advances.sciencemag.org/cgi/content/full/2/6/e1600154/DC1
Supplementary Materials for
A Devonian predatory fish provides insights into the early evolution of modern sarcopterygians
Jing Lu, Min Zhu, Per Erik Ahlberg, Tuo Qiao, You’an Zhu, Wenjin Zhao, Liantao Jia
Published 3 June 2016, Sci. Adv. 2, e1600154 (2016) DOI: 10.1126/sciadv.1600154
The PDF file includes:
Supplementary Materials and Methods fig. S1. The anterior cranial portion of Qingmenodus (IVPP V16003.5). fig. S2. Rendered anterior cranial portion of Qingmenodus (IVPP V16003.5). fig. S3. The posterior cranial portions of Qingmenodus. fig. S4. Rendered posterior cranial portion of Qingmenodus (holotype, IVPP V16003.1) showing the position of the hyomandibula. fig. S5. Tentative restoration of the cranium of Qingmenodus in right lateral view. fig. S6. Rendered brain cavity with the transparent braincase of Qingmenodus in left lateral view. fig. S7. Comparative brain cavity morphology of selected Palaeozoic osteichthyans. fig. S8. Digital restorations of the anterior cranial portion of Qingmenodus. fig. S9. Comparison of the tubule system in selected sarcopterygians. fig. S10. Previously sarcopterygian phylogenic hypotheses showing the different positions of onychodonts. fig. S11. Strict consensus of 845 most parsimonious trees resulting from a modified data set. fig. S12. Phylogenetic placement of Qingmenodus shown in a 50% majority consensus tree of the 845 most parsimonious trees. fig. S13. One selected most parsimonious tree. Supplementary Material and Methods
Specimen collection During 2009-2012 field trips, we collected some new sarcopterygain cranial materials from the type site of Qingmenodus yui (7), including a completely ossified anterior cranial portion (IVPP V16003.5), and a posterior cranial portion (IVPP V16003.6).
These two specimens are assigned to Qingmenodus yui based on the shared ornamentation and comparable size with the holotype (IVPP V16003.1).
Phylogenetic Analyses a. Character list This dataset is adopted from (2, 3, 5, 7, 19, 44, 45). Characters 65, 66, 232-242 are newly added characters.
Dermal bones of skull roof
1 Postrostral: 0. absent (0) 1. postrostral mosaic of small variable bones 2. large median postrostral, with or without accessory bones 3. paried E bones
2 Mesial margin of nasal: 0. not notched 1. notched 3 Number of nasals: 0. many 1. one or two
4 Processus dermintermedius: 0. absent 1. present
5 Position of posterior nostril: 0. external, far from jaw margin 1. external, close to jaw margin 2. palatal
6 Posterior nostril: 0. associated with orbit 1. not associated with orbit
7 Posterior nostril enclosed posteriorly by preorbital or preorbital process of premaxilla: 0. absent 1. present
8 Supraorbital (sensu Cloutier & Ahlberg 1996, including posterior tectal of Jarvik): 0. absent 1. present
9 Number of supraorbitals: 0. one 1. two 2. more than two
10 Supraorbital, preorbital and nasal: 0. unfused 1. fused
11 Contact between parietal and supraorbital: 0. present 1. absent
12 Posterior or posteriormost supraorbital (postfrontal) extends anterior of orbit: 0. yes 1. no
13 Relative size of anterior (or anteriormost) supraorbital (prefrontal, posterior tectal of Jarvik) and posterior (or posteriormost) supraorbital (postfrontal): 0. similar 1. prefrontal much bigger
14 T-shaped dermosphenotic: 0. absent 1. present
15 Intertemporal: 0. present 1. absent
16 Tectal (sensu Cloutier & Ahlberg 1996, not counting the ‘posterior tectal’ of Jarvik): 0. absent 1. present
17 Postspiracular: 0. absent 1. present
18 Anterior margin of parietal: 0. between or in front of orbits 1. slightly posterior to orbits 2. much posterior to orbits
19 Pineal foramen: 0. present 1. absent
20 Pineal eminence (in those taxa with no pineal foramen): 0. absent 1. present
