Supplementary information I. Clades & supporting characters at major nodes in Fig. 4a




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SUPPLEMENTARY INFORMATION
I. Clades & supporting characters at major nodes in Fig. 4a. (Note: Lower level nodes in taxa with * are not depicted in Fig.4)

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Node Clade Supporting characters

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Node 1. (Acanthodes+Ctenacanthus)+(Psarolepis+Osteichthyes) 147

Node 2. Psarolepis+Osteichthyes 149

Node 3. Osteichthyes No synapomorphy

Node 4. Sarcopterygii 4,18,42,49,54,63(2),88,105,120,128

Node 5. Crossopterygii (sensu ref. 4) No synapomorphy

Node 6. Powichthys+{Porolepiformes+[(Actinistia+Onychodontida)+Tetrapodomorpha]} No synapomorphy

Node 7. Porolepiformes+[(Actinistia+Onychodontida)+Tetrapodomorpha] 89

Node 8. (Actinistia+Onychodontida)+Tetrapodomorpha 137; reversals 2, 41, 43

Node 9. TETRAPODOMORPHA* (= Choanata of ref. 4) 44,71,119(2),122

Rhizodontida* (Barameda, Strepsodus)

Osteolepidae* (Beelarongia, Gyroptychius, Osteolepis)

Eusthenopteron

Elpistostegalia* (Elpistostege, Panderichthys)

Tetrapoda* (Acanthostega, Crassigyrinus, Ichthyostega, Ventastega)

Node 10. Acanthodes+Ctenacanthus Reversal 141

Node 11. Actinopterygii 6; reversals 52,93(2->0),110

Node 12. DIPNOI* (Diabolepis, Diphnorynchus, Dipterus, Speonesydrion, Uranolophus) 17A,30,65,80,107

Node 13. POROLEPIFORMES* (Glyptolepis, Holoptychius, Porolepis) 51,55,63(2->1),75,78A,101

Node 14. ACTINISTIA* (Diplocercides kayseri, D. heiligenstockiensis) 76,93(2–>1),95,97,138

Node 15. Actinistia+Onychodontida No synapomorphy

Node 16. ONYCHODONTIDA* (Barameda, Strepsodus) 41(2)


II. Clades & supporting characters at major nodes in Fig. 4b. (Note: Lower level nodes in taxa with * are not depicted in Fig.4)

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Node Clade Supporting characters

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Node 1. (Acanthodes+Ctenacanthus)+(“Actinopterygii”+Psarolepis+Sarcopterygii) 147

Node 2. “Actinopterygii”+Psarolepis+Sarcopterygii 149

Node 3. Cheirolepis+[Polypterus+(Psarolepis+Sarcopterygii)] No synapomorphy

Node 4. Polypterus+(Psarolepis+Sarcopterygii) 46,63(2),69,98,134

Node 5. Psarolepis+Sarcopterygii 4,42,49,88,93(2),110,128

Node 6. Sarcopterygii 18,54,105,120

Node 7. Onychodontida+Rhipidistia (sensu ref. 14) No synapomorphy

Node 8. Rhipidistia (sensu ref. 14) 56

Node 9. TETRAPODOMORPHA* 44,71,119(2),122, reversal 2

Rhizodontida* (Barameda, Strepsodus);

Osteolepidae* (Beelarongia, Gyroptychius, Osteolepis);



Eusthenopteron;

Elpistostegalia* (Elpistostege, Panderichthys)

Tetrapoda* (Acanthostega, Crassigyrinus, Ichthyostega, Ventastega)

Node 10. Acanthodes +ctenacanthus Reversal 141

Node 11. Mimia+(Howqualepis+Moythomasia) 7

Node 12. ACTINISTIA* (Diplocercides kayseri, D. heiligenstockiensis) 76,93(2->1),95,97,138

Node 13. ONYCHODONTIDA* (Barameda, Strepsodus) 41(2)

Node 14. POROLEPIFORMES* (Glyptolepis, Holoptychius, Porolepis) 51,55,75,101

Node 15. Dipnomorpha (sensu ref. 14) 41,43,130

Node 16. Dipnoiformes (sensu ref. 14) 77,100,119

Node 17. Youngolepis+Dipnoi 17, 45

Node 18. DIPNOI* (Diabolepis, Diphnorynchus, Dipterus, Speonesydrion, Uranolophus) 30,65,80,107


III. Characters and character states defining major nodes in Fig. 4a,b. (from ref. 14 except for characters 141–149).

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2. Mesh canals. 0 = pore cavity with horizontal partition; 1 = pore cavity without horizontal cavity.

