Supplementary information (Zhu et al

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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
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