1

Supplementary information

for “Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Evolution in the Early History of Jawed Vertebrates.”

Benedict King, Tuo Qiao, Michael S.Y. Lee, Min Zhu, John A. Long

Contents

2-5 Figures S1-S4

6 Prior distributions

7-13 Taxon list

14 Stratigraphic ranges used in sampling test

15-63 Character list

64-70 Supplementary references

2

Figure S1. Weighted mean evolutionary rates in each time slice in a BEAST2 analysis in which placoderms are constrained to be paraphyletic. The overall pattern of rates is the same as the unconstrained analysis, with higher rates in the Silurian and a subsequent decline. 3

Figure S2. Weighted mean evolutionary rates in each time slice in a BEAST2 analysis in which certain taxa are given an age range rather than a fixed age. The overall pattern of rates is the same as in the focal analysis, with higher rates in the Silurian and a subsequent decline. 4

Figure S3. Weighted mean evolutionary rates in each time slice in a BEAST2 analysis in which all taxa occurring after the Frasnian are deleted. The overall pattern of rates is the same as in the focal analysis, with higher rates in the Silurian and a subsequent decline. 5

Figure S4. Comparison of rate heterogeneity patterns between a tree with placoderm monophyly (constrained) and placoderm paraphyly (constrained). This figure shows that the pattern in figure 6D was not an artefact of constraining the topology. A and B) Guide trees showing the branches on which rates of evolution would be expected to be affected between the two trees (A placoderm monophyly, B placoderm paraphyly). Both topologies were constrained such that the only difference is the root position. Dark grey branches (triangles) would be shortened in the paraphyly tree and black branches (diamonds) lengthened, thus increasing and decreasing rates respectively. Star (with arrow) indicates the root in placoderm paraphyly. C) The pattern of rate heterogeneity in the constrained placoderm monophyly tree resembles that of the unconstrained placoderm monophyly tree (fig. 6D). This shows that the pattern of rate heterogeneity in the constrained paraphyly tree is due to paraphyly and not an artefact of topological constraints. Single and double headed arrows indicate weighted and unweighted mean rates respectively. 6

Priors

Origin: Uniform 0-1000

Birth Rate: Lognormal with mean (real space) 0.14 and standard deviation 0.9

The prior on birth rate matches the distribution rates found across living ray-finned fish (Rabosky et al. 2013).

Death rate: Exponential with mean 0.1

Sampling rate: Exponential with mean 0.03

The proportion of known species included in the analysis can be used to place an upper bound on the sampling rate. (Sallan and Galimberti 2015) list 1124 Devonian-Mississippian taxa, said to be ~90% of named species, and 531 from the Lochkovian to the Frasnian. The dataset contains 107 and 97 taxa from taxa from these intervals respectively, placing an upper bound in the sampling proportion of between 0.0856. and 0.164. The exponential distribution employed here places the 97.5% quantile at 0.111. This amounts to an uninformative prior since the number of named species is still much lower than the true diversity.

Gamma shape: Uniform 0-10

Mean rate: Exponential with mean 0.003 and offset 0.0016

The offset of the exponential sistribution is placed at the rate calculated by taking the mean number of steps per character from the parsimony analysis and dividing by the total branch length obtained when the parsimony tree is time-scaled in R using timePaleoPhy in the R package paleotree (Bapst 2012) with minimum ghost ranges. This provides a minimum rate estimate. The exponential is broad enough that the 95% quantile is at 0.0106, 6.3 times the estimated rate from parsimony. The median of this distribution is 0.0037, the rate generated by dividing the minimum estimate by the proportion of non-missing data.

Ucld standard deviation: Exponential with mean 1

7

Taxa, sources formations and age used in analysis

Taxon Source(s) Formation Age for analysis Hemicyclaspis (Stensiö 1932) Ludlow, Shropshire. 421 murchisoni Downtownian (Pridoli) Zenaspis salweyi (Stensiö 1932) Lower old red 412 sandstone. Skirrid Fawr, Senni/St Maughans formation Cephalaspis lyelli (Stensiö 1932, White Lower old red 412 1958) sandstone, Glammis Benneviaspis (Janvier 1985a) Ben Nevis formation, 413 holtedahli Red bay group. Boreaspis (Janvier 1985a) Wood bay formation 411 macrorhynchus Norselaspis glacialis (Janvier 1981) Wood bay formation 411 Nectaspis areolate (Wängsjö 1952, Janvier Wood bay formation 411 1981) Procephalaspis (Robertson 1939, Saaremaa, Estonia. 427 oeselensis Denison 1951, Janvier Wenlockian and 1985b) Ludlowian Tremataspis (Robertson 1938a, Saaremaa 427 mammillata Robertson 1938b, Denison 1947, Denison 1951, Janvier 1985b) Waengsjoeaspis (Wängsjö 1952, Janvier Fraenkelryggen 416 excellens 1985a) formation Escuminaspis laticeps (Janvier et al. 2004) Escuminac formation 380 Eugaleaspis changi (Liu 1965, Zhu and Gai Xitun formation, 412 2007) Liaojaoshan Hanyangaspis (Zhu and Gai 2007) Guodingshan 436 guodingshanensis formation. Telychian Polybranchiaspis (Liu 1965, Liu 1975) Xishancun and Xitun 415 liaojiaoshanensis formations Bannhuanaspis (Janvier et al. 1993) Bac Bun formation 411 vukhuci Wenshanaspis (Zhao et al. 2001) Posongchong 409 zhichangensis formation, Wenshan. Pragian Shuyu zhejiangensis (Gai et al. 2011) Maoshan formation. 433 Late Telychian to early Wenlock Polybranchiaspid sp. (Wang et al. 2005) Xishancun and Xitun 415 (histological samples) formations Yunnanolepis sp. (Zhang 1980, Zhu 1996) Xishancun and Xitun 415 (various taxa from formations same formations) Parayunnanolepis (Zhang et al. 2001, Zhu Xitun formation 412 xitunensis et al. 2012) 8

Microbrachius dicki (Hemmings 1978, Long Eday flagstone and 386 et al. 2015) John O’Groats sandstone. Lower- Middle Givetian Bothriolepis sp. (Young 1984) Gogo formation 383 MVP230985 Bothriolepis (Downs and Donoghue Escuminac formation 380 canadensis 2009, Béchard et al. 2014) Pterichthyodes milleri (Hemmings 1978) Achanarras horizon, 389 under upper Stromness flagst. Late Eifelian Remigolepis walkeri (Johanson 1997) Canowindra. 366 Famennian Diandongpetalichthys (Zhu 1991) Xishancun formation 417 liaojiaoshanensis Quasipetalichthys (Liu 1991) Kunming; Shixiagou 385 haikouensis formation, Ninxia. Givetian Eurycaraspis incilis (Liu 1991) Haikou formation. 385 Givetian Lunaspis broili (Gross 1961) Hunsrueck slate. Late 408 Pragian to early Emsian Macropetalichthys (Stensiö 1925, Stensiö Onondaga limetone. 390 rapheidolabis. 1963b, Stensiö 1969) Eifelian (including Macropetalichthys sp. specimens used in 1963 and 1969) Wuttagoonaspis (Ritchie 1973, Miles and Mulga Downs group. 393 fletcheri Young 1977). Emsian-Eifelian AMF53610, AMF53631, AMF53591, Groenlandaspis sp. MVP48873(AMF59808) , Mt. Howitt 385 AMF59814, MVP48877/8 (AMF59811/2), AMF62534A, AMF59809 Cowralepis mclachlani (Ritchie 2005, Carr et al. Merriganowry shale. 383 2009) Late Givetian to early Frasnian Gavinaspis convergens (Dupret et al. 2009) Xitun formation. 412 Sigaspis lepidophora (Goujet 1973) Wood bay formation 412 (extreme base) Kujdanowiaspis (Stensiö 1963a, Dupret Dnister series, Podolia. 411 podolica 2010) Upper Lockhovian- lower Pragian Dicksonosteus arcticus (Goujet 1975, Goujet Wood bay formation 411 1984) 9

Buchanosteus (Burrow and Turner Buchan. Mid-late 408 confertituberculatus 1998, Long et al. 2014) Pragian Parabuchanosteus (White and Toombs Taemas-Wee Jasper 401 murrumbidgeensis 1972, Young 1979, Burrow and Turner 1998) Holonema westolli (Miles 1971) Gogo formation 383 Coccosteus cuspidatus (Miles and Westoll Achanarras and 388 1968) edderton fish bed. Eifelian-Givetain boundary Incisoscutum ritchiei (Dennis and Miles 1981, Gogo formation 383 Giles et al. 2013) Eastmanosteus (Dennis-Bryan 1987) Gogo formation 383 calliaspis Compagopiscis (Gardiner and Miles Gogo formation 383 croucheri 1994) Materpiscis (Long et al. 2008, Gogo formation 383 attenboroughi Trinajstic et al. 2012) Austroptyctodus (Long 1997a) Gogo Formation 383 gardineri Campbellodus (Long 1997a) Gogo formation 383 decipiens Rhamphodopsis (Miles 1967, Long Edderton fish beds. 388 threiplandi 1997b) Eifelian-Givetian boundary Brindabellaspis (Young 1980). Taemas-Wee Jasper 401 stensioi ANUV3247 Romundina stellina (Ørvig 1975, Dupret et Lockhovian. Prince of 415 al. 2014) Wales island. Jagorina pandora (Stensiö 1969, Young Kellwasserkalk, Bad 375 1986) Wildungen. Late Frasnian Gemuendina stuertzi (Gross 1963) Hunsrueck slate 408 Entelognathus (Zhu et al. 2013) Kuanti formation 424 primordialis Janusiscus schultzei (Giles et al. 2015b) Lower member, 415 Kureika formation. Middle Lockhovian. Ramirosuarezia (Pradel et al. 2009) Icla formation. Early 392 boliviana Eifelian Acanthodes bronni (Gross 1935, Watson Lebach ironstone. 298 1937, Miles 1973b, Early Permian Miles 1973a, Coates 1994, Davis et al. 2012, Brazeau and de Winter 2015) Brachyacanthus (Watson 1937) Lower old red 415 scutiger sandstone, Farnell. Lockhovian 10

