Supplementary Information (ZHU and YU: A primitive fish close to the common ancestor of tetrapods and lungfish)

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1 1 Supplementary Information (ZHU and YU: A primitive fish close to the common ancestor of tetrapods and lungfish) I. List of 158 characters used for phylogenetic analysis. [From ref 10 (Zhu, Yu and Ahlberg, 2001: A primitive sarcopterygian fish with an eyestalk. Nature, 410, 81-84) Supplementary Information.] 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

2 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 (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 pit-lines 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. Preopercular-maxillary contact: present (0); absent (1). 51. Jugal-quadratojugal contact: absent (0); present (1). 52. Preoperculosubmandibular: absent (0); present (1). 53. Foramina on dermal cheek bones: absent (0); present (1). 54. Vertical bar-like 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). 2

3 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 otico-occipital 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 otico-occipital and ethmosphenoid blocks of braincase: absent (0); present (1). 99. 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). 3

4 103. 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 (fenestra ventro-lateralis): 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) Basipterygoid (postorbital) pilla: absent (0); present (1) 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) Basicranial fenestra with arcual plates: absent (0); present (1) Unconstricted cranial notochord: absent (0); present (1) Supraotic cavity: absent (0); present (1) Posttemporal fossae: absent (0); present (1) Anocleithrum: element developed as postcleithrum (0); element developed as anocleithrum sensu stricto (1); element absent (2) Presupracleithrum: absent (0); present (1) Dorsal cleithrum (AL of the Placodermi), ventral cleithrum (AVL of the Placodermi) and pectoral spine (SP of the Placodermi): not fused (0); fused (1) Cleithrum: absent (0); present (1) Dorsal end of cleithrum: pointed (0); broad and rounded (1) Paired pectoral spines: absent (0); present (1) Clavicle (IL of the Placodermi): absent (0); present (1) 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) Interclavicle: absent (0); present (1) Triradiate scapulocoracoid: absent (0); present (1) Subscapular foramen: absent (0); present (1) Endoskeletal supports in pectoral fin: multiple elements articulating with girdle (0); single element ("humerus") articulating with girdle (1) Pectoral propterygium: absent (0); present (1) Deltoid and supinator processes: absent (0); present (1) Axis of pectoral fin skeleton: no more than 5 axial elements (0); more than 5 axial elements (1) Pectoral fin radials: not jointed (0); jointed (1) Pectoral fin radials: most axial elements bearing only preaxial radials (0); symmetrical array of preaxial and postaxial radials (1) Dorsal fin: double (0); single (1) Dorsal and anal fins: present (0); absent (1) Basal scutes on fins: absent (0); present (1) Basal fulcra: absent (0); present (1) Median fin spines: absent (0); present (1) Epichordal lepidotrichia in tail: absent (0); present (1). 4

5 141. 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) Supraneural spines: present on thoracic and abdominal vertebrae (0); restricted to a few vertebrae at anterior end of column, or absent (1) Well-ossified ribs: absent (0); present (1) Scales: rhombic (0); rounded (1) Peg on rhombic scale: narrow (0); broad (1) Anterodorsal peg-like process on scale: absent (0); present (1) Endochondral bone: absent (0); present (1) Cosmine: absent (0); present (1) Cosmine with large pore ornamentation: absent (0); present (1) Enamel lining of pore canals: absent (0); present (1) 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). 5

