Supplementary Information Phylogeny of the Ichthyopterygia incorporating the recent discoveries from South China CHENG JI,1,2 DA-YONG JIANG,*, 2, 3 RYOSUKE MOTANI,4 OLIVIER RIEPPEL,5 WEI-CHENG HAO,2 and ZUO-YU SUN2 1Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China, [email protected]; 2Laboratory of Orogenic Belt and Crustal Evolution, Ministry of Education; Department of Geology and Geological Museum, Peking University, Beijing 100871, People’s Republic of China, [email protected]; 3State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China; 4Department of Geology, University of California, Davis, California 95616, U.S.A., [email protected]; 5Section of Earth Sciences, Integrative Research Center, The Field Museum, Chicago, Illinois 60605-2496, U.S.A., [email protected] RH: JI ET AL.—PHYLOGENY OF THE ICHTHYOPTERYGIA *Corresponding author INGROUP TAXA SELECTION We aim at conducting a comprehensive phylogengetic analysis incorporating the recent discoveries during the past fifteen years. However, some genera are known from only partial skeleton and many characters are coded as “?” (Table 1S). Therefore, we provide two analyses in the text based on different combinations of ingroup taxa. In the first analysis, all the taxa in Table 1S are included and results in many polytomies. In the second analysis, the taxa which can not be coded for more than 1/3 (54.3 characters) are removed and the topology is highly resolved. Table S1. Comparison on the numbers of characters that could be coded for each taxon. Abbreviations: Mix, Mixosaurus. Pha, Phalarodon. Cym, Cymbospondylus. ‘C’, Callawayia. Sho, Shonisaurus. Qian, Qianichthyosaurus. Lep, Leptonectes. Pla, Platypterygius. Oph, Ophthalmosaurus. Petrolacosaurus 155 Guanlingsaurus 128 Acamptonectes 48 Thadeosaurus 90 Shastasaurus 96 Maiaspondylus 40 Claudiosaurus 141 Sho.popularis 88 Arthropterygius 43 Hovasaurus 116 Sho.sikanniensis 48 Athabascasaurus 61 Hupehsuchus 120 Californosaurus 58 Sveltonectes 117 Utatsusaurus 151 Toretocnemus 80 Brachypterygius 64 Grippia 110 Qian.zhoui 127 Caypullisaurus 83 Gulosaurus 80 Qian.xingyiensis 101 Pla.australis 140 Chaohusaurus 147 Callawayia 126 Pla.americanus 85 Mix.panxianensis 144 Hudsonelpidia 52 Cryopterygius 83 Mix.cornalianus 138 Macgowania 75 Oph.icenicus 156 Mix.kuhnschnyderi 23 Suevoleviathan 134 Oph.natans 110 Pha.atavus 104 Lep.tenuirostris 149 Malawania 40 Pha.fraasi 62 Lep.moorei 97 Chacaicosaurus 37 Pha.callawayi 49 Lep.solei 81 Mollesaurus 37 Cym.piscosus 132 Excalibosaurus 118 Parvinatator 53 Cym.buchseri 62 Eurhinosaurus 145 Leninia 30 Cym.nichollsi 46 Hauffiopteryx 108 Thalattoarchon 41 Xinminosaurus 95 Ichthyosaurus 162 Palvennia 31 Besanosaurus 85 Stenopterygius 161 Sisteronia 20 Guizhouichthyosaurus 137 Temnodontosaurus 159 ‘C’.wolonggangensis 90 Aegirosaurus 114 CHARACTER EVALUATION Most of the characters in Motani (1999) are followed or modified here. We try to avoid the gradually changed and proportional characters since the cladistics analyses require discrete characters. We also adopt most of the characters from Fischer et al. (2013) since it is so far the most complete phylogenetic analysis for the Thunnosauria. Some characters are removed or modified because they either already exist in our old matrix or appear to be inappropriate which will be explained below. Thus, each character is coded within four discrete character states. The followings are the characters that are modified or excluded from the present analysis with a variety of reasons. Motani (1999) char 5: this character describes the posterior extension of premaxilla dorsal process. In the post-Triassic ichthyosaurs, the premaxilla dorsal process is largely reduced and appears shorter than the ventral process, thus, does not separate the nasal from contacting the external naris. In most Triassic ichthyosaurs as Utatsusaurus, Grippia and Guanlingsaurus, the posterior process of premaxilla does not extend far posteriorly and the nasal contacts the external naris at least partially (Fig. 3A; Fig. 4A, F). Cymbospondylus piscosus has a relatively long premaxilla which forms the entire dorsal margin of the external naris, eliminating the nasal from the latter (Fig. 3C; Fig. 4C). However, in Guizhouichthyosaurus, it is quite obvious that the nasal is overlapped by the premaxilla posteriorly and the latter is not completely preserved (Maisch et al., 2006; Fig. 3E; Fig. 4E). Therefore, the premaxilla could have extended farther originally. In other words, this character is easily biased by the preservation especially on large-bodied ichthyosaurs and thus not adopted in this study. Motani (1999) char 15: the exposure