A Taxonomic Reassessment of Piramys Auffenbergi, a Neglected Turtle From

1 Supplementary File S2 for

4 A taxonomic reassessment of Piramys auffenbergi, a neglected turtle

5 from the late Miocene of Piram Island, Gujarat, India

7 Gabriel S. Ferreira, Saswati Bandyopadhyay, Walter G. Joyce 8 correspondece to: Walter G. Joyce, [email protected], [email protected] 9 10

14 This PDF file includes additional information of the phylogenetic analyses

15 1. List of changes to Ferreira et al. (2018)’s matrix

16 2. Strict consensus tree with node numbers

17 3. Bootstrap, Jacknife & Bremer support information

18 4. List of common synapomorphies for Stereogenyina

20 Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

21 1. Changes to Ferreira et al. (2018)’s matrix

22 Char. 5: PF, preorbital skull broad 23 Scoring: Lemurchelys diasphax – 1 > 0 24 Stereogenys cromeri – 1 > 0 25 Shweboemys pilgrimi – 1 > 0 26 Brontochelys gaffneyi – 1 > 0 27 28 Char. 9: FR, interorbital groove 29 Scoring: Mogharemys blackenhorni – 0 > ? 30 Brontochelys gaffneyi – 0 > ? 31 32 Char. 12: FR, prefrontal/frontal 33 Scoring: Bairdemys sanchezi – 1 > 0 34 35 Char. 14: Anteroventral emargination 36 Scoring: Cordichelys antiqua – 1 > 0 37 38 Char. 15: QJ, quadratojugal 39 Scoring: Stereogenys cromeri – ? > 1 40 41 Char. 19: PA, dorsal portion in relation to adductor fossa 42 Scoring: Stereogenys cromeri – 0 > ? 43 44 Char. 23: PA, PA-JU contact 45 Scoring: Shweboemys pilgrimi – 0 > ? 46 47 Char. 25: PA, parietal contacts pterygoid at base of processus trochlearis pterygoidei 48 Scoring: Mogharemys blackenhorni – 0 > 1 49 Brontochelys gaffneyi – 0 > 1 50 Lemurchelys diasphax – 0 > 1 51 Stereogenys cromeri – 0 > 1

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

52 Cordichelys antiqua – 0 > 1 53 Latentemys plowdeni – 0 > 1 54 Bairdemys thalassica – 0 > 1 55 Bairdemys sanchezi – 0 > 1 56 Bairdemys hartsteini – 0 > ? 57 Bairdemys venezuelensis – 0 > ? 58 Shweboemys pilgrimi – 0 > ? 59 60 Char. 26: PA, PA-PT contact in septum orbitotemporale 61 Scoring: Caninemys tridentata – 2 > 0 62 63 Char. 27: PA, interparietal scale 64 Scoring: Bairdemys sanchezi – 1 > ? 65 66 Char. 29: PA, interparietal scale meeting medially 67 Scoring: Bairdemys winklerae – 1 > ? 68 69 Char. 41: PM, pinched snout 70 Scoring: Cordichelys antiqua – 0 > 1 71 Bairdemys hartsteini – 0 > 1 72 73 Char. 43: PM, protrudes cranially in lateral view beyond apertura narium interna dorsal ridge 74 Statement: this character refers to the premaxilla protruding beyond the dorsal ridge (in lateral 75 view) of the apertura narium externa, not interna as originally stated. 76 Scoring: Shweboemys plilgrimi – ? > 1 77 78 Char. 57: MX, triturating surface shape 79 Scoring: Brontochelys gaffneyi – 1 > 2 80 Shweboemys pilgrimi – 1 > 2 81 Stereogenys cromeri – 1 > 2 82 Cordichelys antiqua – 1 > 2