21 Location of pineal foramen/eminence: 0. level with posterior margin of orbits 1. well posterior of orbits 2. level with midway of orbits
22 Parietals surround pineal foramen/eminence: 0. yes 1. no
23 Dermal intracranial joint: 0. absent 1. present
24 Margins of postparietals and parietals participating in dermal intracranial joint: 0. smooth 1. jagged
25 Length of parietal versus postparietal: 0. equal or postparietal longer than Parietal 1. Parietal up to 2 times Postparietal
26 Parietal portion (shield) of skull roof relative to postparietal portion (shield) in length: 0. parietal portion roughly as long as postparietal portion 1. parietal portion much longer than postparietal portion 2. parietal portion much shorter than postparietal portion
27 Postparietal narrowing posteriorly: 0. absent 1. present
28 Length/width index of the postparietal: 0. ≤150 1. 150-300 2. ＞300
29 Complete enclosure of spiracle by bones bearing otic and infraorbital canals: 0. absent 1. present
30 Posterior margin of skull roof: 0. embayed 1. straight or convex
31 Number of marginal bones alongside postparietal: 0. single 1. two or more
32 Extratemporal: 0. absent 1. present
33 Number of extrascapulars: 0. uneven 1. paired
34 Position of orbits: lateral and widely separated (0); dorsal and close together (1).
35 Proportion of skull roof lying anterior to middle of orbits: 0. <50% 1. ≥50%
36 Position of anterior nostril: 0. facial 1. edge of mouth (or marginal) 2. palatal
37 Palatal opening surrounded by premaxilla, maxilla, dermopalatine, and vomer (“choana” sensu stricto): 0. absent 1. present
38 Palatal opening medially enclosed by dermopalatine and vomer (“choana” sensu lato): 0. absent 1. present
39 Number of (anterior) tectals: 0. one 1. two or more
40 B-bone: 0. absent 1. present
41 Paired bones anterior to parietals: 0. absent (0) 1. present (1)
42 Width of ethmoid relative to length from snout tip to posterior margin of parietals: 0. more than 80% 1. 70 - 80% (1) 2. 50 - 70% (2) 3. less than 40%
43 Spiracle: 0. absent-small hole 1. narrow groove 2. wide notch
44 Contact between extratemporal and supratemporal: 0. absent 1. present
45 Posterior margin of tabulars: 0. anterior to posterior margin of postparietals 1. level with posterior margin of postparietals
46 Extrascapular bones: 0. present 1. absent
47 Median extrascapular overlap: 0. median extrascapular overlapped by lateral extrascapulars 1. median extrascapular overlapping lateral extrascapulars 2. median extrascapular abutting lateral extrascapulars
Neurocranium
48 Interorbital space (spectum): 0. broad 1. narrow
49 Internasal pits: 0. undifferentiated or anterior palatal fossa 1. shallow paired pits with strong midline ridge 2. deep pear-shaped pits 3. absent
50 Fenestra ventralis: 0. absent 1. present 2. common ventral fenestra for anterior and posterior nostrils
51 Postorbital process on braincase: 0. present 1. absent
52 Tectum orbitale: 0. narrow 1. extensive
53 Large median opening and several small dorsolateral openings in postnasal wall: 0. absent 1. present
54 Ethmoid articulation for palatoquadrate: 0. placed on postnasal wall 1. majority of facet located anterior to postnasal wall 2. extends posteriorly to the level of N.II
55 Autopalatine fossa bearing unfinished articular surfaces: 0. absent 1. present
56 Eye stalk or unfinished area for similar structure: 0. present 1. absent
57 Postorbital pillar: 0. absent 1. present
58 Basipterygoid process: 0. small knob-like process 1. developed as a broad platform
59 Position of exit of pituitary vein: 0. in front of basipterygoid process 1. dorsal to vertical portion of basipterygoid process 2. posterior to basipterygoid process
60 Unconstricted cranial notochord: 0. absent 1. present
