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1 1 Appendix S1: Complete List of Characters And 1 1 Appendix S1: Complete list of characters and modifications to the data matrix of RC07, with 2 reports of new observations of specimens. 3 The names, the abbreviations and the order of all characters and their states are 4 unchanged from RC07 unless a change is explained. We renumbered the characters we did 5 not delete from 1 to 277, so the character numbers do not match those of RC07. However, 6 merged characters retain the abbreviations of all their components: PREMAX 1-2-3 (our 7 character 1) consists of the characters PREMAX 1, PREMAX 2 and PREMAX 3 of RC07, 8 while MAX 5/PAL 5 (our ch. 22) is assembled from MAX 5 and PAL 5 of RC07. We did not 9 add any characters, except for splitting state 1 of INT FEN 1 into the new state 1 of INT FEN 10 1 (ch. 84) and states 1 and 2 of the new character MED ROS 1 (ch. 85), undoing the merger 11 of PIN FOR 1 and PIN FOR 2 (ch. 91 and 92) and splitting state 0 of TEETH 3 into the new 12 state 0 of TEETH 3 (ch. 183) and the entire new character TEETH 10 (ch. 190). A few 13 characters have additional states or are recoded in other ways. Deleted characters are retained 14 here, together with the reasons why we deleted them and the changes we made to their scores. 15 All multistate characters mention in their names whether they are ordered, unordered, 16 or treated according to a stepmatrix. 17 Taxa are by default mentioned in the same order as in the matrix, at least within the 18 same paragraph. 19 In the interest of making our scoring decisions transparent, the taxa we have added as 20 separate OTUs are mentioned in cases where their scores could be controversial or, of course, 21 when we report previously unknown scores for them based on pers. obs. of specimens. Their 22 names are preceded by an asterisk; the names of taxa that are not included (but mentioned for 23 comparison) are marked with two asterisks. 24 Similarly, scores we have decided not to change are mentioned in cases where they 25 could be controversial. Lack of mention implies lack of change from RC07. 26 “Broiliellus” is B. brevis throughout; other species, including the type species B. 27 texensis, were not considered (as explained in Material and methods: Treatment of OTUs: 28 Taxa added as parts of existing OTUs). 29 30 1. PREMAX 1-2-3: Caudodorsal process of premaxilla: broad, low, indistinct (0); alary 31 process (vaguely triangular, not occupying entire available mediolateral width at its 32 base) (1); moderately tall, vaguely rectangular, or acutely triangular but occupying the 33 entire mediolateral width between the nares and the median suture at its base (2); 34 narrow and long, along the sagittal plane or parasagittal (3) (unordered). Within state 3, 35 the mediolateral position of the process is not considered, because it probably depends on the 36 width of the premaxilla. 37 This character changes states from 0 to 1 in the ontogeny of Apateon gracilis (Schoch 38 & Fröbisch, 2006); we have tried to take this into account when scoring OTUs known only 39 from immature or paedomorphic individuals. 