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

83 Latentemys plowdeni – 1 > 2 84 Bairdemys venezuelensis – 1 > 2 85 Bairdemys hartsteini – 1 > 2 86 Bairdemys sanchezi – 1 > 2 87 Bairdemys winklerea – 1 > 2 88 89 Char. 114: EX-QU contact 90 Scoring: Cordichelys antiqua – 1 > 0 91 Latentemys plowdeni – 1 > 0 92 Bairdemys thalassica – 1 > 0 93 Bairdemys venezuelensis – 1 > 0 94 Bairdemys hartsteini – 1 > 0 95 Bairdemys sanchezi – 1 > 0 96 Bairdemys winklerae – 1 > 0 97 98 New character: 246. PM, median notch in upper jaw: 0, notch absent, mx and pm ventral ridge 99 runs anteroventrally, forming an anterior hook (Peltocephalus dumerilianus); 1, notch absent or 100 very shallow, mx and pm ventral ridge runs anteriorly to the midline (Euraxemys essweini); 2, 101 notch present, mx and pm ventral ridge runs anterodorsally to the midline (Podocnemis unifilis) 102

103 104 105

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

106 2. Strict consensus tree with node numbers

Strict consensus of 270 trees (0 taxa excluded)

0 Proganochelys_quenstedti 2 Notoemys_laticentralis 103 1 Platychelys_oberndorferi 7 Emydura_macquarii 8 Myuchelys_latisternum 102 115 113 6 Elseya_dentata 112 5 Pseudemydura_umbrina 9 Acanthochelys_radiolata 116 Platemys_platycephala 104 111 10 117 13 Mesoclemmys_nasuta 119 Phrynops_geoffroanus 118 12 110 11 Phrynops_hilarii 16 Chelus_fimbriatus 120 15 Chelus_colombianus 109 14 Chelodina_colliei Hydromedusa_maximilliani 114 108 121 18 17 Hydromedusa_tectifera 107 4 Prochelidella_cerrobarcinae 106 3 Bonapartemys_bajobarrealis 105 20 Yaminuechelys_gasparinii 122 19 Yaminuechelys_maior Dirqadim_schaefferi 129 27 26 Euraxemys_essweini 128 Laganemys_tenerensis 127 25 24 Araripemys_barretoi 23 Pelomedusa_subrufa 126 124 22 Pelusios_castanoides 123 21 Pelusios_castaneus 28 Sokatra_antitra 125 29 Atolchelys_lepida 34 Sankuchemys_sethnai 33 Kurmademys_kallamedensis 35 Kinkonychelys_rogersi 130 135 30 Cearachelys_placidoi 132 32 Galianemys_whitei 137 134 31 Galianemys_emringeri 58 Nigeremys_gigantea 158 57 Arenila_krebsi 131 155 51 Acleistochelys_maliensis 133 154 52 Azabbaremys_moragjonesi 153 53 Labrostochelys_galkini 56 Rhothonemys_brinkmani 152 157 55 Ummulisani_rutgersensis 156 151 54 Phosphatochelys_tedfordi 140 50 Taphrosphys_congolensis 150 Taphrosphys_ippolitoi 149 49 136 48 Taphrosphys_sulcatus 38 Polysternon_provinciale 138 37 Foxemys_trabanti 36 Foxemys_mechinorum 139 41 Rosasia_soutoi 143 40 Zolhafah_bella 142 39 Araiochelys_hirayamen 47 Chedighaii_barberi 141 148 46 Chedighaii_hutchisoni 146 45 Bothremys_kellyi 147 44 Bothremys_arabicus 145 Bothremys_cooki 144 43 42 Bothremys_maghrebiana 59 Brasilemys_josai 159 60 Hamadachelys_escuilliei 160 61 Portezueloemys_patagonica 63 Cambaremys_langertoni 161 62 Bauruemys_elegans 163 64 Peiropemys_mezzalirai 164 66 Pricemys_caiera 166 162 65 Lapparentemys_vilavilensis 75 Caninemys_tridentata 168 67 Cerrejonemys_wayuunaiki 167 71 Podocnemis_erythrocephala 165 171 68 Podocnemis_vogli 170 72 Podocnemis_expansa 70 Podocnemis_unifilis 172 69 Podocnemis_lewyana Podocnemis_bassleri 169 173 74 73 Podocnemis_sextuberculata 79 Carbonemys_cofrinii 78 UCMP_42008 174 77 Dacquemys_paleomorpha 76 Stupendemys_geographicus 87 Papoulemys_laurenti 175 86 Neochelys_franzeni 85 Neochelys_arenarum 84 Neochelys_fajumensis 177 81 Kenyemys_williamsi Erymnochelys_madagascariensis 178 83 82 Turkanemys_pattersoni 80 Peltocephalus_dumerilianus 176 88 Mogharemys_blackenhorni 179 93 Cordichelys_antiqua 184 94 Latentemys_plowdeni 96 Bairdemys_healeyorum 183 89 Brontochelys_gaffneyi 182 180 90 Lemurchelys_diasphax 185 101 Piramys_auffenbergi 186 92 Stereogenys_cromeri 181 91 Shweboemys_pilgrimi 100 Bairdemys_winklerae 99 Bairdemys_sanchezi 188 98 Bairdemys_hartsteini Bairdemys_venezuelensis 187 97 107 95 Bairdemys_thalassica 108 Figure S2-1. Strict consensus tree from 270 most parsimonious tress with 1134 steps 109