61 Descending process of sphenoid (with its posterior extremity lacking periostegeal lining): 0. absent 1. present
62 Endoskeletal intracranial joint: 0. absent 1. present
63 Orientation of intracranial joint: 0. anteroventrally slanting (posteriorly reclined) 1. vertical or posteroventrally slanting (anterior reclined)
64 Position of intracranial joint or fissure relative to cranial nerves: 0. joint through profundus foramen 1. joint through or behind trigeminal foramen
65 Processus connectens: [New] 0. absent 1. present
66 Processus connectens: [New] 0. knob-like, not well-develped 1. long, well-developed
67 Proportion of neurocranium: 0. ethmosphenoid shorter than or equal in length to otoccipital 1. ethmosphenoid much longer than otoccipital
68 Articulation facet with hyomandibular: 0. single-headed 1. double-headed
69 Position of the lateral commissure: 0. overlying root of N.V 1. posterior to root of N.V
70 Vestibular fontanelles: 0. absent 1. present
71 Accessory fenestration in otic capsule: 0. absent 1. present
72 Attachment for basicranial muscle: 0. anterior to or level with the lateral commissure 1. posterior to the lateral commissure
73 Basioccipital: 0. separated from the otic capsule by cartilage or a persistent fissure 1. sutured or co-mineralised with the otic capsule
74 Enclosed canal for dorsal aorta within basioccipital region: 0. absent 1. present
75 Otoccipital fissure: 0. absent 1. present
76 Basicranial fenestra: 0. absent 1. present
77 Posttemporal fossae: 0. absent 1. present
78 Extent of crista parotica: 0. does not reach posterior margin of tabular 1. reaches posterior margin of tabular
79 Otical process (an outgrowth from the lateral wall of the braincase penetrated by the branches of the r. oticus lateralis): 0. absent 1. present
80 Supraotic cavity proper: 0. absent 1. present
81 Lateral cranial canal: 0. absent 1. present
Cheek region
82 Foramina (similar to infradentary foramina) on cheek bones: 0. absent 1. present.
83 Number of sclerotic plates: 0. four or less 1. five or more
84 Jugal extends anterior to middle of orbit: 0. no 1. yes
85 Lacrimal: 0. not fused with jugal 1. fused with jugal
86 Contact between postorbital and lacrimal: 0. absent 1. present
87 Squamosal: 0. absent 1. present
88 Quadratojugal: 0. present, small 1. present, large 2. absent
89 Preopercular: 0. large, broad 1. large, bar-like 2. small
90 Quadratojugal, squamosal and preopercular fused: 0. no 1. yes
91 Jugal-quadratojugal contact: 0. absent 1. present
92 Contact between most posterior major bone of cheek bearing preopercular canal ('preopercular') and maxilla: 0. present 1. absent
93 Most posterior major bone of cheek bearing preopercular canal ('preopercular') extending forward, close to orbit: 0. absent 1. present
94 Number of cheek bones bearing preopercular canal posterior to jugal: 0. one 1. two
95 Bone bearing both quadratojugal pit-line and preopercular canal: 0. absent 1. present
96 Subsquamosals: 0. absent 1. present
97 Preoperculosubmandibular: 0. absent 1. present
98 Dermohyal: 0. absent 1. present
Palate
99 Vomeral fangs: 0. absent 1. present
100 Vomeral area with grooves and raised areas: 0. absent 1. present
101 Posterior process of vomers: 0. absent 1. present
102 Articulation of vomers: 0. vomers not articulating with each other 1. vomers articulating with each other
103 Position of parasphenoid: 0. beneath sphenethmoid part of endocranium 1. beneath sphenethmoid and otico-occipital part
104 Denticulated field of parasphenoid: 0. without spiracular groove 1. with spiracular groove
105 Ascending process of parasphenoid: 0. absent 1. present
106 Parasphenoid/vomer: 0. not sutured 1. sutured with each other
107 Shape of parasphenoid: 0. lozenge-shaped 1. broad, splint-shaped 2. slender, splint-shaped
