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