On-line supplementary information 1
Character list (characters as in Sterli (2008), otherwise explained):
0. NasalA
1. NasalB
2. NasalC
3. PrefrontalA
4. PrefrontalB
5. PrefrontalC
6. PrefrontalD
7. PrefrontalE
8. LacrimalA
9. FrontalA
10. ParietalA
11. ParietalB
12. ParietalC
13. ParietalD
14. ParietalE (NEW): Processus inferior parietalis forming the posterior margin of the foramen nervi trigemini. 0= Absent; 1= Present.
15. JugalA
16. JugalB
17. QuadratojugalA
18. QuadratojugalB
19. QuadratojugalC
20. SquamosalA
21. SquamosalB
22. PostorbitalA
23. SupratemporalA
24. PremaxillaA
25. PremaxillaB
26. PremaxillaC
27. PremaxillaD
28. PremaxillaE
29. VomerA
30. VomerB
31. VomerC
32. VomerD
33. PalatineA
34. QuadrateA
35. QuadrateB+C
36. QuadrateD
37. AntrumpostoticumA
38. QuadrateF:
39. QuadrateG
40. EpipterygoidA
41. PterygoidA
42. PterygoidB
43. PterygoidC
44. PterygoidD
45. PterygoidE
46. PterygoidF
47. PterygoidG
48. PterygoidH
49. PterygoidI
50. PterygoidJ (NEW):Intrapterygoid slit. 0=Absent; 1= Present.
51. SupraoccipitalA
52. SupraoccipitalB
53. ExoccipitalA
54. BasioccipitalA
55. OpisthoticA
56. OpisthoticB
57. OpisthoticC
58. OpisthoticD
59. BasisphenoidA
60. BasisphenoidB
61. HyomandibularnerveA
62. StapedialarteryA
63. StapedialarteryB
64. JugularforaminaA
65. CanaliscaroticumB
66. CanaliscaroticumC (Jamniczky and Russell, 2007): 0= Pattern A; 1=Pattern B; 2= Pattern C.
67. FenestraperilymphaticaA
68. DentaryA
69. Splenial
70. TeethA
71. Uppertemporalfossa
72. CarapaceA
73. CarapaceB
74. CarapaceC
75. NuchalA
76. NuchalB
77. NeuralA
78. PeripheralA
79. PeripheralB
80. CostalA
81. CostalB
82. CostalC
83. CervicalA
84. SupramarginalA
85. VertebralA
86. VertebralB
87. VertebralC
88. PlastronA
89. PlastronB
90. PlastronC
91. EntoplastronA
92. EntoplastronB
93. EntoplastronC
94. EntoplastronD
95. EntoplastronE
96. EpiplastronA
97. HyoplastronA
98. MesoplastronA
99. HypoplastronA
100. XiphiplastronA
101. XiphiplastronB
102. PlastralscutesA
103. PlastralscutesB
104. GularA
105. ExtragularA
106. ExtragularB
107. ExtragularC
108. IntergularA
109. HumeralA
110. PectoralA
111. AbdominalA
112. AnalA
113. InframarginalA
114. CervicalribA
115. CervicalvertebraA
116. CervicalvertebraB
117. CervicalvertebraC
118. CervicalarticulationA
119. CervicalarticulationB
120. CervicalarticulationC
121. CervicalarticulationD
122. CervicalarticulationE
123. CervicalarticulationF
124. CervicalarticulationG
125. CervicalarticulationH
126. DorsalribA:
127. DorsalribB
128. DorsalribC
129. DorsalvertebraA:
130. ChevronA
131. CaudalA
132. CaudalB
133. PectoralgirdleA
134. PectoralgirdleB
135. CleithrumA
136. ScapulaA
137. ScapulaB
138. ScapulaC
139. CoracoidA
140. PelvisA
141. IliumA
142. IliumB
143. IliumC
144. IliumD
145. IschiumA
146. HypoischiumA
147. ManusA
148. ManusB
149. ManusC
150. PesA
151. PesB
Character deleted:
Canalis caroticum A; this character is contained in canalis caroticum B.