108 Parasphenoid denticle field with multifid anterior margin: 0. absent 1. present
109 Parasphenoid denticle field with anteriorly divergent lateral margins: 0. absent 1. present
110 Parasphenoid denticle field: 0. terminates at or anterior to level of foramina for internal carotid arteries 1. extends posterior to foramina for internal carotid arteries
111 Posterior carotid opening in parasphenoid: 0. large 1. small 2. absent
112 Posterior margin of palatoquadrate: 0. sloping forward 1. erect or sloping backward
113 Dentition of palatoquadrate complex: 0. marginal teeth 1. tooth plates
114 Fenestra in palatoquadrate marking position of basal articulation: 0. absent 1. present
115 Articulation of pterygoids: 0. pterygoids not articulating with each other 1. pterygoids articulating with each other
116 Entopterygoid: 0. elongated 1. triangular
117 Proportions of entopterygoid: 0. anterior end level with processus ascendens 1. anterior end considerably anterior to processus ascendens
118 Number of dermopalatines: 0. multiple 1. single
Mandibular arch
119 Subterminal mouth: 0. absent 1. present
120 Premaxilla: 0. absent 1. present
121 Enlarged anterior tooth on premaxilla: 0. absent 1. present
122 Premaxillae with inturned symphysial processes: 0. absent 1. present
123 Premaxilla forming part of orbit: 0. absent 1. present
124 Contact of premaxilla with lacrimal: 0. posteriorly 1. ventrally or postoventrally 2. absent
125 Preorbital process of premaxilla: 0. absent 1. present
126 Maxilla: 0. absent 1. present
127 Posterodorsal process of maxilla: 0. present 1. very weak or absent
128 Posterior expansion of maxilla (maxilla cleaver-shaped): 0. present 1. absent
129 Contribution by maxilla to posterior margin of cheek: 0. present 1. absent
130 Strong ascending flexion of symphysial region of mandible: 0. absent 1. present
131 Large ventromesially directed flange of symphysial region of mandible: 0. absent 1. present
132 Infradentary foramina: 0. always present 1. variable 2. always absent
133 Length of dentary: 0. long 1. short
134 Dentary fang pair: 0. absent 1. present
135 Marginal teeth on dentary: 0. present 1. absent
136 Teeth of dentary: 0. reaching anterior end of dentary 1. not reaching anterior end
137 Splenial: 0. absent 1. present
138 Splenial: 0. not sutured to prearticular 1. sutured to prearticular
139 Postsplenial: 0. present 1. absent
140 Angular and prearticular: 0. separated by ventral exposure of Meckelian bone 1. in contact
141 Raised crest on angular: 0. absent 1. present
142 Surangular: 0. absent 1. present
143 Parasymphysial plate: 0. detachable tooth whorl 1. long with posterior corner, sutured to coronoid, denticulated or with tooth row 2. short, rounded, not sutured to coronoid, denticulated 3. absent
144 Enamel ribs on parasymphysial tooth whorl: 0. absent 1. present
145 Number of coronoids: 0. more than three 1. three
146 Fangs of coronoids (sensu stricto): 0. absent 1. present
147 Marginal denticle band on coronoids: 0. broad band, at least posteriorly 1. narrow band with 2-4 denticle rows 2. single tooth row or absent
148 Coronoid proportions: 0. posterior coronoid same length as middle coronoid, or shorter 1. posterior coronoid significantly longer than middle coronoid
149 Condition of most posterior coronoid: 0. not distinctly differentiated from other coronoids 1. well developed and oriented vertically
150 Teeth radial rows on prearticular: 0. absent 1. present
151 Linear, subparallel ridges of remodeled denticles on dermal bones lining the oral cavity: 0. absent 1. present
152 Prearticular-dentary contact: 0. present 1. absent
153 Anterior mandibular (precoronoid) fossa: 0. absent 1. present
154 Labial pit: 0. absent 1. present
155 Large facet or articular condyle posterior to and in line with glenoid, borne on a retroarticular prominence: 0. absent 1. present
