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SUPP Methods & Results 1 ELECTRONIC SUPPLEMENTARY MATERIAL 2 3 The radiation of cynodonts and the ground plan of 4 mammalian morphological diversity 5 Marcello Ruta1,*, Jennifer Botha-Brink2, Stephen A. Mitchell3 and Michael J. Benton3 6 1 School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK 7 2 Karoo Palaeontology, National Museum, P. O. Box 266, Bloemfontein 9300, South Africa, 8 and Department of Zoology and Entomology, University of the Free State, Bloemfontein 9 9300, South Africa 10 3 School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK 11 * Author for correspondence ([email protected]). 1 11 SUPPLEMENTARY MATERIAL AND METHODS 12 (a) Taxon-character dataset 13 Two cladistic matrices [1,2] provided the foundations for a new, revised, and expanded taxon- 14 character data set that includes all major cynodont clades from Late Permian to Early Jurassic. 15 After checking these matrices for instances of character duplications and conflicting codings, 16 we merged them and consulted additional works [2–15] for further character inclusion and/or 17 coding refinements (Datasets S2, S3, S9, S10). If different authors gave conflicting codings of 18 a character, then the most recent codings were scrutinized and either endorsed or changed as 19 appropriate in light of available data from specimens and/or illustrations. J. B. B. checked the 20 majority of characters against original specimens, where possible. After all relevant data had 21 been scrutinised, taxon descriptions were surveyed to glean additional data: Van Heerden [16] 22 for Nanictosaurus; Crompton [17] for Aleodon; Crompton [18], Savage and Waldman [19], 23 Sues [20] and Luo and Sun [21] for Oligokyphus; Brink [22] for Cynosaurus; Crompton [23] 24 for both Scalenodon angustifrons and ‘Scalenodon’ hirschoni; Abdala and Ribeiro [24] for 25 Santacruzodon; Bonaparte and Barberena [25] for Therioherpeton; Bonaparte [26] and 26 Martinelli and Rougier [9] for Chaliminia; Barberena [27] for Traversodon; Hopson [28] for 27 Gomphodontosuchus; Flynn et al. [29] and Kammerer et al. [10] for Menadon; Bonaparte et 28 al. [3] and Soares et al. [30] for Riograndia; Abdala and Teixeira [31] and Abdala and Smith 29 [32] for Luangwa and Aleodon); Sidor and Hancox [7] for Elliotherium; Liu and Powell [33] 30 for Andescynodon; Reichel et al. [11] for Protuberum; Gow [34] for Diarthrognathus; Sues 31 and Jenkins [35] for Kayentatherium; Gao et al. [12] for Beishanodon; Oliveira et al. [14] for 32 Trucidocynodon. 33 Some taxa require comments. Relative to the data matrices in [1,2], Charassognathus 34 adds to Late Permian and basal cynodonts. Nanictosaurus augments Late Permian taxa and 35 also adds to the sample of epicynodonts in general. Beishanodon, Sinognathus, Cricodon and 2 36 Langbergia add to the diversity of Trirachodontidae. Traversodon, Andescynodon, Dadadon, 37 Santacruzodon, Scalenodontoides, Scalenodon attridgei, Arctotraversodon, Boreogomphodon 38 and Nanogomphodon add to Traversodontidae. These were diverse and successful tetrapods 39 in the Triassic, but were poorly represented in the cladistic matrices in [1,2]. Traversodon is a 40 Ladinian-Carnian traversodontid. Andescynodon is possibly transitional between Olenekian– 41 Anisian and Ladinian–Carnian traversodontids. Scalenodontoides is Rhaetian, and represents 42 the only known record of a South African traversodontid. Menadon and Protuberum are both 43 known from fairly complete specimens; Protuberum displays an unusual morphology relative 44 to other traversodontids. Trucidocynodon was included in our matrix as it is a close relative of 45 Ecteninion. Despite the incompleteness of Therioherpeton, this genus has diagnostic cranial, 46 dental and postcranial (a humerus) features, and belongs to a group not represented in either 47 of the data matrices in [1,2]. Tritylodon and Bienotherium add to the Tritylodontidae. Finally, 48 Riograndia, Chaliminia, Diarthrognathus and Elliotherium are fairly complete members of 49 Tritheledontidae, and cover the geographical range of this clade: Riograndia and Chaliminia 50 are from South America, whilst Diarthrognathus and Elliotherium are from South Africa. 51 52 (b) Stratigraphic assignments 53 The time scale of the Triassic is poorly resolved with very few radiometric dates to calibrate 54 against [3,36–38]. We endeavoured to bin the species as precisely as possible within a time 55 bin (whether that was the lower, middle or upper part of a stage or the stage in total) and date 56 the age of the taxa as being the midpoint of that time bin. The duration and age boundaries of 57 stages were based on the timescale from [40], though modified in agreement with recent work 58 [37] suggesting a longer Norian and shorter Carnian durations [38] than formerly thought. All 59 stratigraphic data can be found in Datasets S1, S11. 