4. Peg on rhombic scale. 0 = narrow; 1 = broad.

6. Ganoine. 0 = absent; 1 = present.

7. Acrodin caps on teeth. 0 = absent; 1 = present.

17. Position of premaxilla 0 = marginal; 1 = ventral part turned in (17A uses codings from ref. 4).

18. Relation of premaxilla to the orbit. 0 = forming part of orbit; 1 = not forming part of orbit.

30. B-bone. 0 = absent; 1 = present.

41. Median extrascapular. 0 = overlapped by lateral extrascapular; 1 = overlapping lateral extrascapular; 2 = abutting lateral extrascapular.

42. Tectals. 0 = absent; 1 = present.

43. Number of tectals (not counting the "posterior tectal" of Jarvik). 0 = one; 1 = three or more.

44. Anterior and posterior nares. 0 = both present; 1 = only anterior naris present.

45. Position of posterior naris. 0 = external, far from jaw margin; 1 = external, close to jaw margin; 2 = palatal.

46. Position of posterior naris in relation to the orbit. 0 = associated with orbit; 1 = not associated with orbit.

49. Number of sclerotic plates. 0 = four or less; 1 = more than four.

51. Prespiracular. 0 = absent; 1 = present.

52. Dermohyal. 0 = present; 1 = absent.

54. Squamosal and preopercular. 0 = one bone ("preopercular"); 1 = two separate bones.

55. Subsquamosals. 0 = absent; 1 = present.

63. Number of branchiostegal rays per side. 0 = 10 or more; 1 = two to seven; 2 = one.

65. Width of submandibulars. 0 = narrow; 1 = broad.

69. Size of lateral gular. 0 = similar to branchiostegal rays; 1 = covering about half the intermandibular space.

71. Articulation of vomers. 0 = not articulating with each other; 1 = articulating with each other.

75. Buccohypophysial foramen of parasphenoid. 0 = single; 1 = double.

76. Rostral organ. 0 = absent; 1 = present.

77. Rostral tubuli. 0 = absent; 1 = present.

78. Fossa autopalatina. 0 = absent; 1 = present (78A uses codings from ref. 4).

80. Labial cavity. 0 = absent; 1 = present.

88. Condition of hyomandibular. 0 = with one proximal articular head; 1 = two proximal articular head.

89. Posttemporal fossa. 0 = absent ; 1 = present.

93. Number of infradentaries. 0 = one; 1 = two; 2 = four.

95. Condition of most posterior coronoid. 0 = not distinctly differentiated from other coronoids; 1 = well developed and oriented vertically.

97. Articulation or symplectic with articular. 0 = absent ; 1 = present.

98. Trajectory of supraorbital canal. 0 = passing between anterior & posterior nares; 1 = passing anterior to both naries.

100. Relationship of infraorbital canal to premaxilla. 0 = entering Pmx; 1 = following dorsal margin of Pmx.

101. Trajectory of otic canal. 0 = not passing through growth center of postparietal ; 1 = passing through.

105. Preopercular canal. 0 = ending at dorsal margin of preopercular; 1 = not ending at dorsal margin of preopercular.

107. Position of infraorbital canal. 0 = ventral to anterior naris; 1 = dorsal to anterior naris.

110. Trajectory of mandibular canal. 0 = passing through dentary; 1 = not passing through dentary.

119. Proximal articular surface of humerus. 0 = concave; 1 = flat; 2 = convex.

120. Endoskeletal supports in pectoral fins. 0 = multiple elements articulating with girdle; 1 = single element.

122. Deltoid and supinator processes. 0 = absent ; 1 = present.

128. Basal plates in dorsal fin supports. 0 = absent ; 1 = present.

130. Posterior branched radial complex in posterior dorsal fin. 0 = absent ; 1 = present.

134. Epichordal lepidotrichia in tail. 0 = absent ; 1 = present.

137. Supraneural spines. 0 = present on thoracic and abdominal vertebrae; 1 = restricted to a few anterior vertebrae or absent.

