APPENDIX 1.
Changes to character scores
Changes to OTUs
Axestemys infernalis, supplement scoring with specimen MAB13742
Changes to scores
Axestemys infernalis
Character 31 (1 -> 1&2)
Apertura narium externum is dorsolaterally excavated in some specimens, especially in DMNH 130951
Character 44 (1 -> 2)
Premaxilla unossified in specimen MAB13742
Character 99 (? -> 2)
Observed in specimen MAB13742
Character 33
Likely character states are swapped in character 33. Absence (state 1) in outgroup Adocus (e.g., Meylan and Gaffney 1989), that is correct. Presence (state 2) correctly coded in Carretochelys insculpta (e.g., Walther 1922; Joyce 2014). But in remaining extant taxa, the coding is swapped. Absence of basisphenoid-palatine contact is diagnostic among extant trionychids for Rafetus euphraticus (Meylan 1987), but in the matrix of Evers et al. (2023) is only extant taxon coded with presence (state 2).
Cyclanorbis elegans
Character 33 (1 -> 2)
Cyclanorbis senegalensis
Character 33 (1 -> 2)
Cycloderma aubryi
Character 33 (1 -> 2)
Cycloderma frenatum
Character 33 (1 -> 2)
Lissemys punctata
Character 33 (1 -> 2)
Trionyx triunguis
Character 33 (1 -> 2)
Chitra indica
Character 33 (1 -> 2)
Pelochelys bibroni
Character 33 (1 -> 2)
Rafetus euphraticus
Character 33 (2 -> 1)
Apalone ferox
Character 33 (1 -> 2)
Apalone spinifera
Character 33 (1 -> 2)
Apalone mutica
Character 33 (1 -> 2)
Dogania subplanus
Character 33 (1 -> 2)
Nilssonia formosus
Character 33 (1 -> 2)
Nilssonia hurum
Character 33 (1 -> 2)
Nilssonia gangetica
Character 33 (1 -> 2)
Amyda cartilaginea
Character 33 (1 -> 2)
Palea steindachneri
Character 33 (1 -> 2)
Pelodiscus sinensis
Character 33 (1 -> 2)
Gobiapalone orlovi
Character 33 (1 -> 2)
Presence observed in MPC 25/160 (Danilov et al. 2014)
REFERENCES
Danilov, I.G., Hirayama, R., Sukhanov, V.B., Suzuki, S., Watabe, M., and Vitek, N.S. 2014. Cretaceous soft-shelled turtles (Trionychidae) of Mongolia: new diversity, records and a revision. Journal of Systematic Palaeontology, 12(7):799–832.
https://doi.org/10.1080/14772019.2013.847870
Evers, S.W., Chapelle, K.E.J., and Joyce, W.G. 2023. Cranial and mandibular anatomy of Plastomenus thomasii and a new time-tree of trionychid evolution. Swiss Journal of Palaeontology, 142:1–40.
https://doi.org/10.1186/s13358-023-00267-5
Joyce WG. 2014. A review of the fossil record of turtles of the clade Pan- Carettochelys. Bulletin of the Peabody Museum of Natural History 55: 3-33
Meylan, P.A. 1987. The phylogenetic relationships of soft-shelled turtles (family Trionychidae). Bulletin of the American Museum of Natural History, 186: 1–101.
Meylan, P.A. and Gaffney, E.S. 1989. The skeletal morphology of the Cretaceous cryptodiran turtle, Adocus, and the relationships of the Trionychoidea. American Museum Novitates, 2941:1–60
Walther, W.G. 1922. Die Neu-Guinea-Schildkröte Carettochelys insculpta Ramsay: Dissertation zur Erlangung der Doktorwürde bei der Philosophischen Fakultät der Hessischen Ludwigs-Universität zu Giessen
APPENDIX 2.
List of characters
Updates to character matrix (Evers et al. 2023)
Reworded characters
Character 44. Premaxilla absent. 1: no, 2: occasionally, 3: usually
to:
Character 44. Premaxilla ossified. 1: yes, 2: usually, 3: occasionally
Character 100 of Evers et al. (2023) was not transferred to actual character matrix.