Brochoadmones milesi (Hanke and Wilson MOTH 415 2006) Cassidiceps (Gagnier and Wilson MOTH 415 vermiculatus 1996) Cheiracanthus (Watson 1937, Miles Middle old red 388 latus/murchisoni 1973a) sandstone, Moray firth. Nodular fish beds, Eifelian-Givetian Climatius reticulatus (Watson 1937, Miles ‘Turin hill’ 415 1973a) Culmacanthus stewarti (Long 1983) Mt Howitt 385 Euthacanthus (Watson 1937, Miles ‘Turin hill’ 415 macnicoli 1973a, Newman et al. 2014) Gladiobranchus (Hanke and Davis 2008) MOTH 415 probation Homalacanthus (Gagnier 1996) Escuminac formation 380 concinnus Ischnacanthus gracilis (Watson 1937, Miles ‘Turin hill’ 415 1973a) Kathemacanthus (Gagnier and Wilson MOTH 415 rosulentus 1996, Hanke and Wilson 2010) Latviacanthus (Schultze and Zidek Ventspils. Kemeri 404 ventspilensis 1982) stage Lupopsyrus pygmaeus (Hanke and Davis 2012) MOTH 415 Mesacanthus mitchelli (Watson 1937, Miles ‘Turin hill’ and Farnell 415 1973a) Obtusacanthus (Hanke and Wilson MOTH 415 corroconis 2004) Parexus recurvus (Watson 1937, Miles ‘Turin hill’ 415 1973a, Burrow et al. 2013) Poracanthodes (Valiukevicius 1992) Severnaya Zemlya 417 menneri formation. Lower Lockhovian. Promesacanthus (Hanke 2008) MOTH 415 eppleri Ptomacanthus anglicus (Miles 1973a, Brazeau Wayne Herbert 415 2012) quarry, Lockhovian Diplacanthus striatus (Watson 1937, Miles Moray firth and 388 1973a) Achanarras. Eifelian- Givetian boundary Tetanopsyrus (Gagnier et al. 1999, MOTH 415 lindoei/breviacanthus Hanke et al. 2001) Vernicomacanthus (Miles 1973a) Wayne Herbert quarry 415 waynensis Cladodoides (Maisey 2005) Wildungen limestone, 375 wildungensis Upper Frasnian 11

Akmonistion zangerli (Coates and Sequeira Manse Burn 327 1998, Coates et al. formation, Bearsden. 1998, Coates and Serpukhovian Sequeira 2001) “Cobelodus” (Maisey 2007) Fayetteville formation. 325 Chesterian Cladoselache (Harris 1938, Bendix- Cleveland member of 360 kepleri/fyerli Almgreen 1975, Ohio Shale. Late Schaeffer 1981, Maisey Famennian 2007) Chondrenchelys (Moy-Thomas 1935, Glencartholm, 338 problematica Finarelli and Coates Scotland. Visean 2011, Finarelli and (Holkerian) Coates 2014) Helodus simplex (Moy-Thomas 1936) Fenton, Staffordshire. 311 Moscovian Debeerius ellefseni (Grogan and Lund 2000) Bear Gulch limestone. 320 Upper Chesterian Doliodus (Miller et al. 2003, ‘Atholville beds’, 395 problematicus Maisey et al. 2009) Campbellton formation. Emsian or Emsian-Eifelian Hamiltonichthys (Maisey 1989) Hartford limetone, 302 mapesi Hamilton quarry. Middle Virgilian Onychoselache (Dick and Maisey 1980, Glencartholm volcanic 336 traquari Coates and Gess 2007) beds and Wardie shales. Holkerian- Asbian Orthacanthus sp. (Schaeffer 1981) Admiral formation. 290 Wolfcampian Pucapampella (Maisey 2001) Sica sica formation, 388 rodrigae/sp. Bolivia. Eifelian- Givetian Tamiobatis vetustus (Schaeffer 1981, Cleveland shale 360 Williams 1998) (Famennian) and Salem limestone (Early Visean) Tristychius arcuatus (Dick 1978, Coates and Wardie shales and 336 Gess 2007) Manse burn formation, Bearsden Dialipina (Schultze 1968, Schultze Bear Rock formation. 401 salgueiroensis and Cumbaa 2001) Emsian Ligulalepis toombsi (Schultze 1968, Burrow Taemas-Wee Jasper 401 1994, Basden et al. 2000, Basden and Young 2001) Cheirolepis canadensis (Pearson and Westoll Escuminac formation 380 1979, Arratia and Cloutier 1996) 12

Cheirolepis trailli (Pearson and Westoll Achanarras limestone, 388 1979, Giles et al. 2015a) Tynet burn and Gamrie. Late Eifelian Howqualepis (Long 1988) Mt. Howitt 385 rostridens Mimipiscis toombsi (Gardiner and Bartram Gogo formation 383 1977, Gardiner 1984, Giles and Friedman 2014) Moythomasia (Gardiner 1984) Gogo formation 383 durgaringa Kentuckia deani (Rayner 1952, Giles and New Providence Shale 347 Friedman 2014) member, Stockdale formation. Latest Tournasian or earliest Visean Osorioichthys marginis (Taverne 1997) Femenne formation. 367 Early Femennian Meemannia eos (Zhu et al. 2006, Zhu et Xitun formation 412 al. 2010) Guiyu oneiros (Zhu et al. 2009, Qiao Kuanti formation 424 and Zhu 2010) Psarolepis romeri (Yu 1998, Zhu et al. Xishancun, Xitun and 416 1999, Zhu and Yu 2004, Yulongsi formations. Zhu and Yu 2009) Also Silurian. Most material used to score characters is from Xishancun formation. Achoania jarvikii (Zhu et al. 2001, Zhu Xitun formation 412 and Yu 2004, Zhu and Yu 2009) Onychodus (Andrews et al. 2005) Gogo formation, 383 jandemarrai Saddler formation Miguashaia bureaui (Cloutier 1996, Forey Escuminac formation 380 1998) Styloichthys changae (Zhu and Yu 2002, Xitun formation 412 Friedman 2007) Diabolepis speratus (Chang and Yu 1984, Xitun formation 412 Chang 1995) Youngolepis (Zhang and Yu 1981, Xitun formation 412 praecursor Zhang 1982, Chang 1991) Powichthys (Jessen 1980) Late lockhovian or 411 thorsteinssoni early Pragian. Prince of Wales island Porolepis sp. (includes (Jarvik 1972, Clement Wood bay formation 411 elongate, brevis and 2004) spitzbergensis) 13

Glyptolepis (Jarvik 1972, Ahlberg Red siltstone member 388 groenlandica 1989) of the Nathorst Fjord group. Late Eifelian- Early Givetian Kenichthys campbelli (Chang and Zhu 1993, Chuangdong 396 Zhu and Ahlberg 2004) formation. Late Emsian Osteolepis (Westoll 1936, Thomson Tynet burn. Late 388 macrolepidotus 1965, Jarvik 1980) Eifelian Gogonasus andrewsi (Long 1985, Long et al. Gogo formation 383 1997, Long et al. 2006, Holland 2013, Holland 2014) Eusthenopteron foordi (Jarvik 1980) Escuminac formation 380

14

Stratigraphic ranges used for sensitivity analysis (uniform priors on tip dates)

Wenlockian-Ludlowian (423-433 Mya)

Peocephalaspis oeselensis, Tremataspis mammillata

Lochkovian (411-419 Mya)

Yunnanolepis sp., Romundina stellina, Brachyacanthus scutiger, Brochoadmones milesi, Cassidiceps vermiculatus, Climatius reticulatus, Euthacanthus macnicoli, Gladiobranchus probaton, Ischnacanthus gracilis, Kathemacanthus rosulentus, Lupopsyrus pygmaeus, Mesacanthus mitchelli, Obtusacanthus corroconis, Parexus recurvus, Promesacanthus eppleri, Ptomacanthus anglicus, Tetanopsyrus (lindoei and breviacanthias), Vernicomacanthus waynensis, Psarolepis romeri

Emsian (393-408 Mya)

Doliodus problematicus, Dialipina salgueiroensis

Emsian-Eifelian (388-408 Mya)

Wuttagoonaspis fletcheri

Eifelian-Givetian (383-393 Mya)

Pucapampella rodrigae

Famennian (359-372 Mya)

Remigolepis walker

Late Famennian and early Visean (340-360 Mya)

Tamiobatis vetustus

Moscovian (307-315 Mya)

Helodus simplex 15

Character List

Histology

1. DFC1 Tessellate prismatic calcified cartilage 0 absent 1 present

2. GFB2 Prismatic calcified cartilage 0 single layered 1 multi-layered

3. DFC2 Perichondral bone 0 present 1 absent

4. DFC3 Extensive endochondral ossification 0 absent 1 present

5. GFB8 Extensive pore canal network 0 absent 1 present

6. Three-layered exoskeleton 0 absent 1 present Sansom 2009 character 72. Donoghue et al. (2000) character 71.

7. Cephalic dermoskeletal bone 0 cellular 1 acellular Sansom 2009 character 73. Donoghue et al 2000 character 67.

8. Perforated horizontal lamina in the sensory line canals and vascular system 0 absent 1 present Sansom 2009 character 85

9. Galeaspedin 0 absent 1 present Sansom 2009 character 87.

10. DFC4 Dentine 0 absent 1 present

11. GFB11 Bone cell lacunae in body scale bases 0 present 1 absent 16

12. DFC5 Dentine kind 0 mesodentine 1 semidentine 2 orthodentine

13. GFB12 Main dentinous tissue forming fin spine 0 osteodentine 1 orthodentine

14. ZHU139 Resorption and redeposition of odontodes 0 lacking or partially developed 1 developed

15. GFB5 Enamel(oid) present on dermal bones and scales 0 absent 1 present

16. GFB6 Enamel 0 single-layered 1 multi-layered

17. GFB7 Enamel layers 0 applied directly to one another (ganoine) 1 separated by layers of dentine

18. Superficial glassy layer of dermal armour 0 absent 1 present Sansom 2009 character 80.

Neurocranium and associated dermal ossifications

19. DFC54 Precerebral fontanelle 0 absent 1 present

20. DFC56 Nasal opening(s) 0 dorsal, placed between orbits 1 ventral and anterior to orbits

21. DFC57 Olfactory tracts 0 short, with olfactory capsules situated close to telencephalon cavity 1 elongate and tubular (much longer than wide)

22. Extended preorbital region between eyes and nasal capsule 0 present 1 absent 17

The original definition of this character stated that a prominent expansion was when the neurocranium extended far anterior to the nasal capsules. In antiarchs and acanthothoracids, this condition is present because of the posteriorly placed nostrils and anteriorly positioned jaws and associated attachments. In Macropetalichthys, Chondrenchelys and Debeerius the neurocranium does not extend far anteriorly to the nasal capsules, but rather there is an extended region between the nasal capsules and the orbits. Therefore this character was apparently previously scored as present in taxa either with posteriorly placed or extremely anteriorly placed nasal capsules, and absent in those with an intermediate condition. The definition of this character is therefore altered to apply only to taxa with very anteriorly placed nasal capsules, as posterior nasal capsules are dealt with in another character.