60 3 61 (c) Phylogenetic analyses 62 We used identical settings for all maximum parsimony analyses with PAUP* [39] and TNT 63 [40], as follows: heuristic searches with 5000 random stepwise addition sequences, holding a 64 single tree in memory during each step, using a tree bisection-reconnection branch swapping 65 algorithm, and collapsing all tree branches that have minimum length of zero. After this initial 66 run, we applied a new search to all the trees in memory, but with the option of saving multiple 67 trees. These settings were employed in three analyses: 1) analysis with unordered and equally 68 weighted characters; 2) analysis with all characters reweighted using the maximum values of 69 their respective rescaled consistency indices (from the first analysis); 3) analysis with implied 70 weights [41]. We ran implied weights analyses several times, each time increasing the integer 71 value for Goloboff’s K constant of concavity [41], until tree shape became stable (for K = 3). 72 Branch support for the implied weights tree was assessed via 1000 bootstrapping replicates in 73 TNT, with a 50% threshold value for bootstrap support. 74 75 (d) Time-calibrated cynodont phylogeny 76 The branch durations for the tree (i.e. branch lengths in millions of years; Myr) were obtained 77 with methods developed in [42,43]. Below, we supply the tree in a format (i.e. object of class 78 ‘phylo’) that is readable by the ‘R’ ape package [44]. The time-calibrated tree is reproduced in 79 figure S3a. 80 81 #NEXUS 82 83 BEGIN TAXA; 84 DIMENSIONS NTAX = 54; 85 TAXLABELS 86 Charassognathus 87 Dvinia 88 Procynosuchus 89 Cynosaurus 90 Progalesaurus 4 91 Galesaurus 92 Nanictosaurus 93 Thrinaxodon 94 Platycraniellus 95 Lumkuia 96 Ecteninion 97 Aleodon 98 Chiniquodon 99 Probainognathus 100 Trucidocynodon 101 Therioherpeton 102 Riograndia 103 Diarthrognathus 104 Pachygenelus 105 Elliotherium 106 Chaliminia 107 Brasilitherium 108 Brasilodon 109 Morganucodon 110 Sinoconodon 111 Oligokyphus 112 Kayentatherium 113 Bienotherium 114 Tritylodon 115 Cynognathus 116 Diademodon 117 Beishanodon 118 Sinognathus 119 Trirachodon 120 Cricodon 121 Langbergia 122 Andescynodon 123 Pascualgnathus 124 Scalenodonangustifrons 125 Luangwa 126 Traversodon 127 Scalenodonattridgei 128 Scalenodonhirschoni 129 Nanogomphodon 130 Arctotraversodon 131 Boreogomphodon 132 Massetognathus 133 Dadadon 134 Santacruzodon 135 Menadon 136 Gomphodontosuchus 137 Protuberum 138 Scalenodontoides 139 Exaeretodon 140 ; 5 141 END; 142 BEGIN TREES; 143 TRANSLATE 144 1 Charassognathus, 145 2 Dvinia, 146 3 Procynosuchus, 147 4 Cynosaurus, 148 5 Progalesaurus, 149 6 Galesaurus, 150 7 Nanictosaurus, 151 8 Thrinaxodon, 152 9 Platycraniellus, 153 10 Lumkuia, 154 11 Ecteninion, 155 12 Aleodon, 156 13 Chiniquodon, 157 14 Probainognathus, 158 15 Trucidocynodon, 159 16 Therioherpeton, 160 17 Riograndia, 161 18 Diarthrognathus, 162 19 Pachygenelus, 163 20 Elliotherium, 164 21 Chaliminia, 165 22 Brasilitherium, 166 23 Brasilodon, 167 24 Morganucodon, 168 25 Sinoconodon, 169 26 Oligokyphus, 170 27 Kayentatherium, 171 28 Bienotherium, 172 29 Tritylodon, 173 30 Cynognathus, 174 31 Diademodon, 175 32 Beishanodon, 176 33 Sinognathus, 177 34 Trirachodon, 178 35 Cricodon, 179 36 Langbergia, 180 37 Andescynodon, 181 38 Pascualgnathus, 182 39 Scalenodonangustifrons, 183 40 Luangwa, 184 41 Traversodon, 185 42 Scalenodonattridgei, 186 43 Scalenodonhirschoni, 187 44 Nanogomphodon, 188 45 Arctotraversodon, 189 46 Boreogomphodon, 190 47 Massetognathus, 6 191 48 Dadadon, 192 49 Santacruzodon, 193 50 Menadon, 194 51 Gomphodontosuchus, 195 52 Protuberum, 196 53 Scalenodontoides, 197 54 Exaeretodon 198 ; 199 TREE * UNTITLED = [&R] 200 (1:1.0,((2:3.333333333,3:0.3333333333):0.3333333333,(4:1.833333333,((5:1.6,6:1):2.375,(( 201 7:0.4583333333,8:2.458333333):0.4583333333,(9:2.458333333,((10:2.8,(11:18.6,((12:0.2,13 202 :4.2):0.2,(14:4.2,(15:15.46666667,(16:4.733333333,((17:5.911111111,((18:20.5,19:5):10.940 203 74074,(20:9.97037037,21:2.97037037):2.97037037):2.97037037):5.911111111,((22:3.94074 204 0741,23:3.940740741):3.940740741,((24:4.960493827,25:15.96049383):4.960493827,(26:4. 205 960493827,(27:15.80699588,(28:3.653497942,29:3.653497942):3.653497942):3.653497942) 206 :4.960493827):4.960493827):3.940740741):5.911111111):4.733333333):4.733333333):4.2): 207 0.2):0.2):3.838888889,(30:1.819444444,(31:2.455555556,(((32:0.3638888889,33:1.36388888 208 9):0.3638888889,(34:0.3638888889,(35:5.181944444,36:0.1819444444):0.1819444444):0.36 209 38888889):0.3638888889,((37:2.5,38:2.5):3.31875,(39:5.545833333,(40:0.2729166667,(41:7 210 .9546875,((42:1.318229167,(43:0.6591145833,(44:2.329557292,(45:4.414778646,46:4.4147 211 78646):4.414778646):2.329557292):0.6591145833):1.318229167,((47:2.212152778,(48:4.35
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