138. Condition of intercentra. 0 = ossified; 1 = not ossified.

141. Large dermal plates. 0 = absent; 1 = present.

142. Paired pectoral spines. 0 = absent; 1 = present.

143. Median fin spines. 0 = absent; 1 = present.

144. Denticulate postbranchial lamina of the cleithrum. 0 = absent; 1 = present.

145. Wide suborbital ledge. 0 = absent; 1 = present.

146. Eye stalk or unfinished area for similar structure. 0 = absent; 1 = present.

147. Ventral and otico-occipital fissures. 0 = absent; 1 = present.

148. Basipterygoid articulation. 0 = absent; 1 = present.

149. Endochondral bone. 0 = absent; 1 = present.


( See Part IV for the expanded matrix. See ref. 14 for a complete list of the original 140 characters and character states; see ref. 4 for the changed codings for characters 10, 17, 78, 108.)

IV. Expanded matrix with 149 characters for 37 taxa. Note: Characters 1–140 for taxa 1–33 are from ref.14; modified codings at the end of the matrix (10A,17A,78A,108A) are based on ref. 4; 0 = plesiomorphic state; 1,2,3 = apomorphic states; ? = unavailable character or logical impossibility; {01} = polymorphic states (0 and 1).

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1 1111111112 2222222223 3333333334 4444444445

1234567890 1234567890 1234567890 1234567890 1234567890

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Acanthostega 0?0??00000 0111100101 ?0?1100110 000101111? ?101??1110

Allenypterus 0?1?000000 000000011? ?000000120 0101011003 ?1?0010011

Barameda 0?1?100000 011100010? ??00000110 0001101002 01????0??0

Beelarongia 1?010000?? ????0???00 1???0001?0 000110?002 ???10?0??0

Cheirolepis 0?0?010000 0000000{01}00 0000000100 01000{01}0001 ?0?0000000

Crassigyrinus 0?0?000000 0?11100101 ???1100110 000100111? ?101??01?0

Diabolepis 11???0001? 00000011?? ?0??0001?1 2100?010?? ???0111???

Diplocercides kaeseri 0?1?000000 000000011? ??00000120 0101012002 01?0010011

D. heligenstockiensis 0?1?000000 0?0000011? ??00000120 0101012002 ?1?0010?11

Dipnorynchus 1?0100?12? 000?01??1? ??000011?1 2000001003 ?1102120??

Dipterus 111?00011? 000001??1? ??00011111 2100001002 ?1?0212010

Elpistostege 0?010000?? 0???100101 ?000100110 0011011??? ?101??1??0

Eusthenopteron 0?1?100000 0101000100 1010000110 0001001002 0101??0110

Glyptolepis 0?1?000000 1102000101 ?000000100 0101112002 1110010110

Gyroptychius 1?01000000 0101000100 0010000110 0001101002 0101??0??0

Holoptychius 0?1?000000 1102000101 ?000000120 0101112002 1110010110

Howqualepis 0?00011000 0000000000 01?00000?0 000?000001 ?0?0000?00

Ichthyostega 0?1??00000 0111100101 ?0?1100110 000101111? ?101??11?0

Miguashaia 0?1?000000 000000011? ?000000120 0101001002 01?0010?10

Mimia 0?00011000 0000000000 00?00000?0 000?000001 ?0?0000000

Moythomasia 0?00011000 0000000000 01?00000?0 000?000000 ?0?0000000

Onychodus 0?1?000000 1100000100 0000000120 0101111002 2100010?10

Osteolepis 1001000000 010?000100 1010000110 0001101002 0101??0110

Panderichthys 0?01000000 0111100101 ?000100110 0011001102 0101??11?0

Polypterus 0?00010000 000000000? ???01000?0 010?00?000 ?0?001000?

Porolepis 1101000000 0102000101 ?000000100 1100112002 1110010??0

Powichthys 1101000001 ?1010001?? ?0000001?0 1000?01002 1110010???

Speonesydrion 1?0?00012? 000001???? ??00001??1 20000010?? ??????????

Strepsodus 0?1?100000 0111000100 1????0011? ??0???100? ?1????0?10

Strunius 0?1?000000 1?00000100 0000000??0 0101?11002 ?1??????10

Uranolophus 110100?10? 000001??1? ??00011??1 2100001003 ??102120??