23. DFC59 Pronounced sub-ethmoidal keel 0 absent 1 present

24. DFC60 Position of myodome for superior oblique eye muscles 0 posterior and dorsal to foramen for nerve II 1 anterior and dorsal to foramen

25. DFC61 Endoskeletal cranial joint 0 absent 1 present

26. DFC62 Spiracular groove on basicranial surface 0 absent 1 present

27. DFC63 Spiracular groove on lateral commissure 0 absent 1 present

28. DFC64 Subpituitary fenestra 0 absent 1 present

29. DFC65 Supraorbital shelf broad with convex lateral margin 0 absent 1 present

30. DFC66 Orbit dorsal or facing dorsolaterally, surrounded laterally by endocranium 0 present 1 absent

31. DFC67 Extended prehypophysial portion of sphenoid 0 absent 1 present

32. DFC68 Narrow interorbital septum 0 absent 1 present

18

33. DFC70 Hyoid ramus of facial nerve (N. VII) exits through posterior jugular opening 0 absent 1 present

34. DFC71 Glossopharyngeal nerve (N. IX) exit 0 foramen situated posteroventral to otic capsule and anterior to metotic fissure 1 through metotic fissure

35. DFC72 Short otico-occipital region of braincase 0 absent 1 present

36. DFC73 Ethmoid region elongate with dorsoventrally deep lateral walls 0 absent 1 present

37. DFC74 Relationship of cranial endocavity to basisphenoid 0 endocavity occupies full depth of sphenoid 1 endocavity dorsally restricted Follows revision in Giles et al (2015)

38. DFC75 Ascending basisphenoid pillar pierced by common internal carotid 0 absent 1 present

39. DFC79 Canal for efferent pseudobranchial artery within basicranial cartilage 0 absent 1 present

40. DFC77 Canal for lateral dorsal aorta within basicranial cartilage 0 absent 1 present

41. DFC78 Entrance of internal carotids 0 through separate openings flanking the hypophyseal opening or recess 1 through a common opening at the central midline of the basicranium

42. DFC80 Position of basal/basipterygoid articulation 0 same anteroposterior level as hypophysial opening 1 anterior to hypophysial opening

43. DFC81 Postorbital process articulates with palatoquadrate 0 absent 1 present

44. DFC82 Labyrinth cavity 0 separated from the main neurocranial cavity by a cartilaginous or ossified capsular wall 1 skeletal capsular wall absent

45. DFC83 Basipterygoid process (basal articulation) with vertically oriented component 0 absent 19

1 present

46. DFC84 Pituitary vein canal 0 dorsal to level of basipterygoid process 1 flanked posteriorly by basipterygoid process

47. DFC85 External (horizontal) semicircular canal 0 absent 1 present

48. DFC86 Sinus superior 0 absent or indistinguishable from union of anterior and posterior canals with saccular chamber 1 present

49. DFC87 External (horizontal) semicircular canal 0 joins the vestibular region dorsal to posterior ampulla 1 joins level with posterior ampulla

50. DFC89 Posterior dorsal fontanelle 0 absent 1 present

51. DFC90 Shape of posterior dorsal fontanelle 0 approximately as long as broad 1 much longer than wide, slot-shaped

52. DFC91 Dorsal ridge 0 absent 1 present

53. DFC92 Endolymphatic ducts 0 posteriodorsally angled tubes 1 tubes oriented vertically through median endolymphatic fossa

54. DFC96 Ventral cranial fissure 0 absent 1 present

55. DFC97 Metotic (otic-occipital) fissure 0 absent 1 present

56. DFC98 Vestibular fontanelle 0 absent 1 present

57. DFC99 Occipital arch wedged in between otic capsules 0 absent 1 present

20

58. DFC100 Spino-occipital nerve foramina 0 two or more, aligned horizontally 1 one or two, dorsoventrally offset

59. DFC101 Ventral notch between parachordals 0 absent 1 present or entirely unfused

60. DFC102 Parachordal shape 0 broad, flat 1 keeled with sloping lateral margins

61. DFC103 Hypotic lamina (and dorsally directed glossopharyngeal canal) 0 absent 1 present

62. ZHU222, GFB131 Eye stalk or unfinished area on neurocranial wall for eye stalk 0 absent 1 present

63. ZHU227, GFB155 Articulation facet with hyomandibular 0 single-headed 1 double-headed

64. ZHU231, GFB169 Basicranial fenestra 0 absent 1 present

65. ZHU233, GFB155 Lateral cranial canal 0 absent 1 present

66. ZHU234, GFB179 Midline canal in basicranium for dorsal aorta 0 absent 1 present

67. ZHU142 Rostral tubuli 0 absent 1 present

68. ZHU225 Unconstricted cranial notochord 0 absent 1 present

69. ZHU226 Descending process of sphenoid (with its posterior extremity lacking periostegeal lining) 0 absent 1 present

70. ZHU229 Opercular suspension on braincase 0 absent 1 present 21

71. ZHU236 Vomeral area with grooves and raised areas 0 absent 1 present

72. ZHU221 Ethmoid articulation for palatoquadrate 0 placed on postnasal wall 1 extends posteriorly to the level of N.II

73. DUPRET255 optic fissure 0 present 1 absent

74. GFB114 Buccohypophysial canal in parasphenoid 0 single 1 paired

75. GFB125 Transverse otic process 0 present 1 absent

76. GFB126 Jugular canal 0 long (invested in otic region along length of skeletal labyrinth) 1 short (restricted to region anterior of skeletal labyrinth) 2 absent (jugular vein uninvested in otic region)

77. GFB132 Postorbital process 0 absent 1 present

78. GFB133 Canal for jugular in postorbital process 0 absent 1 present

79. GFB134 Series of perforations for innervation of supraorbital sensory canal in supraorbital shelf 0 absent 1 present

80. GFB141 Subcranial ridges 0 absent 1 present

81. GFB154 Horizontal semicircular canal in dorsal view 0 medial to path of jugular vein 1 dorsal to jugular vein

82. GFB159 Synotic tectum 0 absent 1 present

83. GFB161 Shape of median dorsal ridge anterior to endolymphatic fossa 22

0 developed as a squared-off ridge or otherwise ungrooved 1 bears a midline groove

84. GFB166 Branchial ridges 0 present 1 reduced to vagal process 2 absent (articulation made with bare cranial wall)

85. GFB167 Craniospinal process ("supravagal process" in Stensio) 0 absent 1 present

86. GFB176 Stalk-shaped parachordal/occipital region 0 absent 1 present

87. Paired occipital facets 0 absent 1 present

88. GFB178 Size of aperture to notochordal canal 0 much smaller than foramen magnum 1 as large, or larger, than foramen magnum

89. Relative position of jugular groove and hyomandibular articulation 0 hyomandibula dorsal or same level 1 jugular vein passing dorsal or lateral to hyomandibula

90. Medial recess of the posteroventral mydome 0 absent 1 present Sansom 2009 character 103 Assumed to be inapplicable outside osteostracans

91. Number of ‘sel’ canals 0 five 1 less than 5 Sansom 2009 character 109 The presence of ‘sel’ canals themselves is not considered independent of lateral fields and is not included as a separate character here. This character concerns the number of canals, and is inapplicable in taxa lacking them.

92. ‘sel’ 1 canal bifurcation 0 between orbit and field 1 adjacent to field Sansom 2009 character 110 (with modified states).

93. Marginal vein 0 absent 1 present Sansom 2009 character 111. 23

94. Profundus nerve (Young 1980) 0 emerges from the cranial cavity separately from the trigeminal nerve 1 emerges together with the trigeminal nerve This character refers to the roots of the nerves as they leave the cranial cavity (i.e. it does not refer to whether or not the profundus emerges from the braincase through a separate foramen).

95. Transverse otic process 0 Not extending in front of orbits 1 extending in front of orbits Jia et al (2010) character 17. The nomenclature of the postorbital process of antiarchs is changed to be consistent with other characters in this matrix, following Giles et al., (2015).

96. Nasal capsules in anterolateral corners of orbit 0 no 1 yes A unique feature of Brindabellaspis, see Young 1980.

97. Vagal process 0 forked 1 unforked Pan et al., (2015) character 14. The posterior process of placoderms is forked in many arthrodires, petalichthyids and acanthothoracids. Here the wording is changed to vagal process for consistency with other characters, following Giles et al., 2015.

98. Paravagal fossa 0 absent 1 present Pan et al., (2015) character 18. A large fossa is present around the vagus nerve in both Macropetalichthys and Brindabellaspis. This is significantly larger than the fossa between the ‘prongs’ of the forked posterior postorbital process of many other placoderms, although they may be homologous.

99. Rostral processes 0 absent 1 present Paired rod-like cartilages supporting the anterior of the snout are present in ptyctodontids and Debeerius. Although this character was one that was used to argue for a relationship between ptyctodontids and holocephalans, this claim is no longer accepted. However, there is no a priori reason to reject their homology here.

100. Braincase is a series of bilateral ossifications 0 no 1 yes A unique feature of ptyctodontids.

101. Median rostral dorsal process of the braincase 0 absent 1 present. 24

Another feature of the braincase of Jagorina. See Stensio (1969, fig. 27: rk)

102. Tectum orbitale/supraorbital shelf 0 absent or very narrow 1 present Lu et al., (2012) character 43. This character is considered inapplicable to many placoderms with extremely platybasic braincases, and those with dorsally facing orbits. A narrow orbital tectum/supraorbital shelf is present in tetrapodomorphs, Ramirosuarezia and Jagorina.

103. Expanded articular area anterior to basipterygoid process 0 absent 1 present In Glyptolepis groenlandica the basipterygoid attachment area for the palatoquadrate is expanded anteriorly, beyond the level of the optic nerve. See Jarvik (1972 fig. 21A: fus).

104. Hyomandibular facets where they straddle the jugular vein 0 narrowly separated 1 widely separated Lu et al., (2012) character 59. Only applicable to taxa with a double-headed hyomandibular attachment.

105. Parachordal plates 0 separated from the otic capsule 1 sutured or fused with the otic capsule Lu et al., (2012) character 63.

106. Posttemporal fossae 0 absent 1 present Lu et al., (2012) character 67.

107. Rostral organ 0 absent 1 present Lu et al., (2012) character 261. The presence of a rostral organ is determined by the presence of large pores in the snout region. It is a feature of coelacanths, of which Miguashaia is the only one included here.

108. Prespiracular dental plate 0 absent 1 present The palate of Powichthys has paired dermal plates lateral to the parasphenoid, termed parashpenotic dental plates by Jessen (1980, fig. 4: Ps.dp). These were renamed prespiracular dental plates in Youngolepis by Chang (1982, fig. 10: Prsdp). Although it is often partly fused to the parasphenoid in Youngolepis, this character is scored as present in this taxon following the discussion in Chang (1982).

109. Suprapterygoid process 0 absent 1 present 25

Holland (2009) The processus ascendens of the palatoquadrate does not always form an articular process on the braincase, and is assumed to form a ligamentous attachment if it does not. This character is inapplicable in taxa without a processus ascendens, although it is tentatively scored in a number of sarcopterygians in which the palatoquadrate is not preserved due to the similarities of the the braincase with other sarcopterygians.

110. Processus supraorbitalis lateralis 0 absent 1 present A rod-like process projects posteriorly from the dorsal part of the ethmoid in Eusthenopteron. See Jarvik (1980, fig. 88).