40 RC07 treated this character complex as three separate characters: PREMAX 1, “Pre- 41 maxillary alary process: absent (0); present (1)”; PREMAX 2, “Premaxilla alary process shor- 42 ter than wide (0) or as long as/longer than wide (1)”; and PREMAX 3, “Premaxilla alary 43 process less than (0) or at least one-third as wide as premaxilla (1)”. Not only are PREMAX 2 44 and PREMAX 3 inapplicable when PREMAX 1 has state 0; they do not (even together) cover 45 the diversity of shapes of the contact between premaxilla and nasal seen in the taxon sample. 46 Accordingly, we have replaced all three characters by ch. 26 of Marjanović & Laurin (2009), 47 itself based on ch. 2 of Marjanović & Laurin (2008) and the work of Good & Wake (1992). 48 Crassigyrinus and Microbrachis were scored for PREMAX 2 and PREMAX 3 by 49 RC07 in spite of being also scored PREMAX 1(0), which, as mentioned, made PREMAX 2 1 2 50 and PREMAX 3 inapplicable. Some OTUs were scored for the latter two characters in spite of 51 being also scored PREMAX 1(?), which had the same effect. 52 State 0 occurs in Eusthenopteron (Jarvik, 1967; Brazeau & Ahlberg, 2006), 53 Panderichthys (Vorobyeva & Schultze, 1991), Ventastega (Ahlberg et al., 2008), 54 Acanthostega (Clack, 2007), Ichthyostega (Clack & Milner, 2015: fig. 8), Whatcheeria 55 (Lombard & Bolt, 1995), Baphetes and Megalocephalus (Beaumont, 1977), Eucritta (Clack, 56 2001 – it looks like 2 in the reconstruction, but the photo strongly suggests the pieces of bone 57 in question are median rostrals rather than processes of the premaxilla), Chenoprosopus 58 (Langston, 1953), Cochleosaurus (Sequeira, 2004), Neldasaurus (Chase, 1965), Caerorhachis 59 (Ruta, Milner & Coates, 2002 – though 1 and 2 would also be more or less defensible scores), 60 Eoherpeton (Smithson, 1985, though this is somewhat arguable), Proterogyrinus (Holmes, 61 1984), Archeria (Holmes, 1989), Discosauriscus (Klembara & Ruta, 2005a), Keraterpeton, 62 Batrachiderpeton, Ptyonius and Sauropleura (Bossy & Milner, 1998), Ariekanerpeton 63 (Laurin, 1996b; Klembara & Ruta, 2005a) and Utegenia (Laurin, 1996c; Klembara & Ruta, 64 2004a). We have further assigned state 0 to the frogs Notobatrachus (Báez & Nicoli, 2004), 65 Vieraella (Báez & Basso, 1996) and *Liaobatrachus (Dong et al., 2013): their so-called alary 66 processes are entirely ventral to the nares and are laterally bordered by a neomorphic fenestra 67 that is more or less confluent with the naris on the same side. 68 Colosteus and Greererpeton are here tentatively scored 1 (Smithson, 1982; Hook, 69 1983; see Bolt & Lombard, 2010, for grounds for caution). State 1 further occurs in Isodectes 70 (Sequeira, 1998), Trimerorhachis (Schoch & Milner, 2013), Balanerpeton (Milner & 71 Sequeira, 1994), Dendrerpetidae (Holmes, Carroll & Reisz, 1998), Eryops, Acheloma (Polley 72 & Reisz, 2011 – although it is arguably a special case), Ecolsonia (Berman, Reisz & Eberth, 73 1985), Amphibamus (Schoch, 2001), Doleserpeton (Bolt, 1969; Sigurdsen & Bolt, 2010), 74 Platyrhinops (Clack & Milner, 2010), Micromelerpeton (arguably borderline to state 3: 75 Schoch, 2009), Apateon (Schoch & Fröbisch, 2006), Karaurus (Ivachnenko, 1978: fig. 1; D. 76 M. and M. L., pers. obs. of unnumbered MNHN cast of PIN 2585/2), Dolichopareias 77 (Andrews & Carroll, 1991), Capetus (Sequeira & Milner, 1993) and, perhaps surprisingly, 78 *Utaherpeton (Carroll, Bybee & Tidwell, 1991: fig. 6.1, 7). 