Supplementary Information for v410, 081
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I. List of 158 characters used for phylogenetic analysis.
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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).
- 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. Cbone: 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. Bbone: 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. Parietalsupraorbital 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); lyreshaped (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 (2).
37. Contact of otic and supraorbital canals: not in contact (0); in contact (1).
38. Position of anterior pit line: on postparietal (0); on parietal (1).
39. Middle and posterior pitlines on postparietal: posteriorly situated (0), mesially situated(1).
40. 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).
41. Maxilla: absent (0); present (1).
42. Posterior expansion of maxilla: present (0); absent (1).
43. Posteriorly deep maxilla: present (0); absent (1).
44. Preopercular extending forward, close to orbit: absent (0); present (1).
45. Dermohyal: absent (0); present (1).
46. Squamosal, quadratojugal and preopercular bones: separated (0); fused (1).
47. Squamosal: absent (0); present (1).
48. Subsquamosals: absent (0); present (1).
49. Quadratojugal: absent (0); present, small (1); present, large (2).
50. Preopercularmaxillary contact: present (0); absent (1).
51. Jugalquadratojugal contact: absent (0); present (1).
52. Preoperculosubmandibular: absent (0); present (1).
53. Foramina on dermal cheek bones: absent (0); present (1).
54. Vertical barlike preopercular: absent (0); present (1).
55. Anterior portion of preopercular canal: present (0); absent (1).
56. Jugal canal: present (0); absent (1).
57. Dentary: absent (0); present (1).
58. Relative length of dentary: long (0); short (1).
59. Marginal teeth on dentary: present (0); absent (1).
60. Teeth of dentary: reaching anterior end of dentary (0); not reaching anterior end (1).
61. Parasymphysial tooth whorl: absent (0); present (1).
62. Axis of parasymphysial tooth whorl: parallel to dentary (0); perpendicular to dentary (1).
63. Meckelian bone exposed immediately anterior to first coronoid: yes (0); no (1).
64. Splenial: absent (0); present (1).
65. Postsplenial: absent (0); present (1).
66. Surangular: absent (0); present (1).
67. Raised crest on angular: absent (0); present (1).
68. Coronoids (sensu stricto, excluding parasymphysial dental plate or anterior coronoid): present (0); absent (1).
69. Tusks of coronoids (sensu stricto): absent (0); present (1).
70. Dentition on coronoid: broad marginal "tooth field" (0); narrow marginal tooth row (1); single tooth row (2).
71. Anterior end of prearticular: far from jaw symphysis (0); near jaw symphysis (1).
72. Prearticular dentary contact: present (0); absent (1).
73. Teeth radial rows on prearticular: absent (0); present (1).
74. Anterior mandibular (precoronoid) fossa: absent (0); present (1).
75. Labial pit: absent (0); present(1).
76. Foramina on external surface of lower jaw: absent (0); present (1).
77. Middle pit line of lower jaw: not developed into enclosed canal (0); developed into enclosed oral canal or intermediate morphology (1).
78. Anterior pit line of lower jaw: not developed into enclosed canal (0); developed into enclosed canal linking oral and mandibular canals (1).
79. Course of mandibular canal: passing through dentary (0); not passing through dentary (1).
80. Course of mandibular canal: not passing through most posterior infradentary (0); passing through most posterior infradentary (1).
81. Branchiostegal rays: present (0); absent (1).
82. Number of branchiostegal rays per side: ten or more (0); two to seven (1); one (2).
83. Submandibulars: absent (0); present (1).
84. Width of submandibulars: narrow (0); broad (1).
85. Median gular: present (0); absent (1).
86. Size of lateral gular: lateral gular and brachiostegal rays of similar size (0); lateral gular covering approximately half the intermandibular space.
87. Palatal opening surrounded by premaxilla, maxilla, dermopalatine, and vomer: absent (0); present (1).
88. Posterior process of vomer: absent (0); present (1).
89. Articulation of vomers: vomers not articulating with each other (0); vomers articulating with each other (1).
90. Vomerine tusks: absent (0); present (1).
91. Articulation of pterygoids: pterygoids not articulating with each other (0); pterygoids articulating with each other (1).
92. Position of parasphenoid: beneath sphenethmoid part of endocranium (0); beneath sphenethmoid and oticooccipital part (1).
93. Parasphenoid: protruding forward in ethmoid region of endocranium (0); behind ethmoid region (1).
94. Denticulated field of parasphenoid: without spiracular groove (0); with spiracular groove (1).
95. Dental plate: denticles on entopterygoid or naked bone (0); tooth plate on entopterygoid (1); dentine plate on entopterygoid (2).
96. Form of head of hyomandibular: single headed (0); double headed (1).
97. Posterior margin of palatoquadrate: sloping forward (0); erect or sloping backward (1).
98. Dorsal endoskeletal articulation between oticooccipital and ethmosphenoid blocks of braincase: absent (0); present (1).
99. Ventral endoskeletal articulation between oticooccipital and ethmosphenoid blocks of braincase: absent (0); present (1).
100. Orientation of intracranial joint or fissure: vertical or anteroventrally slanting (0); posteroventrally slanting (1).
101. Position of intracranial joint or fissure relative to cranial nerves: joint through profundus foramen (0); joint through trigeminal foramen (1).