111. Anterolateral fenestra in roof of otoccipital 0 absent 1 present This is a characteristic of Eusthenopteron. See Jarvik (1980, fig. 88).

112. Ventral cranial fissure connects with vestibular fontanelles 0 absent 1 present (Coates 1999) character 29 (in part)

113. Bar across spiracular groove 0 absent 1 present In Moythomasia durgaringa an endocranial bar crosses the spiracular groove. See Gardiner (1984 fig. 7).

114. Hypophysial opening in braincase 0 absent 1 present A hypophysial opning is absent on the ventral surface of the braincases of Macropetalichthys and Ramirosuarezia.

115. Pineal opening in braincase 0 absent 1 present Although a character concerning the presence of a pineal opening in the skull roof is already present in the matrix, the presence or absence of a pineal opening in the braincase of taxa without dermal bones may still be informative. The presence of a pineal opening in the skull roof necessarily implies the presence of an opening in the braincase, but the absence of a dermal opening does not necessarily preclude an opening in the braincase. Because of this uncertainty it is decided that two separate characters will be used. A pineal opening on the dorsal surface of the neurocranium is absent in Ramirosuarezia, Acanthodes and chondrichthyans.

116. Ventral rounded processes on preotic part of braincase 0 absent 1 present Two bulbous processes are present on the ventral surface of the endocranium in Ramirosuarezia. See Pradel et al., (2009, fig. 2: vpr). 26

117. Periotic process 0 absent 1 present (Pradel et al. 2011) character 11/12. The character list of Pradel et al., (2011) starts at 0. Therefore character 11 is actually 12 etc.

118. Dorsal otic ridge forming horizontal crest 0 absent 1 present Pradel et al., (2011) character 12/13.

119. Perilymphatic fenestrae 0 absent 1 present Pradel et al., (2011) character 16/17. Dependent on the presence of an endolymphatic fossa.

120. Notochord short and stopped by occipital cotylus 0 absent 1 present Pradel et al., (2011) character 21/22.

121. Hyomandibular articulating with the braincase 0 yes 1 no Pradel et al., (2011) character 23/24 (in part).

122. Ethmoidal articulation 0 absent 1 present Pradel et al., (2011) character 25/26.

123. Orbital/palatobasal articulation 0 posterior to optic foramen 1 anterior to optic foramen Pradel et al., (2011) character 26/27 (in part).

124. Accessory processes extend from ventral surface of nasal capsule 0 absent 1 present. Rodlike extensions project anterolaterally from the nasal capsule in Tristychius. See Dick (1978, fig. 4: acc).

125. Internal carotid meets efferent pseudobranchial in orbit 0 absent 1 present This is a unique feature of ‘Cobelodus’ in which the internal carotid may have entered the orbit to join the efferent pseudobranchial before entering the brain (following the discussion in Maisey 2007, pages 37-40).

27

126. Jugular vein passes through cranioquadrate passage 0 absent 1 present

The cranioquadrate passage is a large foramen in the fused palatoquadrate of holocephalans. It is present in Helodus.

127. Anterior margin of ventral fissure 0 straight 1 sinusoidal. This character is dependent on the presence of a ventral cranial fissure. In Acanthodes the anterior margin of the ventral fissure is M-shaped, with the posterior margin of the basisphenoid extending posteriorly in the midline. See e.g. Davis et al., (2012 fig S14).

128. Bulbous otic and auxiliary condyles for palatoquadrate articulation 0 absent 1 present. In Acanthodes there are two bulbous condyles on the otic capsule wall that form a postorbital articulation with the palatoquadrate. See Davis et al., (2012 fig. 1: Art.p.d; Art.p.v).These are also present in Homalacanthus according to Gagnier (1996).

129. Basal fenestra opening into floor of orbit 0 absent 1 present A large open fenestra in the basicranium communicates with the orbit in Acanthodes. See e.g. Davis et al., (2012 fig. S14: bf). Following the discussion of Miles (1973) this is not considered homologous to the hyopophysial foramen which opens into the posterior of the basal fenestra.

130. Nasal sacs 0 unpaired 1 paired.

131. DFC55 Median dermal bone of palate (parasphenoid) 0 absent 1 present

132. ZHU239, GFB113 Ascending process of parasphenoid 0 absent 1 present

133. ZHU240, GFB111 Shape of parasphenoid denticulated field 0 broad rhomboid or lozenge-shaped 1 broad, splint-shaped 2 slender, splint-shaped

134. ZHU241, GFB112 Parasphenoid denticulated field with multifid anterior margin 0 absent 1 present

135. ZHU237 Parasphenoid 0 protruding forward into ethmoid region of endocranium 28

1 behind ethmoid region

136. ZHU238 Denticulated field of parasphenoid 0 without spiracular groove 1 with spiracular groove

137. ZHU243 Parasphenoid denticle field 0 terminates at or anterior to level of foramina for internal carotid arteries 1 extends posterior to foramina for internal carotid arteries

138. 4 carotid foramina in parashpenoid 0 absent 1 present Lu et al., (2012) character 98 (with modified states). Two pair of foramina are present in the parasphenoid of porolepiformes, interpreted by Jarvik as transmitting anterior and posterior branches of the internal carotids. See Jarvik (1972 fig. 92).

139. Parotic dental plates 0 absent 1 present Dermal plates beneath the otic region are known from Eusthenopteron, Glyptolepis, Moythomasia and Cowralepis.

Hyoid arch and gill skeleton

140. DFC37 Basihyal 0 present 1 absent, hyoid arch articulates directly with basibranchial

141. DFC38 Interhyal 0 absent 1 present

142. ZHU197 Foramen in hyomandibular 0 absent 1 present 143. GFB72 Gill arches 0 largely restricted to region under braincase 1 extend far posterior to braincase

144. GFB75 Hypohyal 0 absent 1 present

145. GFB76 Endoskeletal urohyal 0 absent 1 present

146. Disposition of the interbranchial ridges of the oralobranchial chamber roof 0 oligobranchiate 29

1 orthobranchiate 2 nectaspidoform Sansom 2009 character 62.

147. Number of branchial fossae 0 5-7 1 9-17 2 more than 20 Zhu and Gai 2007 character 49

148. Basibranchial elements 0 unpaired 1 paired In Cowralepis the basibranchial elements form a paired series of ossifications, rather than a single midline series as in other gnathostomes where known.

149. Sublingual rod 0 absent 1 present Lu et al., (2012) character 168.

150. Dense array of hyoid arch rays covers gill area 0 absent 1 present Hyoid arch rays in Tristychius form a gill cover. See Dick (1978, fig.13: HYR).

Dermal skull bones

151. DFC18 Dermal skull roof 0 includes large dermal plates 1 consists of undifferentiated plates or tesserae

152. DFC19 Tesserae morphology 0 large interlocking polygonal plates 1 microsquamose, not larger than body tesserae

153. DFC20 Extent of dermatocranial cover 0 complete 1 incomplete (scale-free and elsewhere)

154. DFC21 Endolymphatic ducts open in dermal skull roof 0 present 1 absent

155. DFC22 Endolymphatic ducts with oblique course through dermal skull bones 0 absent 1 present

30

156. DFC23 Series of paired median skull roofing bones that meet at the dorsal midline of the skull (rectilinear skull roof pattern) 0 absent 1 present

157. DFC24 Consolidated cheek plates 0 absent 1 present

158. DFC25 Pineal opening perforation in dermal skull roof 0 present 1 absent

159. DFC26 Enlarged postorbital tessera separate from orbital series 0 absent 1 present

160. DFC27 Bony hyoidean gill-cover series (branchiostegals) 0 absent 1 present

161. DFC28 Branchiostegal plate series along ventral margin of lower jaw 0 absent 1 present

162. DFC29 Branchiostegal ossifications 0 plate-like 1 narrow and ribbon-like

163. DFC30 Branchiostegal ossifications 0 ornamented 1 unornamented

164. DFC31 Imbricated branchiostegal ossifications 0 absent 1 present

165. DFC32 Opercular cover of branchial chamber 0 complete or partial 1 separate gill covers and gill slits

166. DFC34 Shape of opercular (submarginal) ossification 0 broad plate that tapers towards its proximal end 1 narrow, rod-shaped

167. DFC35 Gular plates 0 absent 1 present

168. DFC36 Size of lateral gular plates 0 extending most of length of the lower jaw 31

1 restricted to theanterior third of the jaw (no longer than the width of three or four branchiostegals

169. ZHU196, GFB67 Median gular 0 present 1 absent

170. ZHU147, GFB46 Dermal intracranial joint 0 absent 1 present

171. ZHU152, GFB116 Posterior nostril 0 associated with orbit 1 not associated with orbit

172. ZHU161, GFB48 Number of marginal bones alongside paired median skull roofing bones over the otico-occipital division of braincase 0 single 1 two or more

173. GFB60 Type of dermal neck-joint 0 overlap 1 ginglymoid

174. Type of ginglymoid neck joint 0) ‘conventional’ 1) reverse

175. ZHU180, GFB90 Posterior expansion of maxilla (maxilla cleaver-shaped) 0 present 1 absent

176. ZHU182, GFB59 Contribution by maxilla to posterior margin of cheek 0 present 1 absent

177. ZHU148 Large unpaired median skull roofing bone anterior to the level of nasal capsules 0 absent 1 present

178. ZHU149 Number of nasals 0 many 1 one or two

179. ZHU150 Mesial margin of nasal 0 not notched 1 notched

180. ZHU151 Dermintermedial process 0 absent 1 present 32

181. ZHU153 Position of posterior nostril 0 external, far from jaw margin 1 external, close to jaw margin

182. ZHU154 Supraorbital (sensu Cloutier and Ahlberg 1996, including posterior tectal of Jarvik) 0 absent 1 present

183. ZHU155 Supraorbital, preorbital and nasal 0 unfused 1 fused

184. ZHU156 Tectal (sensu Cloutier and Ahlberg 1996, not counting the posterior tectal of Jarvik) 0 absent 1 present

185. ZHU157 Lateral plate 0 absent 1 present

186. ZHU158 Location of pineal foramen/eminence 0 level with posterior margin of orbits 1 well posterior of orbits

187. ZHU159 Parietals (preorbitals of placoderms) surround pineal foramen or eminence 0 yes 1 no

188. ZHU160 Complete enclosure of spiracle by skull roof bones 0 absent 1 present

189. ZHU162 paranuchal number 0 one pair 1 two pairs

190. ZHU164 Contact of nuchal or centronuchal plate with paired preorbital plates 0 absent 1 present

191. ZHU167 Number of extrascapulars 0 uneven 1 paired

192. ZHU168 Dermal neck-joint between paired main-lateral-line-bearing bones of skull and shoulder girdle 0 absent 1 present

193. ZHU171 Foramina (similar to infradentary foramina) on cheek bones 33

0 absent 1 present

194. ZHU172 Lacrimal posteriorly enclosing posterior nostril 0 absent 1 present

195. ZHU173 Most posterior major bone of cheek bearing preopercular canal (preopercular) extending forward, close to orbit 0 absent 1 present