Two characters were labelled as Character 111
Modified character list
Character 1: Width-length of nuchal bone. 1 = less than 2; 2 = greater than 2; 3 = greater than 3; 4 = greater than 4.
Character 2: Anterior and posterior costiform processes of nuchal bone united. 1 = no; 2 = yes.
Character 3: Position of anterior edge of first body vertebra relative to nuchal bone. 1 = posterior edge of nuchal; 2 = middle of nuchal; 3 = anterior edge of nuchal.
Character 4: First and second neurals fused. 1 = no; 2 = yes.
Character 5: Total number of peripherals. 1 = 22; 2 = 20; 3 = 14-18; 4 = 0.
Character 6: Prenuchal bone. 1 = absent; 2 = present.
Character 7: Size of eighth pleurals. 1 = large; 2 = reduced or absent.
Character 8: Epiplastral callosity. 0 = absent; 1 = present.
Character 9: Entoplastral callosity. 0 = absent; 1 = present.
Character 10: Hyo/Hypoplastral callosity. 0 = absent; 1 = present.
Character 11: Xiphiplastral callosity. 0 = absent; 1 = present.
Character 12: Supernumerary callosities. 0 = absent; 1 = present.
Character 13: Hyoplastra and hypoplastra fuse just after hatching. 1 = no; 2 = yes.
Character 14: Extended midline contact of xiphiplastral callosities. 1 = absent; 2 = present along much of the midline.
Character 15: Hypo-xiphiplastral union. 1 = xiphiplastra lateral to hypoplastra; 2 = hypoplastra lateral to xiphiplastra.
Character 16: Number of neurals. 1 = eight; 2 = seven; 3 = six or less.
Character 17: Variability in position of neural reversal. 1 = always at same neural; 2 = always at adjacent neurals; 3 = highly variable.
Character 18: Pleurals which meet at midline. 0 = none; 1 = eighth only; 2 = seventh and eighth or eighth only; 3 = sixth, seventh, and eighth or seventh and eighth; 4 = sixth, seventh, and eighth or seventh and eighth.
Character 19: Point of reversal of orientation of neurals. 1 = seven; 2 = six; 3 = five; 4 = four.
Character 20: Suprascapular fontanelles. 1 = closed at hatching; 2 = closed in large adults only; 3 = open throughout life.
Character 21: Epiplastron shape. 1 = J-shaped; 2 = I-shaped.
Character 22: Length epiplastra anterior to entoplastron contact. 1 = short; 2 = intermediate; 3 = long.
Character 23: Depressions on eighth pleurals for contact of ilia. 1 = present; 2 = absent.
Character 24: Bridge length. 1 = long; 2 = short.
Character 25: Largest adult size 200 mm or less (disc length). 1 = no; 2 = yes.
Character 26: Carapace margin straight to concave posteriolaterally. 1 = no; 2 = yes.
*Character 27: Sexual dimorphism in disc length. 1 = no; 2 = yes.
Character 28: Jugal contacts squamosal. 1 = no; 2 = in one half of sample.
Character 29: Jugal contacts parietal on skull surface. 1 = no; 2 = yes.
Character 30: Vomer contacts prefrontal. 1 = yes; 2 = no.
Character 31: Dorsal edge of aperture narium externum laterally emarginated. 1 = no; 2 = weakly; 3 = strongly.
Character 32: Dorsal edge of aperture narium externum medially emarginated. 1 = no; 2 = yes.
Character 33: Basisphenoid contacts palatines. 1 = no; 2 = yes.
Character 34: Vomer divides maxillae. 1 = yes; 2 = no.
Character 35: Vomer reaches intermaxillary foramen. 1 = yes; 2 = no.
Character 36: Vomer contacts basisphenoid. 1 = no; 2 = occasionally.
Character 37: Size of foramen palatinum posterius. 1 = large; 2 = small; 3 = small and divided; 4 = many small openings.
Character 38: Foramen jugulare posterius. 1 = open; 2 = enclosed.