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

110 3. Bootstrap, Jacknife & Bremer support information

GC values, 1000 replicates, cut=1 (tree 1) - Standard Bootstrap

Proganochelys_quenstedti Notoemys_laticentralis 41 Platychelys_oberndorferi Pseudemydura_umbrina 5 Emydura_macquarii 39 Myuchelys_latisternum 62 Elseya_dentata Acanthochelys_radiolata 21 39 Platemys_platycephala 100 21 Mesoclemmys_nasuta 59 Phrynops_geoffroanus 81 15 Phrynops_hilarii Prochelidella_cerrobarcinae Chelus_fimbriatus 85 Chelus_colombianus 2 Chelodina_colliei 73 Hydromedusa_maximilliani 11 99 Hydromedusa_tectifera Bonapartemys_bajobarrealis 19 Yaminuechelys_gasparinii 58 Yaminuechelys_maior Pelomedusa_subrufa 93 Pelusios_castanoides 46 Pelusios_castaneus Laganemys_tenerensis 27 95 Araripemys_barretoi Sokatra_antitra Dirqadim_schaefferi 66 1 Euraxemys_essweini Atolchelys_lepida Sankuchemys_sethnai 15 Kurmademys_kallamedensis 4 Kinkonychelys_rogersi 11 Cearachelys_placidoi 57 Galianemys_whitei 57 Galianemys_emringeri 5 Nigeremys_gigantea 79 Arenila_krebsi 31 30 Azabbaremys_moragjonesi 13 4 Acleistochelys_maliensis 27 Labrostochelys_galkini Rhothonemys_brinkmani 45 55 Ummulisani_rutgersensis 57 21 Phosphatochelys_tedfordi Taphrosphys_congolensis 13 22 Taphrosphys_ippolitoi 23 Taphrosphys_sulcatus 4 Polysternon_provinciale 57 Foxemys_trabanti 3 13 Foxemys_mechinorum Rosasia_soutoi 22 Zolhafah_bella 11 Araiochelys_hirayamen Chedighaii_barberi 38 43 Chedighaii_hutchisoni 54 Bothremys_kellyi 32 Bothremys_arabicus 23 Bothremys_cooki 40 Bothremys_maghrebiana Brasilemys_josai Hamadachelys_escuilliei 5 Cambaremys_langertoni Bauruemys_elegans 7 8 Portezueloemys_patagonica Peiropemys_mezzalirai 6 18 Pricemys_caiera 23 Lapparentemys_vilavilensis Caninemys_tridentata 14 Cerrejonemys_wayuunaiki 25 41 Podocnemis_erythrocephala Podocnemis_vogli 29 Podocnemis_unifilis 8 Podocnemis_lewyana Podocnemis_expansa 18 9 Podocnemis_bassleri 47 Podocnemis_sextuberculata Stupendemys_geographicus Peltocephalus_dumerilianus Carbonemys_cofrinii 2 UCMP_42008 6 27 Dacquemys_paleomorpha Neochelys_franzeni Neochelys_arenarum 3 Neochelys_fajumensis 1 Papoulemys_laurenti 3 13 Kenyemys_williamsi Erymnochelys_madagascariensis 23 Turkanemys_pattersoni Mogharemys_blackenhorni Bairdemys_healeyorum Latentemys_plowdeni 36 Cordichelys_antiqua Brontochelys_gaffneyi Lemurchelys_diasphax 52 3 Piramys_auffenbergi 20 Stereogenys_cromeri 7 Shweboemys_pilgrimi Bairdemys_winklerae 15 Bairdemys_hartsteini Bairdemys_sanchezi 3 Bairdemys_venezuelensis 111 45 Bairdemys_thalassica