Changes to Sterli’s (2008) matrix:
Institutional abbreviations: AMNH, American Museum of Natural History (USA); BMNH, British Museum of Natural History (UK); CUMZ-T, Cambridge University, Museum of Zoology (UK); DCM-G, Dorset County Museum (UK); JM SCHA, Jura Museum (Germany); MACN, Museo Argentino de Ciencias Naturales (Argentina); MH, Naturhistorisches Museum Basel (Switzerland); MHNSR, Museo de Historia Natural de San Rafael (Argentina); MLP, Museo de La Plata (Argentina); MNHN, Muséum National d'Histoire Naturelle(France); MPEF-PV, Museo Paleontólogico Egidio Feruglio, Paleontología Vertebrados (Argentina); MZUSP, Museu de Zoologia da Universidade São Paulo (Brazil); NMS (=SM), Naturmuseum Solothurn (Switzerland); USNM, United States National Museum (USA); YPM, Yale Peobody Museum (USA), ZMB, Zoologie, Universität-Humboldt Museum für Naturkunde (Germany).
Taxa added to Sterli’s (2008) matrix:
Siamochelys pensinsularis: Tong et al. (2002).
Niolamia argentina: MLP 26-40/41/42 and 44.
Elseya latisternun: BMNH 71.9.25.8 and MZUSP 3315.
Chelodina longicollis: MNHN-AC-1911-181, USNM 8894, and USNM 61091.
Chelus fimbriatus: USNM 64154, USNM 117455, MZUSP 2619 and MZUSP 2133.
Chubutemys copelloi: MPEF-PV 1236, 1940-1943.
Trachemys scripta: MACN 30471, MACN 36671, and MACN 36780
Chelonoidis chilensis: MHNSR no number.
Pelodiscus sinensis: Not included in morphological analysis.
Changes to the character coding of some taxa:
Kallokibotion bajazidi(BMNH R4916, BMNH R4921, BMNH R4922, BMNH R4919 (Lectotype), BMNH R4923, BMNH R9382, BMNH R4926, BMNH R4927, BMNH R4931, BMNH R11178, BMNH R5815, BMNH R4920, BMNH R4924, BMNH R4930, BMNH R4917, BMNH R4918, and BMNH R4925).
Nasal C: 1-->?
Parietal C: ?-->0
Jugal A: 1-->?
Squamosal B: 1-->?
Postorbital A: 0-->?
Premaxilla C: 0-->?
Vomer B: 0-->1
QuadrateG: ?-->1
Supraoccipital A: ?-->1
Exoccipital A: 0-->?
Foramen jugulare posterior A: 1-->0
Peripheral A: 1-->?
Supramarginal A: 2-->?
Plastron A: 0-->?
HioplastronA: 1-->?
HipoplastronA: 1-->?
Cervical VertebraeC: ?-->0
Dorsal rib 1: 0-->2
Pectoral girdle A: ?-->1
Scapula B: ?-->0
Coracoides A: ?-->1
Pelvis A: ?-->0
Ilium A: ?-->1
Ilium D: ?-->0
Ischium A: ?-->1
Meiolania platyceps(BMNH R675, BMNH R682, USNM 206, USNM 207, USNM 208, and Gaffney [1983; 1996]).
Parietal C: 0-->-
Foramen jugular A: 1--> 0,1
Mongolochelys efremovi(Sukhanov, 2000)
Parietal C: 0--> ?
Platychelys oberndorferi[NMS 8685 (=SM 55), NMS 8686 (=SM 56), NMS 8687
(=SM 56), NMS 8688 (=SM 56), NMS 8689 (=SM 56), NMS 8690 (=SM 56),
NMS 8691 (=SM 57), NMS 8692 (=SM 58)]
Cervical articulation H: ?-->1
Dorsal rib 1: 1-->0
Chevron A: 1-->?
Notoemys laticentralis[MHNSR without number, de la Fuente and Fernández (1989), Fernández and de la Fuente (1993), Lapparent de Broin et al. (2007)]
Pterygoid A: 1-->?
Pterygoid I: 0-->?
Foramen jugular A: 1-->0
Gular A: ?-->1
Extragular A: ?-->0
Extragular B: ?-->0
Cervical ribs A: ?-->1
Cervical vertebrae A: 0-->1
Cervical articulation D: ?-->0
Manus A: 1-->?
Manus B: 0-->?
Manus C: 0-->?
Pes A: 1-->?
Pes B: ?-->1
Elseya dentata (BMNH 76.5.19.27.0.)
Costal A: 0-->1
Elseya latisternum
Costal A: 0-->1
Chelodina oblonga[BMNH 64.12.22.6. and Burbidge et al. (1974)]
Costal A: 0-->1
Chelonia mydas[ZMB 46557 and Wyneken (2001)]
Parietal C: 0-->2
Foramen Jugular A: 1-->0
Chubutemys copelloi
Parietal C: ?-->1
Foramen Jugular A: 1-->?