Character 39: Contribution of pterygoid to bar separating foramen julare posterius. 0 = absent; 1 = present.
Character 40: Foramen posterius canalis carotici interni relative to lateral crest of basioccipital tubercle. 1 = above; 2 = in it; 3 = below.
Character 41: Maxilla contacts frontal in front of orbit. 1 = no; 2 = yes.
Character 42: Exoccipital contacts pterygoid. 1 = no; 2 = yes.
Character 43: Basisphenoid shape. 1 = not medially constricted; 2 = medially constricted.
Character 44: Premaxilla absent. 1 = no; 2 = occasionally; 3 = usually.
Character 45: Vomer lost. 1 = no; 2 = yes.
Character 46: Jugal contacts orbit. 1 = yes; 2 = no.
Character 47: Epipterygoid, if present, contacts the palatine. 1 = yes; 2 = no.
Character 48: Contact between pterygoid and foramen nervi trigemini occurs when epipterygoid is present. 1 = yes; 2 = no.
Character 49: When epipterygoid is present pterygoid contacts foramen nervi trigemini. 0 = between epipterygoid and quadrate or not at all; 1 = between prootic and epipterygoid or not at all; 2 = between epipterygoid and parietalor not at all.
Character 50: Epipterygoid contacts prootic anterior to foramen nervi trigemini. 1 = no; 2 = yes.
Character 51: Epipterygoid contacts prootic posterior to foramen nervi trigemini. 1 = no; 2 = yes.
Character 52: Epipterygoid fuses to pterygoid. 1 = in subadults; 2 = in adults only; 3 = never.
Character 53: Average ratio of intermaxillary foramen length to length primary palate. 0 = 0.07; 1 = 0.20 to 0.402 = about 0.60.
Character 54: Postorbital bar relative to orbit. 0 = about 2 times orbit diameter; 1 = about equal to orbit to 1/3 of orbit2 = less than 1/5 of orbit.
Character 55: Proportion of processus trochlearis oticum made up by parietal. 1 = 15.6% or less; 2 = 22.1% or more.
Character 56: Ventral keel on 8th cervical present and limited to posterior end. 1 = no; 2 = yes.
Character 57: Strong dorsal processes on cervicals. 1 = no; 2 = yes.
Character 58: Number of ossifications in corpus hyoidis. 1 = 6; 2 = 8.
Character 59: Number of ossifications in comu branchiale II. 1 = 1 only; 2 = 44714; 3 = 7 or more.
Character 60: Ossifications of comu branchiale II broad and strongly sutured. 1 = no; 2 = yes.
Character 61: Basihyals in close contact and projecting anteriorly. 1 = no; 2 = yes.
Character 62: Symphyseal ridge strong and present in a depression. 1 = no; 2 = yes.
Character 63: Foramen intermandibularis caudalis. 0 = absent; 1 = present at least in parts of the population.
Character 64: Ilia curve medially. 1 = no; 2 = yes.
Character 65: Ischia extend into thyroid fenestra. 1 = yes; 2 = no.
Character 66: Metischial processes present and distinct. 1 = yes; 2 = no.
Character 67: Angle of acromion process to scapula approaches that of coracoid to acromion. 1 = no; 2 = yes.
Character 68: Coracoid longest of three pectoral processes. 1 = no; 2 = yes.
Character 69: Development of surface sculpturing of carapace and plastron. 0 = all metaplastic portions of carapace and plastron have trionychid sculpturing; 1 = trionychid pattern grades towards the center of carapacial and plastral disk to a smooth pattern, as developed in Hutchemys rememdium and Hutchemys arctochelys.
Character 70: Nuchal notch. 0 = anterior rim of nuchal convex or slightly notched; 1 = anterior rim of carapace with deep nuchal notch, as developed in H. rememdium.
Character 71: Shape of neural 1 and 2 (neural 2 and 3 of Meylan 1987). 0 = neurals 1 and 2 hexagonal with short posterior sides; 1 = neural 1 circular to rectangular and neural 2 octagonal, as developed in H. rememdium and H. arctochelys.