112 Figure S2-2. GC Bootstrap value of 1000 replicates (cut = 1)

113

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

Group freqs., 1000 replicates, cut=50 (tree 0) - Standard Bootstrap

Proganochelys_quenstedti Notoemys_laticentralis Platychelys_oberndorferi Mogharemys_blackenhorni Papoulemys_laurenti Neochelys_franzeni Neochelys_arenarum Neochelys_fajumensis Erymnochelys_madagascariensis Turkanemys_pattersoni Kenyemys_williamsi Peltocephalus_dumerilianus Carbonemys_cofrinii UCMP_42008 Dacquemys_paleomorpha Stupendemys_geographicus Caninemys_tridentata Podocnemis_bassleri Podocnemis_sextuberculata Podocnemis_expansa Podocnemis_erythrocephala Podocnemis_unifilis Podocnemis_lewyana Podocnemis_vogli Cerrejonemys_wayuunaiki 100 Pricemys_caiera Lapparentemys_vilavilensis Peiropemys_mezzalirai Cambaremys_langertoni Bauruemys_elegans Portezueloemys_patagonica Hamadachelys_escuilliei Brasilemys_josai Labrostochelys_galkini Azabbaremys_moragjonesi Acleistochelys_maliensis Taphrosphys_congolensis Taphrosphys_ippolitoi Taphrosphys_sulcatus Rosasia_soutoi Zolhafah_bella Araiochelys_hirayamen Kinkonychelys_rogersi Sankuchemys_sethnai Kurmademys_kallamedensis Atolchelys_lepida Sokatra_antitra Chelodina_colliei Platemys_platycephala 74 Acanthochelys_radiolata Emydura_macquarii Pseudemydura_umbrina Prochelidella_cerrobarcinae Bonapartemys_bajobarrealis Nigeremys_gigantea 80 Arenila_krebsi Dirqadim_schaefferi 66 Euraxemys_essweini Laganemys_tenerensis 95 Araripemys_barretoi Yaminuechelys_gasparinii 63 Yaminuechelys_maior Hydromedusa_maximilliani 99 Hydromedusa_tectifera Chelus_fimbriatus 86 Chelus_colombianus Myuchelys_latisternum 64 Elseya_dentata Rhothonemys_brinkmani 57 Ummulisani_rutgersensis 57 Phosphatochelys_tedfordi Polysternon_provinciale 57 Foxemys_trabanti Foxemys_mechinorum Cearachelys_placidoi 58 Galianemys_whitei 60 Galianemys_emringeri Pelomedusa_subrufa 93 Pelusios_castanoides Pelusios_castaneus Mesoclemmys_nasuta 61 Phrynops_geoffroanus 81 Phrynops_hilarii Chedighaii_barberi Chedighaii_hutchisoni Bothremys_kellyi 55 Bothremys_arabicus Bothremys_cooki Bothremys_maghrebiana Piramys_auffenbergi Bairdemys_winklerae Bairdemys_sanchezi Bairdemys_hartsteini Bairdemys_venezuelensis Bairdemys_healeyorum 53 Bairdemys_thalassica Latentemys_plowdeni Cordichelys_antiqua Stereogenys_cromeri Shweboemys_pilgrimi Lemurchelys_diasphax 114 Brontochelys_gaffneyi