156 Meckelian bone exposed immediately anterior to first coronoid: 0. yes 1. no
Hyoid and branchial arch elements
157 Hyomandibular: 0. long 1. short
158 Foramen in hyomandibular: 0. absent 1. present
159 Endoskeletal ‘urohyal’: 0. absent 1. present
160 ‘Urohyal’ morphology: 0. dorsoventrally compressed and rod-like, may bifurcate posteriorly 1. vertical plate
Opercular and Gular series
161 Opercular: 0. present 1. absent
162 Branchiostegal rays: 0. present 1. absent
163 Number of branchiostegal rays per side: 0. ten or more 1. two to seven 2. one
164 Median gular: 0. present 1. absent
165 Size of median gular: 0. small 1. large
166 Size of lateral gular: 0. lateral gular and brachiostegal rays of similar size 1. lateral gular covering approximately half the intermandibular space
167 Submandibulars: 0. absent 1. present
168 Width of submandibulars: 0. narrow 1. broad
Lateral line system
169 Pore clusters on cosmine: 0. absent 1. present
170 Ethmoid commissure: 0. present 1. absent
171 Ethmoid commissure: 0. passes through body of premaxilla 1. along dorsal suture of premaxilla
172 Position of anterior pit-line: 0. on postparietal 1. on parietal
173 Middle pit-line: 0. on the same lineation as the tabular pit-line 1. not on the same lineation as the tabular pit-line
174 Middle and posterior pit-lines on postparietal: 0. posteriorly situated 1. mesially situated
175 Course of supraorbital canal: 0. between anterior and posterior nostrils 1. anterior to both nostrils
176 Course of supraorbital canal: 0. straight 1. lyre-shaped
177 Posterior end of supraorbital canal: 0. in postparietal 1. in parietal 2. in intertemporal
178 Contact between otic and supraorbital canals: 0. not in contact 1. in contact
179 Contact of supraorbital and infraorbital canals: 0. in contact rostrally 1. not in contact rostrally
180 Otic canal: 0. runs through skull roof 1. follows edge of skull roof
181 Course of otic canal in relation to anterior portion of postparietal: 0. through marginal bones alongside postparietal 1. through postparietal
182 Sensory canal or pit-line associated with maxilla: 0. absent 1. present
183 Jugal canal: 0. present 1. absent
184 Course of mandibular canal: 0. not passing through most posterior infradentary 1. passing through most posterior infradentary
185 Mandibular sensory canal through the lowermost part of the infradentary series with many tubes: 0. absent 1. present
186 Course of mandibular canal: 0. passing through dentary 1. not passing through dentary
187 Anterior pit-line of lower jaw: 0. not developed into enclosed canal 1. developed into enclosed canal linking oral and mandibular canals
188 Middle pit-line of lower jaw: 0. not developed into enclosed canal 1. developed into enclosed oral canal or intermediate morphology
Postcranial skeleton
189 Extracleithrum: 0. absent 1. present
190 Presupracleithrum: 0. absent 1. present
191 Anocleithrum: 0. element developed as postcleithrum 1. element developed as anocleithrum sensu stricto 2. bone absent
192 Dorsal end of cleithrum or dorsal cleithrum: 0. pointed 1. broad and rounded
193 Dorsal cleithrum (AL of the Placodermi), ventral cleithrum (AVL of the Placodermi) and pectoral spine (SP of the Placodermi): 0. not fused 1. fused
194 Paired pectoral spines: 0. absent 1. present
195 Relationship of clavicle to cleithrum: 0. ascending process of clavicle overlapping cleithrum laterally 1. ascending process of clavicle wrapping round anterior edge of cleithrum, overlapping it both laterally and mesially 196 Interclavicle: 0. absent 1. present
197 Triradiate scapulocoracoid: 0. absent 1. present
198 Subscapular foramen/fossa: 0. absent 1. present
199 Coracoid plate: 0. absent 1. present and extends ventromedially