Character 72: Splitting of costals along distal margin. 0 = costal rim rounded or graded; 1 = dorsal rims split into separately protruding dorsal and visceral portions, as developed in H. rememdium and H. arctochelys.
Character 73: Lateral notch in carapace at the level of costal 5. 0 = absent, lateral carapacial margin rounded; 1 = present, lateral carapacial margin shows a waist, as developed in H. arctochelys.
Character 74: Skin callosity developed on the visceral side of costals 6 and 7. 0 = absent, visceral side smooth; 1 = present, visceral side sometimes develops a callosity, as seen in H. arctochelys.
Character 75: Mid-line contact of hyoplastra, hypoplastra and xiphiplastra. 0 = hyo-, hypo- and xiphiplastra do not contact another fully, even in adults; 1 = hyo-, hypo and xiphiplastra contact another fully along the entire mid-line in adults, as developed in H. rememdium and H. arctochelys.
Character 76: Shape of deep portion of entoplastron. 0 = lateral branches of entoplastron more or less straight and merge anterior at a clear angle; 1 = entoplastron wide and rounded, as seen in P. aff. thomasii.
Character 77: Mobility of entoplastron and anterior development of hyoplastron. 0 = lateral branches of entoplastron abut loosely against hyoplastron, anterior rim of hyoplastron develops no anterior flap/shoulder; 1 = lateral branches of entoplastron abut loosely against hyoplastron, but hyoplastron develops an anterior flap/shoulder, as seen in Plastomenus aff. thomasii; 2 = entoplastron tightly integrated into anterior plastral lobe due to strong development of anterior flap/shoulder, as developed in H. rememdium and H. arctochelys.
Character 78: Peripheral ossification. 0 = lateral bridge ossification of plastron does not significantly extend beyond the lateral processes of hyo- and hypoplastron; 1 = lateral bridge ossification of plastron extends laterally beyond bridge processes of the hyo- and hypoplastron and ossifies the peripheral aspects of the shell, as seen in H. arctochelys.
Character 79: Number of lateral hyoplastral processes. 1 = one; 2 = two; 3 = three or more.
Character 80: Extensive secondary palate consisting of infolded maxillae. 0 = absent; 1 = present, as developed in Plastomenus thomasii.
Character 81: Accessory ridges of upper triturating surfaces. 0 = absent; 1 = present.
Character 82: Dentary symphysis. 0 = short; 1 = extremely long, mandible extremely elongate, as developed in Plastomenus thomasii.
Character 83: Parietal contribution to orbits. 0 = parietals neither contribute to orbit margins or orbit walls; 1 = parietals either contribute to orbit walls, as developed in Gilmoremys lancensis, or orbit margin, as developed in Plastomenus thomasii.
Character 84: Proportions of costals VIII. 0 = wider than long to nearly square; 1 = significantly taller than wide.
Character 85: Hyoplastron with strongly serrated medial edge. 0 = present; 1 = absent.
Character 86: Serrated medial edge of hyoplastron extends nearly to the posterior edge of bone. 0 = present; 1 = absent.
Character 87: Process on medial edge of hypoplastron. 0 = of subequal size and radiating outward from the medial edge of the bone; 1 = with enlarged anterior process separated by a gap from smaller posterior processes.
Character 88: Ossification of basibranchials. 0 = poorly ossified, especially posterior pair; 1 = well ossified.
Character 89: Metaplastic ossification of hypoplastron "rolls" onto posterior aspects of lateral processes. 0 = absent; 1 = present.
Character 90: Free rib ends. 0 = all ribs end free, not covered by metaplastic ossification; 1 = only costal ribs VII and VIII free; 2 = all ribs covered by metaplastic bone.
*Character 91: Carapacial striations in adults. 0 = absent; 1 = present.
Character 92: Contribution of opisthotic to bar separating foramen jugulare posterius: 0 = absent; 1 = present.
Character 93: Contribution of excoccipital to bar separating foramen jugulare posterius: 0 = absent; 1 = present.
Character 94: Fusion of frontals: 0 = absent; 1 = present.