79 State 2 occurs in Tulerpeton (as far as can be told from the isolated premaxilla + 80 vomer; Lebedev & Clack, 1993), Crassigyrinus (Clack, 1998), Albanerpetidae, Eocaecilia 81 (Jenkins, Walsh & Carroll, 2007), Pholiderpeton attheyi (Panchen, 1972), Anthracosaurus 82 (Clack, 1987a), Pholiderpeton scutigerum (Clack, 1987b), Bruktererpeton (Boy & Bandel, 83 1973), Gephyrostegus (Carroll, 1970; Klembara et al., 2014), Seymouria (Laurin, 1996a; see 84 Marjanović & Laurin [2009: Electronic Supplementary Material 1] for discussion), Capto- 85 rhinus (Fox & Bowman, 1966; Heaton, 1979), Petrolacosaurus (Reisz, 1981), Westlothiana 86 (Smithson et al., 1994), Batropetes (Carroll, 1991; Glienke, 2013), Tuditanus, Pantylus, Asa- 87 phestera, Saxonerpeton, Hapsidopareion, Micraroter, Pelodosotis, Cardiocephalus, Hylople- 88 sion and Odonterpeton (CG78), Rhynchonkos (CG78; Szostakiwskyj, Pardo & Anderson, 89 2015), Microbrachis (Vallin & Laurin, 2004), Stegotretus (Berman, Eberth & Brinkman, 90 1988), Diceratosaurus, Diplocaulus, Diploceraspis, Scincosaurus, Adelogyrinus, Silvanerpe- 91 ton (Ruta & Clack, 2006) and Tseajaia (Moss, 1972). 92 State 3 occurs in Phonerpeton (Dilkes, 1990: fig. 3), Eoscopus (Daly, 1994), Valdo- 93 triton (Evans & Milner, 1996), Diadectes (Berman, Sumida & Martens, 1998), Limnoscelis 94 (Reisz, 2007; Berman, Reisz & Scott, 2010), Lethiscus (Pardo et al., 2017) and Orobates 95 (Berman et al., 2004). 96 Unknown (but not scored as such by RC07) in Edops (Romer & Witter, 1942 – the 97 area is reconstructed in MCZ 1378: D. M., pers. obs.), Leptorophus and Schoenfelderpeton 98 (Boy, 1986, 1987), Triadobatrachus (Roček & Rage, 2000), Solenodonsaurus (Laurin & 99 Reisz, 1999), Kotlassia (Bulanov, 2003), Paleothyris (Carroll, 1969b), Adelospondylus 2 3 100 (Andrews & Carroll, 1991), Urocordylus (Bossy & Milner, 1998), Leptoropha & Microphon 101 (Bulanov, 2003 – known to be 0 in juvenile skulls, but this could be ontogenetic), Ossinodus 102 (Warren, 2007), Pederpes (Clack & Finney, 2005); also unknown in *Gerobatrachus 103 (Marjanović & Laurin, 2009: Electronic Supplementary Material 1). 104 Euryodus is polymorphic, possessing states 0 and 2 (CG78). 105 Brachydectes has state 1 or 2 (Wellstead, 1991; Pardo & Anderson, 2016). 106 Oestocephalus (specimen drawings in Carroll, 1998a) and Phlegethontia (Anderson, 107 2007a) have state 2 or 3. 108 *Acanthostomatops is polymorphic, in at least one case (Witzmann & Schoch, 2006a: 109 fig. 3D) showing states 1 and 2 on different sides of the same individual. 110 States 1 and 3 occur in “large adults” of *Glanochthon (Schoch & Witzmann, 2009b: 111 fig. 2). 112 The premaxillae of *Quasicaecilia are unknown, but the nasals make state 3 113 impossible (Pardo, Szostakiwskyj & Anderson, 2015); we have thus scored state 0, 1 or 2. 114 115 2. PREMAX 4: Premaxilla with flat, expanded anteromedial dorsal surface and 116 elongated along its lateral margin but not along its medial margin, when observed in 117 dorsal aspect: absent (0); present (1). This character is a case of non-additive binary coding; 118 it is likely that dividing state 0 (which is defined only as everything that is not state 1) into 119 several states would reveal further phylogenetic signal. 120 State 0 is present in Ventastega (Ahlberg, Lukševičs & Lebedev, 1994). We have kept 121 it for Acanthostega, Ichthyostega and the colosteids because the anteromedial surface is 122 probably not “expanded”, although the lateral margin is much longer than the medial one 123 (Clack, 2007; Bolt & Lombard, 2010; Porro, Rayfield & Clack, 2015; Clack & Milner, 2015); 124 the same holds for *Elginerpeton (Ahlberg, 1995).
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