115 Figure S2-3. Group frequencies Bootstrap values of 1000 replicates (cut = 50)

116

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

GC values, 1000 replicates, cut=1 (tree 1) - Jacknifing (P=36)

Proganochelys_quenstedti Notoemys_laticentralis 49 Platychelys_oberndorferi Pseudemydura_umbrina 1 Emydura_macquarii 42 Myuchelys_latisternum 71 Elseya_dentata 23 Prochelidella_cerrobarcinae Acanthochelys_radiolata 100 49 Platemys_platycephala 31 Mesoclemmys_nasuta 14 67 Phrynops_geoffroanus 84 Phrynops_hilarii Chelus_fimbriatus 93 Chelus_colombianus 5 Hydromedusa_maximilliani 88 99 Hydromedusa_tectifera 12 Chelodina_colliei 1 Bonapartemys_bajobarrealis 24 Yaminuechelys_gasparinii 60 Yaminuechelys_maior Pelomedusa_subrufa 97 Pelusios_castanoides 46 Pelusios_castaneus 41 Laganemys_tenerensis 98 Araripemys_barretoi Dirqadim_schaefferi 72 5 Euraxemys_essweini Sokatra_antitra Atolchelys_lepida 2 Sankuchemys_sethnai 9 Kurmademys_kallamedensis Kinkonychelys_rogersi 3 13 Cearachelys_placidoi 70 Galianemys_whitei 63 Galianemys_emringeri 11 Nigeremys_gigantea 79 Arenila_krebsi 37 28 Azabbaremys_moragjonesi 14 8 Acleistochelys_maliensis 34 Labrostochelys_galkini Rhothonemys_brinkmani 50 60 Ummulisani_rutgersensis 59 21 Phosphatochelys_tedfordi Taphrosphys_congolensis 19 23 Taphrosphys_ippolitoi 23 Taphrosphys_sulcatus 5 Polysternon_provinciale 68 Foxemys_trabanti Foxemys_mechinorum 17 Rosasia_soutoi 27 Zolhafah_bella 16 Araiochelys_hirayamen Chedighaii_barberi 50 52 Chedighaii_hutchisoni 65 Bothremys_kellyi 40 Bothremys_arabicus 28 Bothremys_cooki 45 Bothremys_maghrebiana Brasilemys_josai Hamadachelys_escuilliei 9 Cambaremys_langertoni Bauruemys_elegans 11 Portezueloemys_patagonica Peiropemys_mezzalirai 10 21 Pricemys_caiera 29 Lapparentemys_vilavilensis Caninemys_tridentata 18 Cerrejonemys_wayuunaiki 38 49 Podocnemis_erythrocephala 33 Podocnemis_vogli 1 Podocnemis_unifilis 8 Podocnemis_lewyana Podocnemis_expansa 28 8 Podocnemis_bassleri 51 Podocnemis_sextuberculata Stupendemys_geographicus Carbonemys_cofrinii 3 UCMP_42008 28 Dacquemys_paleomorpha 10 Neochelys_franzeni Neochelys_arenarum 4 Neochelys_fajumensis 1 Papoulemys_laurenti 4 12 Kenyemys_williamsi Erymnochelys_madagascariensis 25 Turkanemys_pattersoni Peltocephalus_dumerilianus 2 Mogharemys_blackenhorni Latentemys_plowdeni 45 Bairdemys_healeyorum Cordichelys_antiqua 61 Brontochelys_gaffneyi Lemurchelys_diasphax 1 1 Piramys_auffenbergi 14 Stereogenys_cromeri 13 Shweboemys_pilgrimi Bairdemys_winklerae 12 Bairdemys_hartsteini Bairdemys_sanchezi 2 Bairdemys_venezuelensis 117 41 Bairdemys_thalassica