Character 95: Jugal, jugal participation in the margin of the upper temporal emargination: 0 = absent; 1 = present, upper temporal emargination extensive.
Character 96: Jugal, contact with the pterygoid: 0 = absent; 1 = present.
Character 97: Postorbital: 0 = completely reduced; 1 = present.
Character 98: Maxilla, well-developed suborbital crest: 0 = absent; 1 = present.
Character 99: Maxilla, Supraalveolar foramen (on the medial surface of the maxilla within the nasal capsule): 0 = absent; 1 = present, with posteriorly developed groove; 2 = present as fenestra-like opening into the supraalveolar canal.
Character 100: Premaxilla/vomer, foramen praepalatinum: 0 = absent; 1 = present.
Character 101: Foramina in vomer (possibly praepalatine foramina): 0 = absent; 1 = present.
Character 102: Anterior palate region, vomer and or premaxillae/maxillae, transversely concave ventral surface (‘tongue groove’) on anterior parts between maxillae: 0 = absent; 1 = present.
Character 103: Quadrate, infolding ridge on the posterior surface of the quadrate ventral to the incisura columella auris: 0 = absent or extremely minor; 1 = ridge present but low; 2 = ridge present and forms massive overhanging flange. Ordered.
Character 104: Pterygoid, pterygoid contribution to foramen palatinum posterius: 0 = absent; 1 = present.
Character 105: Maxilla, maxilla contribution to foramen palatinum posterius: 0 = absent; 1 = present.
Character 106: Pterygoid, lateral flange at lateral margin: 0 = absent; 1 = present.
Character 107: Parabasisphenoid, abducens nerve course: 0 = in fully ossified canal; 1 = in dorsally open groove.
Character 108: Prootic, lateral semicircular canal enclosure by bone: 0 = canal only formed by bone of the opisthotic, the prootic portion of the canal is not ossified and is instead medially confluent with the recessus labyrinthicus prooticus; 1 = prootic and opisthotic both contribute to the formation of the lateral semicircular canal.
Character 109: Position of the foramen posterius canalis carotici interni (fpcci): 0 = the fpcci is located at the ventral surface of the skull in a position far anterior to the margin of the fenestra postotica; 1 = the fpcci is located at the posterior end of the skull, either on the ventral surface of the skull close to the margin of the fenestra postotica, or on the posterior surface of the skull at the ventral margin of the fenestra postotica.
Character 110: Dentary, expansion of lingual margin: 0 = absent; 1 = lingual margin is medially expanded to a shelf, which often is broader along the central part of the mandibular ramus than near the coronoid and symphyseal ends; 2 = lingual margin is so far expanded that it forms a huge, spatulate continuous surface with the symphysis.
Character 111: Dentary, size of foramen dentofaciale majus: 0 = absent, foramen completely reduced; 1 = small, size of a small vessel; 2 = enlarged, foramen is several mm in diameter.
Character 112: Dorsal surangular foramen: 0 = absent; 1 = present.
Character 113: Coronoid, foramen at anterior end, leading from fossa Meckelii into space between mandibular rami: 0 = absent; 1 = present.
Character 114: Prearticular, exposure of foramen alveolare inferius in medial view: 0 = absent, the foramen is covered by expansions of the prearticular and/or coronoid; 1 = present, the foramen can be seen in medial view.
Character 115: Anterior intermandibular foramen: 0 = absent; 1 = present, fully or partially formed between the angular and prearticular along their anterior processes. Note that this character is scored as inapplicable when the anteroventral process of the prearticular is absent.
Character 116: Posterior chorda tympani foramen: 0 = located within the articular notch on the posterior surface of the articular; 1 = located on the posteromedial jaw surface, usually on the prearticular or prearticular-articular contact.
Character 117: Articulation facet, contribution of prearticular: 0 = absent, prearticular completely retracted from articulation facet; 1 = prearticular forms small medial portion of articulation facet.
APPENDIX 3.
Character matrix. Appendices 3-5 are available for download.
APPENDIX 4.
MrBayes script. Appendices 3-5 are available for download.
APPENDIX 5.
Bayesian log file. Appendices 3-5 are available for download.