6 6 II. Modified data matrix with 27 taxa and 158 morphological characters used for phylogenetic analysis. This data matrix is the same as that in ref 10 (Zhu, Yu and Ahlberg, 2001), except for the addition of Styloichthys codings and the revision of 21 codings for Ligulalepis (formerly known as AMF ) and Onychodus based on recently available information from refs 13 and 20. Among the 21 revised codings (shown in bold and underlined numbers below), 14 missing entries for Ligulalepis and 6 missing entries for Onychodus were replaced with either 0 or 1, and one entry for Onychodus (character 109, the eyestalk) was changed from 0 (absent) to?. The analysis was conducted using PAUP under the same conditions as those used in ref = plesiomorphic state; 1,2,3 = apomorphic states;? = unavailable character or logical impossibility. character number: Acanthodes 000??0?00?0?0???????????????0???????????0???0?000??0? Achoania 10100??0????0?0????1??010011???10??1????????????????? Ligulalepis 10?????00?0?00??0000????????????0??00?00????????????? 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? ????????????? Dicksonosteus 100??0?0????0?1????0????????0???0???0???0???0?000??00 Diplocercides ? ??10???10120?? ?00 Dipnorhynchus 100??101111? ?2?021??1?111?101000???????????? Dipterus 100??3011? ?2?021??1?111?211000?? Eusthenopteron ??? Glyptolepis ?0? Ichthyostega ??1?1????0?10002?? Kenichthys ? ? ?001 Miguashaia 1010?100?? ?0?????10????02??120??0?010?0?00 Mimia ?00000?00000? ? Moythomasia ?0?000?00002? ? Onychodus ?0011?0?1000? Osteolepis ?1??? Panderichthys ????0?1?0021? Porolepis ? Powichthys ?0? ?01121?1? Psarolepis 10111?00????010??001??010010? ??00?0?01 Speonesydrion 100??101???? ??2??????1?111?10?00????????????? Uranolophus 100??10111?? ?2?021??1??11?101000???????????? Youngolepis 10100?00????011?1010??010111? ?001 Styloichthys 101?0?00????000??010??0001??? ??001102?0?1

7 character number: Acanthodes 0000??????????1????????1???0??????????????0000??00??? Achoania?????????????????????????????????000?0010???11011?010 Ligulalepis?????????????????????????????????00??0????0?00??1???? Cheirolepis ?? ?01000?000??0000?000????????? Ctenacanthus 0000??????????1??????????????????0????????0000??0000? Diabolepis???11000??11101?? ???????? ??????01001 Dicksonosteus 0?10??????????1??????????????????0????0???0000??0100? Diplocercides ?? ?0?110??? ??? Dipnorhynchus???111?0??11101?? ??????0???111?2?100???100? Dipterus ?0??11101??101? ???111?1?100???100? Eusthenopteron ? Glyptolepis Ichthyostega ? ?111?0?1? ?000??01100 Kenichthys? ? ??0?0000??0111?01010 Miguashaia ?? ?0?11????00??0?1????????? Mimia ? ? ??11000 Moythomasia ? ? ??11000 Onychodus ??101?1011?00?00100?01110?101? Osteolepis ? ? ?? ??0 Panderichthys ? ??01100 Porolepis ? Powichthys??? ?1001?00?00110? Psarolepis ????0?000?0010?001101?1010 Speonesydrion???111?0??11101?? ?110?????111?1??00???100? Uranolophus?1?111?0??11101?? ? ?0??00???100? Youngolepis? ?? Styloichthys? ?? ???????00?0010?1?

8 character number: Acanthodes 0??01020??0?0?0?10?000??????10001???0???00?????00000 Achoania 0?1?111?1????????????????????????????????11?0??????? Ligulalepis??10102??0???????????????????????????0?1?0??????1??? Cheirolepis??????????? ??01???? ??0?010?????01000 Ctenacanthus 0?1000?00?0?0?0?00?0????????00001???0???00?????00000 Diabolepis 100??0???????11??1??????????????0??????? Dicksonosteus 0?1000?0000?000?11??000???????000???0???00??? Diplocercides 0?0110?11?1?0?110100?????????000011?01?010???? Dipnorhynchus 200?1??001??011??1??????????????0????010110?101?0101 Dipterus 200?1??00?? ???10? ? ?00101 Eusthenopteron ?010???? Glyptolepis ? ? ?010???? Ichthyostega 10??10?0??? ? ? ???10?????00120 Kenichthys 100?101?????011101????????????1?0???? ?00110 Miguashaia????1??????10?100111???????? ?01?0?0??????0?00 Mimia ? ???? Moythomasia ??? ???? Onychodus????10??1?? ??100???00?0011?01?010???? Osteolepis 100?10?11?? ???????? ?0 Panderichthys ?11? ? ? ???? Porolepis ?? ?????????000001??? ??00130 Powichthys 110?10111? ?1??????????00???? Psarolepis 001?111?110?? ????????1???????11100??00110 Speonesydrion 200?1???0???011??1??????????????0????0?0110? Uranolophus 200?1??0??? ??????00000?0?0010?101101?0101 Youngolepis 10001?10110??111011?111?????????0???? Styloichthys 1?10111?1????111011?111??????????????