118 Figure S2-4. GC Jacknife values of 1000 replicates (cut = 1)

119

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

Group freqs., 1000 replicates, cut=50 (tree 0) - Jacknifing (P=36)

Proganochelys_quenstedti Notoemys_laticentralis 52 Platychelys_oberndorferi Mogharemys_blackenhorni Papoulemys_laurenti Neochelys_franzeni Neochelys_arenarum Neochelys_fajumensis Erymnochelys_madagascariensis Turkanemys_pattersoni Kenyemys_williamsi Peltocephalus_dumerilianus Carbonemys_cofrinii UCMP_42008 Dacquemys_paleomorpha Stupendemys_geographicus Caninemys_tridentata Pricemys_caiera Lapparentemys_vilavilensis Peiropemys_mezzalirai Cambaremys_langertoni Bauruemys_elegans Portezueloemys_patagonica Hamadachelys_escuilliei Brasilemys_josai 100 Azabbaremys_moragjonesi Acleistochelys_maliensis Rosasia_soutoi Zolhafah_bella Kinkonychelys_rogersi Sankuchemys_sethnai Kurmademys_kallamedensis Atolchelys_lepida Sokatra_antitra Chelodina_colliei Platemys_platycephala Acanthochelys_radiolata Emydura_macquarii Pseudemydura_umbrina Prochelidella_cerrobarcinae Bonapartemys_bajobarrealis Nigeremys_gigantea 80 Arenila_krebsi Dirqadim_schaefferi 72 Euraxemys_essweini Laganemys_tenerensis 98 Araripemys_barretoi Yaminuechelys_gasparinii 63 Yaminuechelys_maior 88 Hydromedusa_maximilliani 99 Hydromedusa_tectifera Chelus_fimbriatus 93 Chelus_colombianus Myuchelys_latisternum 72 Elseya_dentata Polysternon_provinciale 68 Foxemys_trabanti Foxemys_mechinorum Cearachelys_placidoi 70 Galianemys_whitei 65 Galianemys_emringeri Pelomedusa_subrufa 97 Pelusios_castanoides Pelusios_castaneus Mesoclemmys_nasuta 67 Phrynops_geoffroanus 84 Phrynops_hilarii Labrostochelys_galkini Taphrosphys_congolensis 51 Taphrosphys_ippolitoi Taphrosphys_sulcatus Rhothonemys_brinkmani 61 Ummulisani_rutgersensis 59 Phosphatochelys_tedfordi Araiochelys_hirayamen Bothremys_kellyi 51 Bothremys_arabicus 66 Bothremys_cooki Bothremys_maghrebiana Chedighaii_barberi 52 Chedighaii_hutchisoni Podocnemis_expansa Podocnemis_erythrocephala Podocnemis_unifilis 51 Podocnemis_lewyana Podocnemis_vogli Cerrejonemys_wayuunaiki Podocnemis_bassleri 52 Podocnemis_sextuberculata Piramys_auffenbergi Bairdemys_winklerae Bairdemys_sanchezi Bairdemys_hartsteini Bairdemys_venezuelensis Bairdemys_healeyorum 61 Bairdemys_thalassica Latentemys_plowdeni Cordichelys_antiqua Stereogenys_cromeri Shweboemys_pilgrimi Lemurchelys_diasphax 120 Brontochelys_gaffneyi

121 Figure S2-5. Group frequencies Jacknife values for 1000 replicates (cut = 50)

122

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

Bremer supports (from 1659492 trees, cut 0)