196. ZHU174 Number of cheek bones bearing preopercular canal posterior to jugal 0 one 1 two

197. ZHU175 Bone bearing both quadratojugal pit-line and preopercular canal 0 absent 1 present

198. ZHU176 Dermohyal 0 absent 1 present

199. ZHU177 Premaxillae with inturned symphysial processes 0 absent 1 present

200. ZHU178 Premaxilla forming part of orbit 0 absent 1 present

201. ZHU181 Ventral margin of maxilla 0 straight 1 curved

202. ZHU198 Large dermal plates forming outer dental arcade 0 only with denticles 1 with large monolinear tooth row

203. ZHU244 Presupracleithrum 0 absent 1 present

204. ZHU170 Number of sclerotic plates 0 four or less 1 more than four

205. GFB29 Dermal ornamentation 0 smooth 1 ridges 34

2 tuberculate

206. GFB36 Cranial spines 0 absent 1 present, multicuspid 2 present, monocuspid

207. GFB40 Endolymphatic duct relationship to median skull roof bone (i.e. nuchal plate) 0 within median bone 1 on bones flanking the median bone (e.g. paranuchals)

208. GFB42 Dermal plate associated with pineal eminence or foramen 0 contributes to orbital margin 1 plate bordered laterally by skull roofing bones

209. GFB44 Broad supraorbital vaults 0 absent 1 present

210. GFB49 Suture between paired skull roofing bones (centrals of placoderms; postparietals of osteichthyans) 0 straight 1 sinusoidal

211. GFB50 Medial processes of paranuchal wrapping posterolateral corners of nuchal plate 0 absent 1 present 2 paranuchals precluded from nuchal by centrals 3 no median posterior skull roof bone

212. GFB51 Paired pits on ventral surface of nuchal plate 0 absent 1 present

213. GFB52 Sclerotic ring 0 absent 1 present

214. GFB54 Cheek plate 0 undivided 1 divided (i.e., squamosal and preopercular)

215. GFB55 Subsquamosals in taxa with divided cheek 0 absent 1 present

216. GFB56 Preopercular shape 0 rhombic 1 bar-shaped

217. GFB89 Premaxilla 35

0 extends under orbit 1 restricted anterior to orbit

218. Median rostral extension of the headshield 0 absent 1 present (Sansom 2009) character 1 Anterior median processes of the headshield are present in various osteostracans and galeaspids. Only present in Boreaspis in the taxa considered here. The extension of the headshield in Brindabellaspis is not here considered as a discrete process.

219. Lateral fields 0 absent 1 present. Sansom 2009 character 4.

220. Division of lateral fields 0 absent 1 divided once 2 divided twice Sansom 2009 characters 5-6

221. Lateral fields extend posterior to pectoral sinus 0 absent 1 present Sansom 2009 character 10

222. Lateral fields extend onto cornua 0 absent 1 present Sansom 2009 character 11 (with modified states).

223. Median field 0 absent 1 present Sansom 2009 character 13.

224. Median field separation from pineal plate or foramen 0 absent 1 present Sansom 2009 character 15

225. External endolymphatic duct openings’ location in relation to median field 0 internal 1 external Sansom 2009 character 17.

226. Median dorsal opening 0 absent 1 present 36

Sansom 2009 character 29. (Zhu and Gai 2007) character 1

227. External nasal opening 0 single median 1 paired Sansom (2009) character 25.

228. Nasohypophyseal opening shape 0 unconstricted 1 constriction between nasal and hypophysial divisions; 2) split into nasal and hypophysial divisions. Sansom 2009 character 29 (with modified states).

229. Cornual extensions 0 absent 1 present Sansom 2009 character 36. Zhu and Gai 2007 character 14. Posterolateral extensions of the headshield in osteostracans and galeaspids. Here the ‘corners’ of galeaspids (Zhu and Gai 2007) are considered equivalent to the corneal extension of osteostracans (Sansom 2009). Assumed to be absent (alternatively could be considered inapplicable) in gnathostomes.

230. Fused scale rows on posterior of headshield 0 absent 1 present Sansom 2009 character 43.

231. Dorsal spinal process of headshield 0 absent 1 present Sansom 2009 character 44. Assumed to be absent (alternatively could be considered inapplicable) in gnathostomes.

232. Oralobranchial covering 0 tesserae 1 plates Sansom 2009 character 60 (with revised states). Assumed to be inapplicable in gnathostomes.

233. Shape of median dorsal opening 0 transverse slit-like 1 oval-like 2 slender longitudinal oval Zhu and Gai 2007 character 6

234. Spines on corneal extension 0 absent 1 present Zhu and Gai 2007 character 18.

235. Headshield enclosed posteriorly behind oralobranchial chamber 37

0 no 1) yes In some osteostracans the headshield forms a continuous ring around the body behind the oralobranchial opening. This is present in Tremataspis, Benneviaspis, Boreaspis, Norselaspis and Procephalaspis in the taxa considered here.

236. Enlarged tubercles form symmetrical pattern on posterior part of headshield 0 absent 1 present. Tremataspis has a distinctive pattern of tubercles behind the median field. See for example Robertson 1937 plate II.

237. T-shaped rostral plate 0 absent 1 present (Carr and Hlavin 2010) character 5 (with modified states). A T-shaped rostral is found in many eubrachythoracid arthrodies. The placoderm rostral is here considered equivalent in position to the posterior median rostral of osteichthyans so this character can be scored as absent in a large number of taxa.

238. Centronuchal plate 0 absent 1 present Dupret et al., (2009) character 17

239. Postnuchal plates 0 absent 1 present Dupret et al., (2009) character 45. The terminology of Zhu et al (2013) regarding the ‘extrascapular’ plates of placoderms is followed. Since the nuchal and paranuchal plates of placoderms are considered to be homologous with the extrascapular plates of osteichthyans, the term postnuchals is used for the ‘extrascapular’ plates of placoderms. Postnuchal plates are defined as loosely attached plates posterior to the nuchal plates. In some taxa there are overlap surfaces on the median dorsal plate which may be for the postnuchal plate (Dupret et al., 2009 character 43). Taxa with this character are scored as unknown for the presence of postnuchal plates.

140. Cu.s.o on suborbital plate 0 absent 1 present The so-called ‘cutaneous sense organs’ recognised by (Ørvig 1960) are pits present in a number of arthrodires

241. Cu.s.o on postsuborbital plate 0 absent 1 present The posterior cu.s.o of Parabuchanosteus (Young 1979 figure 13, cusop) is here considered a postsuborbital cuso, as the suborbital and postsuborbital plates have likely fused in this taxon.

242. Cu.s.o on skull roof posterior to orbits 38

0 absent 1 present The Cu.s.o in Romundina (Ørvig 1975). A much smaller cu.s.o was described in a similar position in Brindabellaspis (Young 1980), but these are variably developed, and are no wider than the sensory line canals. Since the sensory lines are variably developed as canals or grooves in Brindabellaspis it is not clear that these ‘cutaneous sensory organs’ are not continuations of the sensory lines, so this character is scored as unknown in Brindabellaspis. A cluster of Cu.s.o pits is also labelled in a posterior region in Eurycaraspis (Liu 1991). Since these are a cluster in an unusual position Eurycaraspis is currently scored as unknown for this character.

243. Parietals or Preorbital plates at anterior edge of skull roof 0 no 1 yes In some placoderms the dermal bones of the snout (rostral, pineal) have been lost or reduced such that the preorbital plates (equivalent to the parietals of Sarcopterygians) sit at the anterior edge of the skull. This is the case in ptyctodontids, Cowralepis, Eurycaraspis and Quasipetalichthys.

244. Sclerotic ring incorporated into skull roof 0 absent 1 present In Entelognathus the sclerotic ring is incorporated into the skull roof and is immovable. Described in Zhu et al 2013.

245. Rostrocaudal groove on the inner surface of the premedian plate 0 absent 1 present (Jia et al. 2010) character 3 Present in Remigolepis. See Johanson (1997 fig. 4e, rcgr, fig. 5).

246. Preorbital depression 0 absent 1 present Jia et al (2010) character 6

247. Preorbital recess 0 absent 1 present Jia et al (2010) character 8 (in part). Following Zhu (1996) and Jia et al (2010), the preorbital depression and preorbital recess are not considered homologous despite the complementary codings in the taxa considered here.

248. Preorbital recess 0 restricted to premedian plate 1 extends onto lateral plates Jia et al (2010) character 8 (in part).

249. Nuchal plate 0 without orbital facets 1 with orbital facets Jia et al (2010) character 14. 39

250. Submarginal articulation 0 absent 1 present Jia et al (2010) character 16. See e.g. Young 1990 fig. 5-6.

251. Prelateral plate 0 absent 1 present Considered applicable only in taxa with a lateral plate (i.e. antiarchs).

252. Posterior descending lamina of skull roof 0 absent 1 present (Pan et al. 2015) character 6. A posterior descending lamina of the skull roof is found in some petalichthyids (Pan et al., 2015 fig. 3, pdl), including Eurycaraspis among those considered here. A similar lamina is found in Materpiscis and Austroptyctodus.

253. Paraorbital plate separating suborbital from orbit: 0) absent; 1) present. A dermal plate that is not associated with the palatoquadrate and runs lateral to the orbit is present in Wuttagoonaspis, and possibly Brindabellaspis.

254. Mesial lamina of marginal plate 0 absent 1 present A pair of laminae on the internal surface of the marginal plate, presumably for contact with the braincase, is present in ptyctodonts with suitable preservation. See e.g. Long (1997 fig. 4, mes.lam).

255. Transverse external groove behind pineal opening 0 absent 1 present A character of Dicksonosteus and Diandongpetalichthys. See e.g. Zhu (1991, fig. 1: srcp)

256. Nostrils enclosed in dermal skull roof 0 yes 1 no In eubrachythoracid arthrodires, the snout is assumed to continue in soft tissue, so that the nostrils are not enclosed within dermal bone. Where only the posterior nostril is enclosed, taxa are scored as yes, as are taxa with dorsal nostrils (acanthothoracids, antiarchs etc.)

257. Lacrimal 0 absent 1 present The lacrimal is here defined as a bone ventral/lateral to the orbit, anterior to the suborbital/jugal, that does not bear the supraorbital canal. It may or may not border the posterior nasal opening.

258. Large median bone directly anterior to parietals 0 absent 1 present 40

Related to Dupret et al., (2009) character 5 and (Lu et al. 2012). This character describes the presence of a rostral bone in placoderms and a median postrostral in osteichthyans, which are equivalent in position and therefore coded as the same bone.