Ventastega 0????00000 0111100101 ?0?????1?? ??0????1?? ?1?1??11?0

Youngolepis 1101000001 ?101001100 10?0000??0 110?10100? ???0110??0

Psarolepis 11???000?1 ?101000000 01?0000??0 100??????? ???00100?0

Dicksonosteus 0????00??? 0000?1??1? ?????000?0 ?00?????01 ?0?????00?

Ctenacanthus 0????00??? 000001??1? ?????000?0 ??0??????? ?0?????0??

Acanthodes 0?0??00??? 000001??1? ?????000?0 ??0??????? ?0?????00?

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1

5555555556 6666666667 7777777778 8888888889 9999999990



1234567890 1234567890 1234567890 1234567890 1234567890

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Acanthostega 0101011101 11?0?1?1?0 1101?0?000 0000???110 0021010100

Allenypterus 0111001100 01?0?1?010 0011010??? 111??????? 101?111??0

Barameda 010??????0 ?????00010 101??0???? 1????????? 00?????100

Beelarongia 01010??0?0 0????????? ?????????? 1????????? 0?????????

Cheirolepis 0010002?00 0000?0000? ?0??0????? 0??????0?? 00000000?0

Crassigyrinus 0101011101 11?0?1?1?1 1011?0??00 0?000????? 0021010???

Diabolepis ?????????? ?????????0 0010001?01 0????????? 102????10?

Diplocercides kaeseri?111001100 01?0?1?01? ?0?1010000 1111111111 101?1111??

D. heligenstockiensis 0111001100 01?0?1?01? ???1?10??? 111??????? 101?111???

Dipnorynchus ?????????? ?????????? ?101?01??1 00000????? 102???011?

Dipterus 0101011100 00211??01? ?101001??1 00000????? 102???011?

Elpistostege ?????????? ???1001??? ?????????? 0????????? 0?????????

Eusthenopteron 0111011000 0021000011 1011000000 1111110111 0021010100

Glyptolepis 1101111010 001101?010 0000100110 1111110111 0121010100

Gyroptychius 0101011000 0021000011 101100??00 111111???? 002?0?0100

Holoptychius 1101111010 001101?010 0000100110 11111101?? 0121010100

Howqualepis 0000000000 0000?0000? ?0?000???0 0?0??0?0?? 0000010000

Ichthyostega 0101011101 11?0?1?1?0 110100?000 00001????? 0021010100

Miguashaia 0111001100 01?0?1?01? ?0??0????? 1????????? 101?11???0

Mimia 0000000000 0000?00000 0000000000 000000?000 0000000000

Moythomasia 0000000000 0000?00000 0000000000 000000?000 0000000000

Onychodus 0101002?00 01?101?01? ?0?1000010 111?110??? 0121010??0

Osteolepis 0101011000 002100001? ?0?1?000?0 11111101?? 002?0??100

Panderichthys 0101011100 0021001011 1011?00000 0??????1?? 0021010100

Polypterus ?0?00?1?00 01?0?1?010 ?010?00000 000001?001 0002000100

Porolepis 1101111010 0011000010 000010?110 11111101?1 0121010100

Powichthys ????????10 00???00010 00?0001010 0111101?00 0121010101

Speonesydrion ?????????0 00?11000?? ?101001??? 000?0????? 102????11?

Strepsodus ???1?????? ???10??01? ?????????? 1????????? 0?2???????

Strunius 01?100??00 01?101?01? ?????????? 1????????? 01???????0

Uranolophus ?????????? ?021100010 ?101?01??1 0000?????? 102?????1?

Ventastega 0??101110? ?????????0 110??0??00 ?????????? 002201?100

Youngolepis ???10?10?0 ???1000010 0010001110 0000101100 0121010101

Psarolepis ???000???? ?????????? 000100?010 111?1?1??0 0120010?10

Dicksonosteus 010?0?1?0? ?????????0 ????000?00 0000???000 ????????1?

Ctenacanthus ?1???????? ?????????0 ?????00?00 0000????00 ????????1?

Acanthodes 010?0?1?0? ?00??????0 ????000?00 0000????00 ??????????