of the frontal is related with the posterior extension of the nasal and the medially extension of postfrontal since the frontal is overlapped by the both. In Utatsusaurus, Grippia and Mixosaurus, the nasal does not extend far posteriorly and postfrontal is restricted along the lateral margin of the upper temporal fenestra (Fig. 4A, B). Thus, the frontal is exposed relatively large and the widest position is located on the posterior edge. The Late Triassic ichthyosaurs such as Guizhouichthyosaurus and Guanlingsaurus have a medially enlarged postfrontal and a deep V-shaped nasal frontal suture, leaving the frontal wider posteriorly than anteriorly (Fig. 4E, F; Maisch et al., 2006). Although they are both coded by the same state, the skull patterns are actually different. In Shastasaurus and Ichthyosaurus, the frontal exposure is restricted within the center of the skull roof due to the large postfrontal and the widest position is located anteriorly at the nasal suture (Fig. 4G). In ‘Callawayia’ wolonggangensis, Cymbospndylus piscosus and C. nichollsi, the frontal is exposed mostly lateral to the parietals due to the huge nasal extension and it is difficult to define the widest position (Fig. 4C, D). In Callawayia neoscapularis, Stenopterygius and Platypterygius, the frontal is overlapped by the nasal anteriorly and postfrontal postero-laterally, leaving the widest position in the middle rather than at the nasal or parietal suture. Here, this character is replaced by char 14 in the present analysis because the nasal extension is hard to define accurately. Motani (1999) char 59, 60, 62, 63, 65, 68, 71, 92: Reduction pattern of the shaft in long bones is significant through ichthyopterygian evolution and has been proposed to be related with the swimming ability (Motani, 1997a). In Motani (1999), it was divided into three states: present and complete, notch or largely reduced and absent because notch is proposed to represent a middle state of the shaft reduction. In addition, notch has been reported to be correlated with ontogenetic stages (Caldwell, 1997). However, as a matter of fact, notch occurs more optionally and randomly that it can not be accurately predicted. For example, on three specimens of Guizhouichthyosaurus of similar size, radiale notch occurs on two individuals while distal carpal II and metacarpal II notch occurs on only one individual. Similar phenomenon happens on some post-Triassic groups, too. Moreover, the radius of Shastasaurus clearly shows a notch on the leading edge while the whole element appeared as a flat discoidal element, lacking a shaft, indicating that notched and shaft absent can not be distinctly separated. Another counter example is that the radius of Mixosaurus panxianensis has two notches on the leading edge and this feature is consistent on plenty of specimens. Therefore, the notches of long bones might not be strictly resulted from the shaft reduction. Besides, as the peripheral margins of the epipodial of Toretocnemus and Qianichthyosaurus show an intermediate state between a complete shaft and a notch as Motani (1999) mentioned, it is not easy and objective to separate the two states. Therefore, the shaft of long bone is described by only two states here including: “(0) complete” such as the radius of Utatsusaurus and Grippia and “(1) largely reduced or absent” such as the radius of Shastasaurus and post-Triassic ichthyosaurs. Some characters are proposed based on the new described taxa since the publication of Motani (1999) and Maisch and Matzke (2000) and personal observations on some unpublished specimens from south China. (8) shallow groove anterior to the external naris: (0) absent; (1) present. Anterior to the external naris, a shallow and long groove is present in “Callwayia” wolonggangensis and Guizhouichthyosaurus (Fig. 3D, E). It is much narrower than the external naris and becomes narrower and pointed anteriorly. The length of the groove is about 3 times of that of the external naris. In the holotype of Guizhouichthyosaurus, it is possibly present on the right side of the skull based on the irregular suture anterior to the external naris while it is not so obvious on the left side. However, since this skull is dorsoventrally compressed, its presence is not unambiguous and we tentatively code it as “0/1”. This feature has not been found in other species so far. (18) postfrontal medially extension: (0) not over the anterior margin of upper temporal fenestra; (1) over the anterior margin of upper temporal fenestra. In Grippia, Utatsusaurus and Mixosaurus, the postfrontal locates lateral to the upper temporal fenestra and does not extend medially