200 Glenoid orientation: 0. posterior and/or ventral orientation 1. lateral component to glenoid orientation
201 Pectoral fin endoskeleton: 0. extends far beyond body wall (fins lobate) 1. barely extends beyond body wall (fins not lobate)
202 Endoskeletal supports in pectoral fin: 0. multiple elements articulating with girdle 1. single element ("humerus") articulating with girdle
203 Pectoral propterygium: 0. absent 1. present
204 Axis of pectoral fin skeleton: 0. no more than 5 axial elements 1. more than 5 axial elements
205 Pectoral fin radials: 0. most axial elements bearing only preaxial radials 1. symmetrical array of preaxial and postaxial radials (archipterygial pectoral fin)
206 Pectoral fin radials: 0. jointed 1. unjointed
207 Dorsal fin: 0. double 1. single
208 Dorsal and anal fins: 0. present 1. absent
209 Median fin spines: 0. absent 1. present
210 Pelvic fin: 0. long (0) 1. short insertion
211 Pelvic fin endoskeleton: 0. extends far beyond body wall (fins lobate) 1. barely extends beyond body wall (fins not lobate)
212 Caudal fin: 0. heterocercal 1. triphycercal 2. diphycercal
213 Relative size of epichordal and hypochordal lobes of caudal fin: 0. epichordal lobe less developed than hypochordal 1. epichordal and hypochordal lobes equally developed 2. epichordal lobe developed than hypochordal
214 Supraneural spines: 0. present 1. absent
215 Well-ossified ribs: 0. absent 1. present
216 Expanded ribs: 0. absent 1. present
Postcranial skeleton
217 Scales: 0. rhombic 1. intermediate between rhombic and round 2. round
218 Scales with interlocking pegs and sockets: 0. absent 1. present
219 Peg on rhombic scale: 0. narrow 1. broad
220 Anterodorsal peg-like process on scale: 0. absent 1. present
221 Epichordal lepidotrichia in caudal fin: 0. absent 1. present
222 Fringing fulcra: 0. absent 1. present as modified distal tips of lepidotrichia 2. present as ‘true’ fringing fulcra
223 Basal scutes on fins: 0. absent 1. present
Histology
224 Dermal bone surface with large openings of pore canals: 0. absent 1. present
225 Ganoine (defined as single or multilayered enamel covering with fine tubercles or very smooth surface, with no pores or very fine pores of vascular cavities): 0. absent 1. present
226 Rostral organ: 0. absent 1. present
227 Ramified tubules in the snout of braincase: 0. absent 1. present
228 Westoll-lines: 0. absent 1. present
229 Acrodin: 0. absent 1. present
230 Plicidentine: 0. absent 1. simple or generalized polyplacodont 2. labyrinthodont 3. dendrodont
231 Syndentine: 0. absent 1. present
Brain features
232 Nasal capsule: [New] 0. round or triangular shaped 1. deep and enlongate
233 Olfactory tracts: [New] 0. short, no longer than forebrain 1. longer than forebrain
234 Anterior angle between olfactory tracts of both sides olfactory tracts: [New] 0. <90° 1. ≥90°
235 Pineal and parapineal organ: [New] 0. side by side situated 1. anterior posterior situated
236 Hypophysial fossa: [New] 0. ventrally extended 1. anteroventrally extended
237 Hypophysial fossa: [New] 0. with posterior lobe 1. without posterior lobe
238 Mesencephalon: [New] 0. developed 1. narrow and short
239 Sacculus of inner ear: [New] 0. not bulging laterally 1. bulging laterally
240 The length of mesencephalon: [New] 0. similar length to diencephalon 1. longer than diencephalon
241 The exit of oculomotor and trochlear nerves: [New] 0. in mesencephalon 1. in diencephalon
242 The top of the labyrinth cavity in lateral view: [New] 0. lower than or about the same level with that of the brain cavity 1. higher than that of the brain cavity
b. Characters and character states defining major clades in fig. S13. Asterisks indicate ambiguous character states resolved using DELTRAN (delayed transformation). Character state is “1”, unless marked otherwise.