9 III. The 50% majority rule consensus tree calculated from 24 equally parsimonious trees of length 328 steps (Consistency Index = 0.549, Homoplasy Index = 0.451, Retention Index = and Rescaled Consistency Index = 0.416). The operating algorithms used are the same as those used in ref 10. 9

10 IV. Selected portions of the 24 most parsimonious trees divided into 6 topological groups showing variable positions of Styloichthys and Powichthys. The large dot represents the node for Dipnomorpha. 10

11 11 V. A selected most parsimonious tree (#18) supporting the topology shown in Fig.3. Tree length = 328; Consistency index (CI) = 0.549; Homoplasy index (HI) = 0.451; Retention index (RI) = 0.759; Rescaled consistency index (RC) = VI. Characters and character states defining major clades shown above. Asterisks indicate ambiguous character states resolved using DELTRAN. Character state is (1), unless marked otherwise. Node 1, Osteichthyes: 3, 41, 57, 68(0), 111*, 121, 126*, 147 Node 2, Actinopterygii: 45, 56*, 119, 120*, 135*, 138, 155 Node 3: 102*, 146 Node 4: 49*, 63*, 94*, 109(0)*, 154 Node 5, Sarcopterygii: 20, 27*, 32*, 38*, 60*, 61*, 64*, 65*, 66*, 71*, 72*, 79*, 93*, 98, 99, 105, 113, 115, 116, 148, 156

12 12 Node 6, Achoania + Crown-group Sarcopterygii: 4(0), 5(0), 28 Node 7, Crown-group Sarcopterygii: 6*, 9*, 11*, 21*, 29*, 34(0)*, 36(2)*, 44(0)*, 47*, 55*, 86*, 96*, 100, 114*, 118*, 120*, 129*, 130(0)*, 140* Node 8, Actinistia + Onychodontida: 12(2) *, 15, 37*, 81, 85, 144, 148(0) Node 9, Actinistia: 39, 40(2), 41(0), 58, 60(0), 61(0), 65(0), 66(0), 67, 97 Node 10, Styloichthys + (Tetrapodomorpha + Dipnomorpha): 19*, 26, 31*, 33, 35, 49(2), 62(0), 107, 122, 125*, 127*, 128*, 145*, 152*, 157* Node 11, Tetrapodomorpha + Dipnomorpha: 17*, 24*, 42*, 50*, 69*, 82(2)*, 83*, 90*, 109(0)*, 149(0) Node 12, Dipnomorpha: 14, 16(0), 94, 132*, 133, 134, 150 Node 13, Dipnoiformes: 15*, 20(0), 36, 98(0), 99(0),106,114(0), 153* Node 14, Dipnoi + Diabolepis: 13, 14(2), 58, 61(0), 68, 72(0), 73, 75, 90(0), 95, 105(0), 151, 152(0), 157(0), 158 Node 15, Dipnoi: 3(0), 8, 17(0)*, 21(3)*, 23(2)*, 26(2), 30, 34, 41(0)*, 59, 77, 78, 80(0)*, 84*, 91, 92, 97*, 107(2), 115(0)* Node 16, Dipnorhynchus + Speonesydrion 15(0) Node 17, Porolepiformes: 22*, 26(0), 37*, 43, 48, 52*, 108 Node 18, Glyptolepis + Porolepis 15*, 18, 19(0), 24(0), 35(0), 39, 40(2), 70(2), 74, 82*, 101(0), 157(3) Node 19, Tetrapodomorpha: 6(2), 10(0), 12*, 37*, 60(0), 61(0), 74, 93(0)*, 137 Node 20, Tetrapodomorpha above Kenichthys: 25, 31(2), 35(0), 54*, 87*, 101(0)*, 142*

13 13 Node 21, Tetrapodomorpha above Osteolepis: 17(0), 70(2)*, 89*, 104*, 105(0)*, 110*, 117*, 131*, 143, 148(0) Node 22, Tetrapodomorpha above Eusthenopteron: 2, 7, 20(0), 43, 51, 136, 137(0), 141(2)*, 157(2)

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