Dorsetochelys delairi(DCM-G 23, holotype).
Prefrontal D: 0-->1
Postorbital A: 0-->?
Premaxilla C: 0-->?
Pterygoid I: ?-->1
Basioccipital A: 2-->1
Opisthotic B: 2-->1
Basisphenoid B: 0-->1
Hyomandibular nerve A: 0-->?
Canalis caroticus A: 1-->0
Foramen Jugular A: 1-->0
Pleurosternon bullockii[BMNH 28618, BMNH R3727, BMNH 28433, BMNH R4317, BMNH R1889, BMNH R911 (Holotype), BMNH R3413 y CUMZT1041.]
Parietal A: 0-->1
Pterygoid B: 1-->2
Pterygoid D: 1-->?
Supraoccipital A: 0-->?
Opisthotic C: 2-->1
Hyomandibular nerve A: 0-->?
Foramen Jugular A: 1-->?
Cervical A: 0-->1
HypoplastronA: ?-->1
Cervical vertebrae A: 0-->1
Dorsal rib B: ?-->0
Pelvis A: ?-->0
Ischium A: ?-->1
Glyptops plicatulus[AMNH 336, AMNH 6099 (Holotipo), USNM 5458, YPM
1687, YPM 1784, YPM 6060 and Gaffney (1979)]
Foramen Jugular A: 1-->0
Dinochelys whitei [YPM 6057, YPM 6069 and Gaffney(1979)]
Foramen Jugular A: 1-->?
Neurankylus eximius[USNM 8344 and Gaffney (1972; 1982)]
Foramen Jugular A: 1-->?
Trinitichelys haitti [Gaffney (1972, 1982)]
Foramen Jugular A: 1-->0
Plesiobaena antiqua[Gaffney (1972, 1982) and Brinkman (2003)]
Foramen Jugular A: 1-->0
Boremys pulcra [Gaffney (1972, 1982) and Brinkman and Nicholls (1991)]
Foramen Jugular A: 1-->0
Caudal B: 2-->1
Baena arenosa[USNM 103 (Holotipo), USNM 974, AMNH 5977 and Gaffney (1972,
1982)].
Foramen Jugular A: 1-->0
Chisternon undatum[AMNH 5961, USNM 12839, YPM 3930 and Gaffney (1972, 1982)]
Foramen Jugular A: 1-->0
Caudal B: 2-->1
Portlandemys mcdowelli[BMNH R2914 (Holotype), BMNH R3163, BMNH R3164 and Gaffney (1975a; 1976).]
Quadratojugal C: 0-->?
Supraoccipital A: 1-->?
Supraoccipital B: 0-->?
Opisthotic C: 2-->1
Foramen Jugular A: 1-->0
Plesiochelys etalloni[MH 435, SM 134, SM 136, SM 594 y Gaffney (1975a,
1976)]
Pterygoid H: - -->0
Opisthotic C: 2-->1
Pectoral girdle A: ?-->1
Foramen Jugular A: 1-->0
Solnhofia parsonsi[JM SCHA 70, Gaffney (Gaffney, 1975b) and Joyce (2000)]
Foramen Jugular A: 1-->0
Santanachelys gaffneyi[Hirayama (1998)]
Parietal C: 0-->2
Foramen Jugular A: 1-->?
Hangaiemys hoburensis[Sukhanov y Narmandakh (1974) and Sukhanov (2000)]
Foramen Jugular A: 1-->0
Ordosemys leios[Brinkman and Peng (1993a)]
QuadrateD: 1-->0
Foramen Jugular A: 0-->?
Judithemys sukhanovi[Parham and Hutchison (2003).]
Foramen Jugular A: 1-->?
Sinemys lens[Brinkman and Peng (1993b)]
QuadrateD: 1-->0
Foramen Jugular A: 1-->?
Toxochelys latiremys[AMNH 1042, AMNH 1496, AMNH 1497, Zangerl (1953; 1980)and Nicholls (1988)]
Foramen Jugular A: 1-->0
Caretta caretta[MHNSR without number, ZMB 46511 and Wyneken (2001)]
Parietal C: 0-->2
Foramen Jugular A: 1-->0
Dermochelys coriacea[Wyneken (2001)]
Foramen Jugular A: 1-->0
Sequence alignment
Sequences were compiled from several previous analyses for each partition (see On-line supplementary information 3) and were aligned using ClustalX (Thompson et al., 1997) with the default values of gap opening (10/100) and gap extension (0.1). After alignment, the leading and trailing ends of the sequences with no homologous sequences in other species were deleted.