259. Snout region fragmented into mosaic of small plates 0 no 1 yes Lu et al., (2012) character 5 (in part). This is a characteristic of Powichthys, Diabolepis, and early lungfishes. etc

260. Choana 0 absent 1 present. Lu et al., (2012) character 12.

261. B-bone 0 absent 1 present Lu et al., (2012) character 13. A large median bone between the postparietals. Present in Diabolepis and some early lungfishes.

262. Number of supraorbitals 0 one 1 two 2 many Lu et al character 14.

263. Series of bones lateral to supratemporal 0 absent 1 single bone 2 two bones This character describes the presence of skull roof bones lateral to the series that bears the sensory canals. In Osteichthyans there is the extratemporal, while in placoderms there is the postmarginal. In Guiyu, there is an accessory extratemporal, so it scored as state 2.

264. Foramina on cheek bones 0 absent 1 present Lu et al., (2012) character 70. 3 large foramina are present on the cheek units of Youngolepis and Kenichthys. See e.g. Chang (1991 fig. 6: p.SQP)

265. Contact between most posterior major bone of cheek bearing preopercular canal and maxilla 0 present 1 absent Lu et al., (2012) character 79.

266. Number of branchiostegal rays per side 0 10 or more 1 2-7 2 one 41

Lu et al., (2012) character 170 (with modified states).

267. Pore clusters 0 absent 1 present Lu et al., (2012) character 175.

268. Westoll lines 0 absent 1 present Lu et al., (2012) character 259. Considered inapplicable in taxa lacking cosmine.

269. Prerostral plate 0 absent 1 present In Guiyu, there is a median dermal bone rostral to the premaxilla, termed the prerostral plate.

270. Size of cosmine pores 0 small 1 large Zhu et al (2001) character 149. Large cosmine pores are known in Meemannia, Achoania, Psarolepis and Styloichthys.

271. Interparietal 0 absent 1 present A median dermal bone between the parietals is found in Onychodus.

272. Premaxilla contributes to posterior nostril 0 absent 1 present (Swartz 2009) character 6.

273. Supratemporal contact with postparietal 0 absent 1 present Swartz 2009 character 15 (modified wording). Supratemporal refers to the actinopterygian intertemporal, sarcopterygian supratemporal and placoderm marginal.

274. Supratemporal contact with nasal 0 absent 1 present Swartz (2009) character 16.

275. Notch in anterior margin of jugal 0 absent 1 present Swartz (2009) character 19.

42

276. Quadratojugal 0) present 1) absent Swartz (2009) character 26. A quadratojugal is here defined as a small separate dermal bone associated with the quadrate. This includes the postsuborbital of placoderms.

277. Number of paired extrascapulars 0 one pair 2 two pairs Swartz (2009) character 28. Romundina is here considered to have two pairs due to the presence of a medial paranuchal.

278. Accessory operculum 0 absent 1 present Swartz (2009) character 32.

279. Dermal bone (sarcopterygian postorbital) between jugal and intertemporal 0 absent 1 present. The intertemporal is the sarcopterygian intertemporal (i.e. dermosphenotic of actinopterygians and postorbital of placoderms). The infraorbital canal crosses an additional bone in many sarcopterygians before reaching the jugal, and this is termed the postorbital. Since there is no similar bone between the suborbital of placoderms and the placoderm postorbital (which is equivalent to the intertemporal of sarcopterygians not the postorbital), this character is scored as absent in placoderms. The placoderm suborbital is here assumed to correspond to the osteichthyan jugal.

280. Lacrimal notch 0 absent 1 present A lacrimal notch is present in Osorioichthys.

281. Cheek plates fragmented into many small plates 0 absent 1 present In Dialipina the cheek is a mosaic of small plates that cannot be easily homologised with those of a standard osteichthyan cheek.

282. Orbital process of maxilla 0 absent 1 present This is a unique feature of Dialipina. See Schultze and Cumbaa (2001 fig. 18.1: o.pMx). Although there is a dorsal flange on the maxilla of many tetrapodomorphs (e.g. (Lebedev 1995) fig. 8I: dmax), this is not here considered equivalent as it is internal (not covered in ornament, whereas the orbital process of Dialipina is external (with ganoine ridges).

Sensory lines 43

Producing characters describing the sensory canals of the cheek region in early vertebrates is challenging because of the difficulty in establishing homologies between different groups. Here, simple morphological definitions are used to define characters. Terminology follows, in part, (Northcutt 1989). The following figure shows a generalised fish head showing all the canals for which characters are formed.

SO: supraorbital canal IO: infraorbital canal ET: ethmoid commissure O: otic canal PM: postmarginal canal POP: preopercular canal Although the postmarginal canal of placoderms has been argued to be homologous with the preopercular canal (Stensio 1947), this interpretation has been challenged (e.g. Young 1980; Holgren and Pehrson 1949). It is here noted that the preopercular canal of osteichthyans generally links up with the mandibular canal, while the postmarginal canal branches from the main lateral line canal and ends blindly. It also noted that the postmarginal canal is found dorsomedial to the spiracular opening while the preopercular canal runs ventrolateral to it. These criteria can be used to produce a purely morphological definition that can be scored in fossils. A postmarginal canal is characteristic of placoderms, although a similar canal appears to be present in Cheirolepis trailli, where it is found in addition to a preopercular canal. The preopercular canal connects to the mandibular canal. It may or may not connect to the infraorbital canal or the otic canal. H: horizontal canal SOR: supraoral canal A canal that runs ventrally or posteroventrally from the infraorbital canal, leaving the edge of the cheek or entering the maxilla (in Entelognathus). Characteristic of many placoderms, and also found in Onychodus. “P”: extension of otic canal In some acanthodians, the otic canal continues forward above the orbit anterior to the junction with the infraorbital canal. This is the canal labelled “P” by Northcutt (1989, fig. 3.3: “P”). This can occur in conjunction with a supraorbital canal: e.g. in Acanthodes. See Watson (1937 fig. 20).

283. DFC16 Sensory line network 0 preserved as open grooves 1 pass through canals enclosed within dermal bones 44

284. DFC17 Jugal portion of infraorbital canal joins supramaxillary canal 0 present 1 absent

285. ZHU166 Junction of posterior pitline and main lateral line 0 far in front of posterior margin of skull roof 1 close to posterior margin of skull roof

286. ZHU183 Course of ethmoid commissure 0 middle portion through median rostral 1 sutural course 2 through bone center of premaxillary

287. ZHU184 Position of anterior pit-line 0 on paired median skull roofing bones over the otico-occipital division of braincase 1 on paired median skull roofing bones over the sphenoid division of braincase

288. ZHU185 Middle and posterior pit-lines on postparietal 0 posteriorly situated 1 mesially situated

289. ZHU186 Position of middle and posterior pit lines 0 close to midline 1 near the central portion of each postparietal

290. ZHU187 Course of supraorbital canal 0 between anterior and posterior nostrils 1 anterior to both nostrils

291. ZHU188 Course of supraorbital canal 0 straight 1 lyre-shaped

292. ZHU189 Posterior end of supraorbital canal 0 extends back to level of posterior/middle pitlines 1 terminates anterior to level of posterior/middle pit lines 2 extends posterior to pit-lines In the previous formulation of this character, states were not independent from differences in dermal bone pattern between taxa and therefore did not really address the supraorbital canal itself. Here the character is simplified to three states: 0) extends back to level of posterior/middle pit lines; 1) terminates anterior to the level of the posterior/middle pit lines; 2) extends posterior to pit-lines. This is therefore independent from dermal bone pattern. This character is considered inapplicable in taxa where the supraorbital canal and otic canal are continuous. State 2 is found in Ligulalepis.

293. ZHU190 Contact between otic and supraorbital canals 0 not in contact 1 in contact

294. ZHU191 Contact of supraorbital and infraorbital canals 45

0 in contact rostrally 1 not in contact rostrally

295. ZHU192 Otic canal 0 runs through skull roof 1 follows edge of skull roof

296. ZHU193 Infraorbital canal follows premaxillary suture 0 no 1 yes

297. ZHU194 Sensory canal or pit-line associated with maxilla 0 absent 1 present

298. ZHU217 Course of mandibular canal 0 not passing through most posterior infradentary 1 passing through most posterior infradentary

299. ZHU218 Course of mandibular canal 0 passing through dentary 1 not passing through dentary

300. Supraorbital canals and posterior pitlines cross as an X 0 absent 1 present The previous formulation of this character was Central dermal skull bone (nuchal) with converging posterior pit-line canals and supraorbital canals: 0) absent; 1) converging but not meeting; 2) cross as an X. State 1 overlaps with ‘posterior end of the supraorbital canal’ character. The definition of this character should also be independent of skull roof patterns.

301. GFB31 Sensory canals/grooves 0 contained within the thickness of dermal bones 1 contained in prominent ridges on visceral surface of bone

302. GFB34 Anterior pit line of dermal skull roof 0 absent 1 present

303. GFB47 Otic canal extends through postparietals 0 absent 1 present

304. Infra-orbital sensory line 0 Crosses lateral field 1 does not cross lateral field. Sansom 2009 character 31.

305. Festooned pattern of sensory canals 0 absent 1 present 46

Sansom 2009 character 32. Zhu and Gai 2007 character 2.

306. Multiply branched sensory canal system associated with the posterior end of the supraorbital canal 0 absent 1 present This is an autapomorphy of Wenshanaspis zhichangensis. See (Zhao et al. 2001), fig.3:mtc1.

307. Supraorbital sensory canals 0 absent 1 present Sansom et al., (2009) character 35; Zhu and Gai (2006) character 39

308. Branching end of lateral transverse canals 0 absent 1 present Zhu and Gai 2007 character 33. This character is assumed to be applicable only to galeaspids in which the festooned pattern of sensory canals leaves many lateral transverse canals that are blind-ending, and these can be branched or unbranched.

309. Anterior supraorbital canal 0 absent 1 present Zhu and Gai 2007 character 38. Paired anterior canals that are separate from the main supraorbital canal are present in Eugaleaspis and Lunaspis (rostraler Sinneskanal, Gross 1961).

310. Median dorsal canal 0 absent 1 present Zhu and Gai 2007 character 43 (with modified states) Here only taxa considered to have a ‘developed’ canal by Zhu and Gai are scored as present.

311. Infraorbital and cephalic main sensory line grooves run along mesial margin of marginal plate 0 no 1 yes (Dupret et al. 2009) character 16.

312. Central sensory lines 0 absent 1 present Dupret et al. (2009) character 31. Central sensory lines are orientated in a posteromesial direction from the otic canal near the junction with the infraorbital canal and project toward the centre where the middle and posterior pit lines also terminate. It is present in arthrodies, Romundina, Diplacanthius and Cheirolepis trailli.

313. Semicircular pit line 0 absent 1 present 47

Jia et al (2010) character 23.

314. Horizontal sensory line canal on cheek 0 absent 1 present Adapted from Carr and Hlavin (2010) character 81 A canal on the suborbital plate that connects the postsuborbital canaland the infraorbital canal (although it may not run the entire way) is present in Parabuchanosteus and Holonema as well as a number of arthrodires not scored in this matrix.