Proganochelys_quenstedti Notoemys_laticentralis 4 Platychelys_oberndorferi Emydura_macquarii Myuchelys_latisternum 1 2 Elseya_dentata 1 Pseudemydura_umbrina Acanthochelys_radiolata 10? 2 Platemys_platycephala 1 2 Mesoclemmys_nasuta 3 Phrynops_geoffroanus 1 2 Phrynops_hilarii Chelus_fimbriatus 5 Chelus_colombianus 1 Chelodina_colliei 6 1 Hydromedusa_maximilliani 7 Hydromedusa_tectifera 1 Prochelidella_cerrobarcinae 1 Bonapartemys_bajobarrealis 3 Yaminuechelys_gasparinii 3 Yaminuechelys_maior Dirqadim_schaefferi 4 Euraxemys_essweini 1 Laganemys_tenerensis 9 Araripemys_barretoi Pelomedusa_subrufa 3 7 Pelusios_castanoides 2 Pelusios_castaneus Sokatra_antitra 1 Atolchelys_lepida Sankuchemys_sethnai Kurmademys_kallamedensis Kinkonychelys_rogersi 1 1 Cearachelys_placidoi 3 Galianemys_whitei 1 1 Galianemys_emringeri Nigeremys_gigantea 3 Arenila_krebsi 1 3 Acleistochelys_maliensis 1 1 Azabbaremys_moragjonesi 1 Labrostochelys_galkini Rhothonemys_brinkmani 3 2 Ummulisani_rutgersensis 1 1 Phosphatochelys_tedfordi 2 Taphrosphys_congolensis 1 Taphrosphys_ippolitoi 1 1 Taphrosphys_sulcatus Polysternon_provinciale 3 Foxemys_trabanti Foxemys_mechinorum 1 Rosasia_soutoi 1 Zolhafah_bella 1 Araiochelys_hirayamen Chedighaii_barberi 1 2 Chedighaii_hutchisoni 3 Bothremys_kellyi 2 Bothremys_arabicus 1 Bothremys_cooki 1 Bothremys_maghrebiana Brasilemys_josai 1 Hamadachelys_escuilliei 1 Portezueloemys_patagonica Cambaremys_langertoni 1 Bauruemys_elegans 1 Peiropemys_mezzalirai 1 Pricemys_caiera 1 1 Lapparentemys_vilavilensis Caninemys_tridentata 1 Cerrejonemys_wayuunaiki Podocnemis_erythrocephala 2 2 1 Podocnemis_vogli 1 Podocnemis_expansa Podocnemis_unifilis 1 Podocnemis_lewyana 2 Podocnemis_bassleri 1 Podocnemis_sextuberculata Carbonemys_cofrinii UCMP_42008 1 Dacquemys_paleomorpha Stupendemys_geographicus Papoulemys_laurenti 1 Neochelys_franzeni Neochelys_arenarum Neochelys_fajumensis 1 Kenyemys_williamsi Erymnochelys_madagascariensis 1 Turkanemys_pattersoni Peltocephalus_dumerilianus 1 Mogharemys_blackenhorni 1 Cordichelys_antiqua 2 Latentemys_plowdeni Bairdemys_healeyorum 1 Brontochelys_gaffneyi Lemurchelys_diasphax 1 1 1 Piramys_auffenbergi 1 Stereogenys_cromeri 1 Shweboemys_pilgrimi Bairdemys_winklerae Bairdemys_sanchezi 1 Bairdemys_hartsteini Bairdemys_venezuelensis 123 1 Bairdemys_thalassica 124 Figure S2-6. Bremer support values using TBR from existing trees retaining suboptimal trees by 125 10 steps 126

