(0)*, 110*, 128*, 131*, 143, 148(0) Tetrapodomorpha above Eusthenopteron: 2, 7, 20(0), 43, 51, 136, 137(0), 141(2)*, 157(2) Actinopterygii: 102* Actinopterygii above AMF 101607: 45*, 56*, 119*, 120*, 135*, 138*, 155* Actinopterygii above Cheirolepis (or Mimia + Moythomasia): 49*, 63*, 94*, 109(0)*, 146, 154