102. Processus descendens of sphenoid or oticosphenoid bridge: absent (0); present (1).
103. Autopalatine articulates with postnasal wall: absent (0); present (1).
104. Anterior palatal fenestra (fossa apicalis): absent (0); present (1).
105. Paired internasal cavity: absent (0); present (1).
106. Vomeral area with grooves and raised areas: absent (0); present (1).
107. Fenestra ventralis: absent (0); present (1); common ventral fenestra for anterior and posterior nostrils (2).
108. Large median opening and several small dorsolateral openings in postnasal wall: absent (0); present (1).
109. Eye stalk or unfinished area for similar structure: absent (0); present (1).
110. Postorbital process on braincase: present (0); absent (1).
111. 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. Wellossified ribs: absent (0); present (1).
144. Scales: rhombic (0); rounded (1).
145. Peg on rhombic scale: narrow (0); broad (1).
146. Anterodorsal peglike 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. Westolllines: absent (0); present (1).
152. Pore clusters: absent (0); present (1).
153. Rostral tubuli: absent (0); present (1).
154. Acrodin: absent (0); present (1).
155. Ganoine: absent (0); present (1).
156. True enamel on teeth: absent (0); present (1).
157. Plicidentine: absent (0); simple (1); labyrinthodont (2); dendrodont (3).
158. 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.
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character00000000000000000000000000000000000000000000000000000
number:00000000011111111112222222222333333333344444444445555
12345678901234567890123456789012345678901234567890123
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Acanthodes000??0?00?0?0???????????????0???????????0???0?000??0?
Achoania10100??0????0?0????1??010011???10??1?????????????????
AMF10160710?????0????0??????0?????????????????????????????????
Cheirolepis101??1000?1?001?0?000?0?000000?001000??010011?00?0000
Ctenacanthus000??0?00?0?0???????????????????????????0???0?000??0?
Diabolepis10100?00??1?1210?010??1?0111?01110110100?????????????
Dicksonosteus100??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
Mimia101110000?00000?00000?00000000000100000010011?0010000
Moythomasia101110000?0?000?00002?00000000000100000010011?0010000
Onychodus 10100100111200111111120?0011?0?1?00?11001000101000000
Osteolepis 10100200101100011011100?1???1021100211001100001021000
Panderichthys1110011010110001001010011????0?1?0021?001110001021100
Porolepis 1010010011100110110111000011?001100111121110001121010
Powichthys1010010011100100101011010011?0?1101211001110?01121?1?
Psarolepis 10111?00????010??001??010010?001010001011001??00?0?01
Speonesydrion 100??101????12000010??2??????1?111?10?00?????????????
Uranolophus100??10111??121000103?2?021??1??11?101000????????????
Youngolepis10100?00????011?1010??010111?01110110100110001102?001
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character00000000000000000000000000000000000000000000001111111
number:55555566666666667777777777888888888899999999990000000
45678901234567890123456789012345678901234567890123456
--
Acanthodes0000??????????1????????1???0??????????????0000??00???
Achoania?????????????????????????????????000?0010???11011?010
AMF101607?????????????????????????????????00??0????0?00??1????
Cheirolepis00110000??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?
Diplocercides01011000??100100011000000111?0?110???0000011111101???
Dipnorhynchus ???111?0??11101??1010101110??????0???111?2?100???100?
Dipterus 010111?0??11101??101?1011100211010???111?1?100???100?
Eusthenopteron11010000?01110012110100001102100111110000010111001100
Glyptolepis 01010011001110012110100001101101100010011010111001010
Ichthyostega11010000?111100021100000?111?0?1?101110100?000??01100
Kenichthys?1010000?011100101101000011021001??0?0000??0111?01010
Miguashaia01011000??100100011000000111?0?11????00??0?1?????????
Mimia 00110000?100000000000000001000?000000000100000??11000
Moythomasia 00110000?100100000000000000000?000000000100000??11000
Onychodus010100111?1110000110?00??101?1011????00100?01110?101?
Osteolepis11010000?01110011?1010000110210011??10000010111001??0
Panderichthys11010000?0111001211010000110210011111000001011??01100
Porolepis 010100110011100121101000011011001?0010011010111001010
Powichthys???1001100111001011000100110?1001?00?00110?0110111010
Psarolepis000100111011100111100010011????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
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character1111111111111111111111111111111111111111111111111111
number:0001111111111222222222233333333334444444444555555555
7890123456789012345678901234567890123456789012345678
Acanthodes 0??01020??0?0?0?10?000??????10001???0???00?????00000
Achoania0?1?111?1????????????????????????????????11?0???????
AMF101607??10102??0???????????????????????????????0??????????
Cheirolepis ???????????011100101??01????1001000??0?010?????01000
Ctenacanthus0?1000?00?0?0?0?00?0????????00001???0???00?????00000
Diabolepis 100??0???????11??1??????????????0???????110110100101
Dicksonosteus0?1000?0000?000?11??000???????000???0???00???0000000
Diplocercides0?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
Glyptolepis110010111?110111011?101001110000010001?010????000130
Ichthyostega10??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
Osteolepis100?10?11??101110111????????0010010100101100010001?0
Panderichthys100110?11?1101110111?1101000?1000121101010????000120
Porolepis110110111??10111011?????????000001???01011010??00130
Powichthys110?10111?010111011?1??????????00????010110101100110
Psarolepis001?111?110??01011110001????????1???????11100??00110
Speonesydrion200?1???0???011??1??????????????0????0?0110?10100101
Uranolophus200?1??0???10111011111??????00000?0?0010?101101?0101
Youngolepis10001?10110??111011?111?????????0????010110101100110
III. Characters and character states defining major clades shown in Fig.3a. Based on a selected mostparsimonious 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 + Crowngroup Sarcopterygii:
4(0), 5(0), 28
Crowngroup 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