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

127 4. List of common synapomorphies for Stereogenyina

128 Mogharemys blackenhorni: 159 Char. 182: 1 --> 2 129 All trees: 160 Char. 192: 1 --> 0 130 Char. 53: 0 --> 1 161 Char. 205: 0 --> 1 131 Char. 113: 0 --> 1 162 Some trees: 132 Char. 117: 1 --> 0 163 Char. 233: 1 --> 0 133 164 134 Brontochelys gaffneyi: 165 Latentemys plowdeni: 135 All trees: 166 All trees: 136 No autapomorphies: 167 Char. 40: 1 --> 0 137 168 Char. 245: 1 --> 2 138 Lemurchelys diasphax: 169 139 All trees: 170 Bairdemys thalassica: 140 Char. 110: 1 --> 0 171 All trees: 141 172 Char. 102: 0 --> 1 142 Shweboemys pilgrimi: 173 143 All trees: 174 Bairdemys healeyorum: 144 No autapomorphies: 175 All trees: 145 176 Char. 180: 0 --> 1 146 Stereogenys cromeri: 177 Char. 241: 1 --> 0 147 All trees: 178 148 Char. 129: 1 --> 2 179 Bairdemys venezuelensis: 149 Some trees: 180 All trees: 150 Char. 42: 1 --> 0 181 No autapomorphies: 151 182 152 Cordichelys antiqua: 183 Bairdemys hartsteini: 153 All trees: 184 Some trees: 154 Char. 8: 0 --> 1 185 Char. 124: 1 --> 0 155 Char. 32: 1 --> 0 186 156 Char. 76: 0 --> 1 187 Bairdemys sanchezi: 157 Char. 169: 0 --> 1 188 All trees: 158 Char. 181: 2 --> 1 189 Char. 17: 1 --> 2

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

190 Char. 110: 1 --> 0 223 All trees: 191 Some trees: 224 Char. 88: 0 --> 1 192 Char. 11: 1 --> 0 225 193 Char. 18: 0 --> 1 226 Node 183: 194 Char. 40: 1 --> 0 227 All trees: 195 Char. 58: 1 --> 0 228 Char. 90: 0 --> 1 196 Char. 129: 1 --> 2 229 197 230 Node 184: 198 Bairdemys winklerae: 231 All trees: 199 Some trees: 232 Char. 54: 1 --> 0 200 Char. 18: 0 --> 1 233 Char. 55: 1 --> 2 201 234 Char. 69: 0 --> 1 202 Piramys auffenbergi: 235 Char. 74: 1 --> 2 203 All trees: 236 Char. 75: 0 --> 1 204 Char. 8: 0 --> 1 237 Char. 89: 0 --> 1 205 Some trees: 238 Char. 127: 0 --> 1 206 Char. 119: 0 --> 1 239 207 240 Node 185: 208 Node 179: 241 All trees: 209 All trees: 242 Char. 76: 0 --> 1 210 Char. 73: 0 --> 1 243 211 Char. 78: 0 --> 1 244 Node 186: 212 Char. 110: 0 --> 1 245 Some trees: 213 246 Char. 32: 1 --> 0 214 Node 180: 247 Char. 77: 0 --> 2 215 All trees: 248 Char. 79: 0 --> 1 216 Char. 53: 0 --> 1 249 Char. 114: 1 --> 2 217 250 Char. 245: 1 --> 2 218 Node 181: 251 219 All trees: 252 Node 187: 220 Char. 140: 1 --> 0 253 All trees: 221 254 Char. 77: 0 --> 1 222 Node 182: 255 Char. 87: 1 --> 0

Taxonomic reassessment of Piramys auffenbergi: Supplementary File S2

256 Some trees: 257 Char. 129: 1 --> 2 258 259 Node 188: 260 All trees: 261 Char. 34: 0 --> 1 262 Char. 35: 0 --> 1 263 Some trees: 264 Char. 11: 0 --> 1 265 Char. 58: 0 --> 1 266 Char. 70: 12 --> 0 267 Char. 124: 0 --> 1