315. Postmarginal canal 0 absent 1 present

316. Preopercular canal 0 absent 1 present

317. Preopercular canal meets main canal 0 absent 1 present The preopercular canal joins the cephalic main lateral line canal in some acanthodians: Acanthodes, Brochoadmones and Euthacanthus.

318. Supraoral canal: 0) absent; 1) present.

319. Extension of otic canal beyond infraorbital canal (“P” canal) 0 absent 1 present This character is not applicable when the supraorbital canal is confluent with the otic canal.

320. Ethmoid commissure fused into midline canal 0 absent 1 present This is a unique feature of Brindabellaspis seen in currently unpublished specimens (specimen number ANUV3247).

321. Posterior pitline and postmarginal canal 0 staggered 1 confluent In Entelognathus the postmarginal canal and posterior pitline are confluent, thus forming an ‘X’ shape with the cephalic main lateral line canal.

322. Supraorbital canal joins infraorbital canal 0 anterior to supraoral canal 1 posterior to supraoral canal Only applicable in taxa with a supraoral canal. Can be scored as 0 when the most anterior point of the supraorbital canal is clearly anterior to the supraoral canal. This character effectively captures the elongation of the preorbital region in Wuttagoonaspis. The suborbital plate extends so far forward that the supraoral canal leaves the infraorbital canal anterior to the meeting of the infraorbital canal and the supraorbital canal. 48

323. Sensory line commissure across extrascapular bones 0 absent 1 present This character describes the presence or absence of a sensory canal across the extrascapular (or nuchal-paranuchal) series of bones.

324. DFC15 Sensory line canal 0 passes between or beneath scales 1 passes over scales and/or is partially enclosed or surrounded by scales 2 perforates and passes through scales

325. Dorsal branch of main lateral line canal on PDL plate 0 absent 1 present

326. Sharp downward bend in PDL sensory line 0 absent 1 present Among the taxa considered here, Groenlandaspis (this character is also present in all groenlandaspids) , Buchanosteus and Holonema have sharply downturned canals on their posterior dorsolateral plates. Only applicable in taxa with PDL plates with a sensory line.

Dentition and jaws

327. DFC39 Oral dermal tubercles borne on jaw cartilages 0 absent 1 present

328. DFC40 Tooth whorls 0 absent 1 present

329. DFC41 Bases of tooth whorls 0 single, continuous plate 1 some or all whorls consist of separate tooth units

330. DFC42 Enlarged adsymphysial tooth whorl 0 absent 1 present

331. DFC43 Teeth ankylosed to dermal bones 0 absent 1 present

332. DFC44 Dermal jaw plates on biting surface of jaw cartilages 0 absent 1 present

49

333. DFC45 Maxillary and dentary tooth-bearing bones 0 absent 1 present

334. DFC46 Large otic process of the palatoquadrate 0 absent 1 present

335. DFC47 Insertion area for jaw adductor muscles on palatoquadrate 0 ventral 1 lateral

336. DFC48 Oblique ridge or groove along medial face of palatoquadrate 0 absent 1 present

337. DFC49 Fenestration of palatoquadrate at basipterygoid articulation 0 absent 1 present

338. DFC50 Perforate or fenestrate anterodorsal (metapterygoid) portion of palatoquadrate 0 absent 1 present

339. DFC51 Pronounced dorsal process on Meckelian bone or cartilage 0 absent 1 present

340. DFC52 Preglenoid process 0 absent 1 present

341. DFC53 Jaw articulation located on rearmost extremity of mandible 0 absent 1 present

342. ZHU140, GFB80 Acrodin 0 absent 1 present

343. ZHU141, GFB86 Plicidentine 0 absent 1 simple or generalized polyplacodont

344. ZHU201, GFB106 Number of coronoids 0 more than three 1 three

345. ZHU202, GFB94 Fangs of coronoids (sensu stricto) 0 absent 1 present 50

346. ZHU199 Tooth-bearing median rostral 0 absent 1 present

347. ZHU200 Teeth of dentary 0 reaching anterior end of dentary 1 not reaching anterior end

348. ZHU203 Marginal denticle band on coronoids 0 broad band, at least posteriorly 1 narrow band with 2-4 denticle rows

349. ZHU204 infradentary 0 absent 1 present

350. ZHU205 Infradentary foramina 0 present 1 absent

351. ZHU206 Large ventromesially directed flange of symphysial region of mandible 0 absent 1 present

352. ZHU207 Flange like extension of mandible composed of prearticular and Meckelian ossification 0 absent 1 present

353. ZHU208 Strong ascending flexion of symphysial region of mandible 0 absent 1 present

354. ZHU209 Parasymphysial plate 0 detachable tooth whorl 1 long with posterior corner, sutured to coronoid, denticulated or with tooth row 2 absent

355. ZHU210 Anterior end of prearticular 0 far from jaw symphysis 1 near jaw symphysis

356. ZHU211 Prearticular - dentary contact 0 present 1 absent

357. ZHU212 Meckelian bone exposed immediately anterior to first coronoid 0 yes 1 no

358. ZHU213 Dermal plates on mesial (lingual) surfaces of Meckels cartilage and palatoquadrate 51

0 absent 1 present

359. ZHU214 Biconcave glenoid on lower jaw 0 absent 1 present

360. ZHU235 Vomerine fangs 0 absent 1 present

361. ZHU215 Contact between palatoquadrate and dermal cheek bones 0 continuous contact of metapterygoid and autopalatine 1 metapterygoid and autopalatine contacts separated by gap between commissural lamina of palatoquadrate and cheek bones

362. ZHU216 Metapterygoid with developed medial ventral protrusion 0 absent 1 present

363. DUPRET254 jaws 0 absent 1 present

364. LONG257 Deep, high supragnathal bone with durophagous occlusal surface 0 absent 1 present

365. GFB79 Enamel(oid) on teeth 0 absent 1 present

366. GFB84 Distribution of tooth whorls 0 upper and lower jaws 1 lower jaws only 2 upper jaws only

367. GFB91 Pair of tooth plates (anterior supragnathals or vomers) on ethmoidal plate 0 absent 1 present

368. GFB93 Extent of infradentaries 0 along much of ventral margin of dentary 1 restricted to posterior half of dentary

369. Position of hyomandibula articulation on neurocranium 0 Anterior postion, suborbital 1 posterior position, behind orbit.

370. GFB97 Autopalatine and quadrate 0 comineralized 52

1 separate mineralizations

371. GFB101 Palatoquadrate fused with neurocranium 0 absent 1 present

372. Fused anterior supragnathals 0 absent 1 present Fused left and right anterior supragnathals are an autapomorphy of Groenlandaspis shown in unpublished Groenlandaspis specimens from Mount Howitt (JL pers. obs.): AMF59809 and AMF62534 (the latter shown in Rise of Fishes book).

373. Posterior superognathal with vertical pipe-like ridges 0 absent 1 present This character describes the distinctive toothplates of Holonema. See Miles (1971).

374. Strongly curved infragnathals with wide flat non-biting region 0 absent 1 present These distinctive lower jaw toothplates are characteristic of those antiarchs in which the toothplates are known: Remigolepis, Pterichthyodes and Bothriolepis among the taxa considered here. See Young (1984 fig. 5) and Johanson (1997, fig. 13d-f).

375. Posterior process of vomers 0 absent 1 present Lu et al., (2012) character 89 (with modified states). Carr and Hlavin (2010) character 68. Posterior processes of the anterior supragnathals/vomers are present in eubrachythoracids and Eusthenopteron.

376. Number of fang pairs on ectopterygoid 0 one 1 two 2 none. Lu et al., (2012) character 103.

377. Proportions of entopterygoid 0 anterior end level with processus ascendens 1 anterior end considerably anterior to processus ascendens Lu et al., (2012) character 104. This character is dependent on the presence of a processus ascendens of the palatoquadrate.

378. Number of dermopalatines 0 one 1 two 2 more than 2 Lu et al., (2012) character 106 (with modified states).

379. Enlarged anterior tooth on premaxilla 53

0 absent 1) present Lu et al., (2012) character 111.

380. Number of tooth rows on outer dental arcade 0 one 1 two Lu et al., (2012) character 123 (with modified states).

381. Number of infradentaries 0 one 1 two 2 more than 2 Friedman (2007) character 54 (with modified states)

382. Coronoids 0 present 1 absent Lu et al., (2012) character 144.

383. Number of fang pairs on posterior coronoid 0 one 1 two 2 none Lu et al., (2012) character 155.

384. Teeth radial rows on prearticular 0 absent 1 present Lu et al., (2012), character 160.

385. Labial pit 0 absent 1 present Lu et al., (2012) character 162.

386. Retroarticular process 0 absent 1 present Lu et al., (2012) character 163.

387. Submandibulars 0 absent 1 present Lu et al., (2012) character 173.

388. ‘Symplectic’ articulation 0 absent 1 present Friedman (2007) character 160.

54

389. Processus ascendens of palatoquadrate: 0) absent; 1) present. An antero-dorsal process of the palatoquadrate anterior to the paratemporal process, which sits over the orbitotemporal region. It is a characteristic feature of Sarcopterygians.

390. Grooved, curved upper toothplates attached to median labial element 0 absent 1 present This character describes the unique, S-shaped toothplates found in Ramirosuarezia.

391. Two divergent processes extending from anterior of palatoquadrate 0 absent 1 present This character describes the unique anterior end of the palatoquadrate in Ramirosuarezia.

392. Extramandibular dentition 0 absent 1 present The presence of extramandibular dentition in Chondrenchelys was the subject of Finarelli and Coates (2011).

393. Bilateral series of labial cartilages 0 absent 1 present Debeerius has a miniumum of five bilateral labial cartilages.

Paired fins and girdles

394. DFC121 Pelvic fins 0 absent 1 present

395. DFC122 Intromittent organ containing bone, not associated with pelvic fins 0 absent 1 present Gemuendina is rescored as ?, based on discussion in Trinajstic et al., (2015).