_____________________________________________________________________________________

1111111111 1111111111 1111111111 1111111111 111111111

0000000001 1111111112 2222222223 3333333334 444444444

1234567890 1234567890 1234567890 1234567890 123456789

_____________________________________________________________________________________

Acanthostega ????110??1 11?01?0021 11?0111??? 0??1201011 100000111

Allenypterus 01?111?001 11100?11?1 ????00011? 0011111100 1000001?1

Barameda 0110??0??1 ???1110?21 01110????? ?2?????0?? 100000???

Beelarongia ???01????? ???0110?21 110??????? 100??????? 100000???

Cheirolepis 00?00000?0 00000000?0 ???00?0??? 000000???0 100100??1

Crassigyrinus ?????????1 12?01?0021 11??111??? 0????01001 100000111

Diabolepis 0010???101 ?????????? ?????????? ?????????? 100000??1

Diplocercides kaeseri 0101110001 1??01001?? ????0????? ?01111?100 100000111

D. heligenstockiensis 0???11?001 1??01001?? ????0?0??? 001111?100 1000001?1

Dipnorynchus 0010??1111 0????????? ?????????? ?????????? 100000111

Dipterus 0110111111 01101101?? ??11000101 01010?0001 100000111

Elpistostege ?????????? ?????????? ?????????? ?????0100? 100000???

Eusthenopteron 0110110001 1100110021 1100000100 1001111011 100000111

Glyptolepis 1111110001 1110110101 0011000111 0001010010 100000111

Gyroptychiu 0110110001 11001?0??? ????0?01?? 100110101? 100000111

Holoptychius 1111110001 11101100?1 ????0?0??? 00010????? 100000111

Howqualepis 0000000000 ?000000??0 ???00?0??? 00000????? 1001001?1

Ichthyostega ????110??1 12?0110021 11??111??? 0??1211011 100000111

Miguashaia 01?011?001 11?00011?? ????0?01?? 00010??100 100000???

Mimia 0000000000 ?0000000?0 00?00000?0 0000000000 100100111

Moythomasia 0000000000 00000000?0 00?00000?0 0000000000 100100111

Onychodus 0110110??1 0110000101 10??0?0??? ?00110?010 100000111

Osteolepis 0110110001 11001100?? ????0?01?0 1001001010 100000111

Panderichthys 01??110001 1100110021 1?000?1??? 0001201001 100000??1

Polypterus 0110000000 1000100100 00?00000?0 0001110??1 100100111

Porolepis 1110110001 11?0110??? ????0?0??? ?????????? 100000111

Powichthys 0110??0001 11???????? ?????????? ?????????? 100000111

Speonesydrion 00?????111 0????????? ?????????? ?????????? 100000111

Strepsodus 01???????? ?111110021 11010?010? 02011????? 100000??1

Strunius 011011?001 1??00001?? ????0?0??? 00011????0 100000??1

Uranolophus 00101??111 ?1101100?? ????0?0??? 000?01?000 10000011?

Ventastega ?????1???1 1????0?0?? ?????1???? ?????????? 100000??1

Youngolepis 0010110101 1??0?10?11 ?????????? ?????????? 100000111

Psarolepis 0010000001 1???0????0 ?????????? ?????????? 111111111

Dicksonosteus ?0???1???? ??????00?0 00?000???? 0??0?????0 110111000

Ctenacanthus ????01?1?? ??????0??? 00?000???? 0??0?????0 0010?1?00

Acanthodes ????01?1?? ??????0??? 00?0000??? 0??0?????0 011000110

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1

1170


0788

AAAA


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Acanthostega 100?

Allenypterus 00?0

Barameda 10??

Beelarongia ????

Cheirolepis 00?0

Crassigyrinus 10??

Diabolepis ?1?0

Diplocercides kaeseri 00?0

D. heligenstockiensis 00?0

Dipnorynchus ???1

Dipterus ???1

Elpistostege ?0??

Eusthenopteron 1000

Glyptolepis 010

Gyroptychius 10?0

Holoptychius 1010

Howqualepis 00?0

Ichthyostega 100?

Miguashaia 00?0

Mimia 0000

Moythomasia 0000

Onychodus ?00?

Osteolepis 1000

Panderichthys 1000

Polypterus 0000

Porolepis 1010

Powichthys 0000

Speonesydrion ???1

Strepsodus 10??

Strunius ?0?0

Uranolophus ???1

Ventastega 10??

Youngolepis 0000

Psarolepis 0000

Dicksonosteus ??0?

Ctenacanthus ??01

Acanthodes ??01



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