Node 1 (Sarcopterygii): 8; 23; 31; 51; 59; 62; 69*; 152*; 172*; 175*; 186*; 225(0) Node 2: 18; 21*; 54(2); 57; 107(0); 110(0); 130; 131 *; 146 *; 147*; 194; 195*; 209 Node 3: 4; 58*; 132(0); 136; 224*; 236* Node 4 (crown sarcopts): 1; 3(0); 7(0); 9; 16; 63*; 65*; 68; 71; 76; 83*; 87; 93(0); 95; 159*; 163(2)*; 176; 177(2); 178; 190(0); 191; 192; 202; 203(0); 210*; 238 Node 5 (Onychodontiformes + Coelacantiformes+Bukkanodus): 28; 144 Node 6 (Onychodontiformes + Coelacantiformes): 11(0)*; 15*; 19*; 52(0)*; 56*; 72*; 88(2)*; 94*; 162*; 164*; 174; 217(2)*; 218(0)*; 220(0)*; 239*; 241* Node 7 (Coelacantiformes): 9(2); 24*; 39*; 49(3); 54; 64; 66*; 109*; 133; 141; 149; 151; 155; 158*; 226 Node 8: 17*; 112*; 116*; 117*; 126(0)*; 139*; 142(0) *; 143(3) *; 157*; 176(0); 189* Node 9: 26*; 31(0); 42(2); 67*; 75(0) *; 77*; 80(0)*; 85*; 180; 181; 212; 213; 234(0)* Node 10 (Onychodontiformes): 26(2)*; 45(0); 122; 124*; 130; 136; 167*; 184(0); 185; 213 Node 11: 27; 28(2); 107(0)*; 110(0)*; 121*; 232*; 237* Node 12: 26*; 49; 50; 58*; 73*; 82*; 88*; 90; 128; 129; 145; 171*; 195*; 198; 219*; 230 Node 13(Rhipidistia): 4; 5*; 32*; 56*; 70; 92*; 99*; 118*; 146*; 158*; 167*; 169*; 196*; 242(0) * Node 14 (Dipnomorpha): 18; 19; 20*; 23(0); 104; 177; 178(0); 227; 233* Node 15: 47*; 82(0); 90(0); 94; 95(0); 97; 204*; 205*; 206(0) *; 214(0) *; 220(0) * Node 16: 5(0); 49(2)*; 53; 96; 111; 136; 163*; 236*; 237* Node 17: 4(0); 15; 23; 31(0); 55; 73(0); 127(0)*; 147*; 153; 171(0); 173; 174; 178;
181; 227(0); 230(3) Node 18 (Dipnoi): 18(2); 40; 49(0)*; 51(0); 62(0)*; 99(0); 113; 133; 143(3); 152(0); 154; 169(0); 228; 230(0); 231 Node 19: 4(0); 5(2); 20(0); 32(0) *; 36(2) *; 41; 50(2); 70(0) *; 76(0) *; 103;112*; 115; 120(0); 126(0) *; 135; 168*; 170; 179*; 187; 188 Node 20 (Tetrapodomorpha): 22(0); 59(0); 143; 153; 220(0) * Node 21: 11(0) *; 38 *; 49(0); 107(2); 124(2) * Node 22: 5(2); 37; 52(0); 71(0) *; 77 *; 78(0) *; 82(0); 89 *; 90(0); 94; 95(0); 111(2) *; 147 *; 171(0); 223 *; 233 *; 235 * Node 23: 42; 43(2); 102 *; 160 * Node 24: 32(0); 67; 101; 106; 117; 138; 143(2); 148 Node 25: 21; 23(0); 34; 36; 41; 42(3); 91; 119; 127(0); 134; 140; 158(0); 165; 199; 200; 208; 212(2)*; 213(2)*; 215; 216; 223(0); 230(2)
Node 26: 13; 15; 35; 84 Node 27: 12; 46*; 89(2)*; 161*; 162*; 206(0)* Supplementary Figures
fig. S1. The anterior cranial portion of Qingmenodus (IVPP V16003.5). In dorsal (A and B, line drawing), ventral (C and D, line drawing) and lateral (C and D, line drawing) views. Scale bars, 2 mm.
fig. S2. Rendered anterior cranial portion of Qingmenodus (IVPP V16003.5). Anterior cranial portion in lateral view with transparent matrix block (A), right lateral view with the matrix block removed (B), posterior view (C), posterior view with the matrix block removed (D). Scale bars, 2 mm.
fig. S3. The posterior cranial portions of Qingmenodus. IVPP V16003.6 in dorsal (A), left lateral (B), and ventral (C and D, line drawing) views. IVPP V16003.1 (holotype) in ventral (E and F, line drawing) view. Scale bars, 2 mm.
fig. S4. Rendered posterior cranial portion of Qingmenodus (holotype, IVPP V16003.1), showing the position of the hyomandibula. In ventral (A, and with transparent braincase B), and lateral (C, and with transparent braincase D) views. Scale bars, 2mm.
fig. S5. Tentative restoration of the cranium of Qingmenodus in right lateral view. (A) Anterior (IVPP V16003.5) and posterior (IVPP V16003.6) cranial portions in lateral view. (B) Two digital cranial parts fitted together by using the perimeter of notochordal facet as reference, using the shape of the notochordal facet as a guide, the laterally compressed anterior part of the anterior cranial part has been restored as well. (C) Line drawing of fitted two digital cranial parts. Not to scale.
fig. S6. Rendered brain cavity with the transparent braincase of Qingmenodus in left lateral view. (A) Digital anterior and posterior cranial endocasts. (B) Two cranial parts fitted together by using the perimeter of notochordal facet as reference. Main color key: blue, cranial cavity; yellow, cranial nerves; light orange, tubule system; and light purple, inner ear cavity. Not to scale.
fig. S7. Comparative brain cavity morphology of selected Palaeozoic osteichthyans. (A) Actinopterygian Mimipiscis. (B) Coelacanth Diplocercides. (C) Onychodont Qingmenodus. (D) Dipnomorph Youngolepis. (E) Lungfish Chirodipterus. (F) Tetrapodomorph Eusthenopteron. Abbreviations: Die, diencephalic cavity; Mes, mesencephalic cavity; II, optic nerve; III, oculomotor nerve; IV, trochlear nerve; V, trigeminal nerve; VII, facial nerve; IX, glossopharyngeus nerve; X, vagus nerve. Color key: green, telencephalic cavity; red, diencephalic cavity; blue, mesencephalic cavity; yellow, rhombencephalic cavity; and orange, labyrinth cavity. Illustrations are modified from (15, 17, 29, 32, 47). Not to scale, anterior is to the left.
fig. S8. Digital restorations of the anterior cranial portion of Qingmenodus. (A-C) Digital endocasts in slightly laterodorsal (A), lateroventral (B) views, and dorsal view with transparent braincase (C). (D) Selected horizontal CT scan slice through the rostral region of endocranial cavity, showing the tubules. Green arrows show the connection between the tubule system and the supraorbital sensory canal; black arrows indicate the superficial ophthalmic nerve entering the cranial cavity which forms the tubule system. Main color key: purple, sensory canal; light orange, tubule system. For other color keys see Fig.3. Not to scale. fig. S9. Comparison of the tubule system in selected sarcopterygians. (A) Digital restoration of the tubule system in Qingmenodus. Reconstructions of the rostral tubuli in Youngoelpis (B), Qingmenodus (C), and Devonian lungfish Griphognathus (D). Illustrations are modified from 36, 38. Not to scale.
fig. S10. Previously sarcopterygian phylogenic hypotheses showing the different position of onychodonts. As sister group of tetrapodomorphs (A) (25), of rhipidistians (B) (43), of stem-sarcopterygian Psarolepis (D) (6), of coelacanths (E) (3, 19), of crown sarcopterygians (F) (5), and uncertain (C) (1).
fig. S11. Strict consensus of 845 most parsimonious trees resulting from a modified data set. The onychodonts excluding Bukkanodus is as the sister group of coelacanths, within the crown sarcopterygians. Bukkanodus is placed as the sister clade of onychodonts plus coelacanths. Numbers at nodes represent Bremer decay indices.
fig. S12. Phylogenetic placement of Qingmenodus shown in a 50% majority consensus tree of the 845 most parsimonious trees.
fig. S13. One selected most parsimonious tree. Tree length = 544; Consistency index = 0.5092; Homoplasy index = 0.4908; Retention index = 0.7488; Rescaled consistency index = 0.3813.