396. LONG258 Intromittent organ with one large J-shaped element 0 absent 1 present

397. LONG259 Intromittent organ ('clasper') consisting entirely of cartilage, formed from distal part of pelvic fin 0 absent 1 present

398. DFC110 Scapular process of shoulder endoskeleton 0 absent 1 present 55

399. DFC111 Ventral margin of separate scapular ossification 0 horizontal 1 deeply angled

400. DFC112 Cross sectional shape of scapular process 0 flattened or strongly ovate 1 subcircular

401. DFC113 Flange on trailing edge of scapulocoracoid 0 absent 1 present

402. DFC114 Scapular process with posterodorsal angle 0 absent 1 present

403. DFC115 Endoskeletal postbranchial lamina on scapular process 0 present 1 absent

404. DFC116 Mineralisation of internal surface of scapular blade 0 mineralised all around 1 unmineralised on internal face forming a hemicylindrical cross-section

405. DFC117 Coracoid process 0 absent 1 present

406. DFC118 Procoracoid mineralisation 0 absent 1 present

407. DFC119 Fin base articulation on scapulocoracoid 0 stenobasal 1 eurybasal

408. DFC120 Perforate propterygium 0 absent 1 present

409. ZHU250, GFB201 Endoskeletal supports in pectoral fin 0 multiple elements articulating with girdle 1 single element ("humerus") articulating with girdle

410. ZHU248 Triradiate scapulocoracoid 0 absent 1 present

411. ZHU249 Subscapular foramen 0 absent 56

1 present

412. ZHU251 Pectoral propterygium 0 absent 1 present

413. GFB190 Scapular infundibulum 0 absent 1 present

414. GFB202 Number of basals in polybasal pectoral fins 0 three or more 1 two

415. GFB204 Number of mesomeres in metapterygial axis 0 five or fewer 1 seven or more

416. GFB205 Biserial pectoral fin endoskeleton 0 absent 1 present

417. GFB207 Filamentous extension of pectoral fin from axillary region 0 absent 1 present

418. Entepicondyle on humerus 0 present 1 absent Dependent on presence of a humerus. The humerus of Onychodus lacks a developed entepicondyle.

419. Horizontal plate of scapulocoracoid 0 absent 1 present Swartz (2009) character 30.

420. Distal articulation of propterygium 0 with fin rays 1 with a second enlarged element 2 no articulation This character is dependent on the presence of a propterygium. In Helodus, a second enlarged element articulates with the propterygium distally (Moy-Thomas 1936 fig. 8: ar), whereas the propterygium of Hamiltonichthys apparently lacks calcified radials.

421. DFC104 Macromeric dermal shoulder girdle 0 present 1 absent

422. DFC105 Dermal shoulder girdle composition 0 ventral and dorsal (scapular) components 1 ventral components only 57

423. DFC106 Dermal shoulder girdle forming a complete ring around the trunk 0 present 1 absent

424. DFC107 Pectoral fenestra completely encircled by dermal shoulder armour 0 present 1 absent

425. DFC108 Median dorsal plate 0 absent 1 present

426. DFC109 Pronounced internal crista (keel) on median dorsal surface of shoulder girdle 0 absent 1 present

427. DFC124 Pectoral fins covered in macromeric dermal armour 0 absent 1 present

428. DFC125 Pectoral fin base has large, hemispherical dermal component 0 absent 1 present

429. DFC128 Paired fin spines 0 absent 1 present

430. ZHU245 Anocleithrum 0 element developed as postcleithrum 1 element developed as anocleithrum sensu stricto

431. ZHU246 Dorsal cleithrum (AL of the Placodermi), ventral cleithrum (AVL of the Placodermi) and pectoral spine (SP of the Placodermi) 0 not fused 1 fused

432. ZHU247 Relationship of clavicle to cleithrum 0 ascending process of clavicle overlapping cleithrum laterally 1 ascending process of clavicle wrapping round anterior edge of cleithrum, overlapping it both laterally and mesially

433. ZHU252 Pelvic girdle with substantial dermal component 0 yes 1 no

434. ZHU253 Pelvic fin spine 0 absent 1 present

58

435. GFB183 Shape of dorsal blade of dermal shoulder girdle 0 spatulate 1 pointed

436. GFB187 Posterior dorsolateral (PDL) plate or equivalent 0 absent 1 present

437. PL and PDL overlap 0 simple 1 insertion Carr and Hlavin (2010) character 42

438. Left and right PDL plates contact below the MD 0 absent 1 present This characterises groenlandaspids (Tiaraspis, Africanaspis, Belgiaspis, Turretaspis, Mulgaspis, Groenlandaspis etc)(Ritchie 1975). Groenlandaspis is the only one included here.

439. PDL plate visible externally 0 absent 1 present Only applicable in taxa in which a PDL plate is known. A small, entirely subdermal PDL is an autapomorphy for Cowralepis in this matrix (Ritchie 2005).

440. Posteriorly produced spine on MD plate 0 absent 1 present Carr and Hlavin (2010) character 37. In Coccosteus the MD plate is drawn out into a narrow spine that projects posteriorly. This is here considered different from the MD plates of many placoderms that form tall dorsal spines e.g. ptyctodontids, acanthothoracids, Groenlandaspis, some antiarchs.

441. Joint in macromeric armoured pectoral fin 0 absent 1 present Jia et al. (2010) character 27. Reworded character so that it is only applicable in taxa with a pectoral fin enclosed in armour (i.e. antiarchs).

442. Cd1 and Cd2 plates 0 in contact 1 separated Jia et al. (2010) character 28. Only applicable to taxa with a macromeric armoured pectoral fin.

443. Clavicles/interolateral plates 0 Large plates, comparable in size to cleithrum 1 reduced to small semilunar plates, paired 2 unpaired semilunar plates Jia et al., (2010) character 44 (with modified states). 59

This character assumes homology between the clavicles of Osteichthyans, the interolateral plates of arthrodires and the semilunar plates of antiarchs. If these bones are not homologous, then character state 0 would simply read “semilunar plates absent” and no changes to codings would be necessary.

444. Chang’s apparatus 0 absent 1 present This is a feature of yunnanolepidoid antiarchs, discussed by Zhu (1996)

445. Number of median dorsal plates 0 one 1 two 2 three (Trinajstic and Long 2009) character 3 (with modified states).

446. Anocleithrum sensu stricto 0 exposed 1 subdermal Lu et al., (2012) character 195.

447. Median ventral trunk plates 0 absent 1 present Related to Lu et al., (2012) character 205. Includes placoderm median ventral plates, osteichthyan interclavicles and acanthodian lorical plates.

448. Extracleithrum 0 absent 1 present The extracleithrum is a characteristic of many coelacanths. It is a shoulder girdle bone that braces the cleithrum and the clavicle, and is not here considered equivalent to any of the posterior bones of the trunk armour in placoderms as it does not border a pectoral opening. It is also not considered equivalent to a pectoral fin spine or spinal plate, as it has a flat, plate-like morphology.

449. Pectoral fin spine small (bivalve-like) 0 absent 1 present Brochoadmones has a small rounded pectoral fin spine, resembling a bivalve. See Hanke and Wilson (2006 fig.3: lt. & rt.pfs.)

Axial skeleton and median fins

450. DFC136 Number of dorsal fins, if present 0 one 1 two

451. Horizontal caudal lobe 0 absent 1 present 60

Sansom 2009 character 70

452. Triphycercal tail 0 absent 1 present A tail with three distinct lobes, regardless of whether or not the tail is heterocercal, is found in Dialipina, Eusthenopteron and Miguashaia among the taxa considered here.

453. DFC138 Caudal radials 0 extend beyond level of body wall and deep into hypochordal lobe 1 restricted to axial lobe

454. GFB235 Supraneurals in axial lobe of caudal fin 0 absent 1 present

455. GFB227 Series of thoracic supraneurals 0 absent 1 present

456. GFB231 Branching radial structure articulating with dorsal fin basal plate 0 absent 1 present

457. DFC126 Dorsal fin spines 0 absent 1 present

458. DFC127 Anal fin spine 0 absent 1 present

459. DFC129 Median fin spine insertion 0 shallow, not greatly deeper than dermal bones / scales 1 deep

460. DFC130 Intermediate fin spines 0 absent 1 present

461. DFC131 Prepectoral fin spines 0 absent 1 present

462. DFC132 Fin spines with ridges 0 absent 1 present

463. DFC133 Fin spines with nodes 0 absent 1 present 61

464. DFC134 Fin spines with rows of large retrorse denticles 0 absent 1 present

465. Synarcual 0 absent 1 present

466. DFC137 Anal fin 0 absent 1 present

467. ZHU145 Fringing fulcra 0 absent 1 present

468. GFB13 Longitudinal scale alignment in fin webs 0 absent 1 present

469. GFB14 Differentiated lepidotrichia 0 absent 1 present

470. ZHU146, GFB236 Epichordal lepidotrichia in caudal fin 0 absent 1 present

471. GFB27 Scute-like ridge scales (basal fulcra) 0 absent 1 present

472. GFB218 Fin spine cross-section 0 round or horseshoe shaped 1 Flat-sided, with rectangular profile

473. GFB219 Intermediate spines when present 0 one pair 1 multiple pairs

474. GFB224 Expanded spine rib on leading edge of spine 0 absent 1 present

475. GFB225 Spine ridges 0 converging at the distal apex of the spine 1 converging on leading edge of spine

476. GFB229 Posterior dorsal fin shape 0 base approximately as broad as tall, not broader than all of other median fins 62

1 base much longer than the height of the fin, substantially longer than any of the other dorsal fins

477. GFB230 Basal plate in dorsal fin (Friedman & Brazeau (2010: character 42).) 0 absent 1 present 478. GFB233 Basal plate in anal fin (Friedman & Brazeau (2010: character 42).) 0 absent 1 present

479. Spine-brush complex 0 absent 1 present. A striking feature defining stethacanthid chondrichthyans, of which Akmonistion is included here. See e.g. Coates and Sequeira (2001, fig. 7).

480. Series of median hexagonal scutes anterior to first dorsal fin 0 absent 1 present This is characteristic of Brachyacanthus. See Watson (1937 p. 66; fig. 5: Med.Sc.).

481. Intermediate spines with finlets 0 absent 1 present Scale-covered finlets are associated with the intermediate spines of Brochoadmones. See Hanke and Wilson (2006, fig. 6B: prp.f.).

482. Median ventral prepectoral spine 0 absent 1 present This character is found in some climatiid acanthodians. The spine may be fused with a lorical plate.

483. Prepectoral spines form ‘necklace’ 0 absent 1 present In Kathemacanthus the pectoral spine is high on the body and the prepectoral spines arranged vertically below it, resembling a ‘spike collar’. See Gagnier and Wilson (1996, fig 3: PPS 1-3).

484. Longitudinal rows of enlarged keeled scutes 0 absent 1 present. These are found on the posterior half of the body in Lupopsyrus. See Hanke and Davis (2012 fig. 1: eks.).

Scales

485. DFC8 Body scale growth pattern 0 monodontode 1 polyodontode

63

486. DFC9 Body scale growth concentric 0 absent 1 present

487. DFC10 Body scales with peg-and-socket articulation 0 absent 1 present

488. DFC11 Body scale profile 0 distinct crown and base demarcated by a constriction (neck) 1 flattened

489. DFC12 Body scales with bulging base 0 absent 1 present

490. DFC13 Body scales with flattened base 0 present 1 absent

491. DFC14 Flank scales alignment 0 vertical rows 1 oblique rows or hexagonal/rhombic packing 2 disorganised

492. ZHU143, DFB19 Peg on rhomboid scale 0 narrow 1 broad

493. ZHU144, GFB20 Anterodorsal process on scale 0 absent 1 present

494. GFB22 Profile of scales with constriction between crown and base 0 neck similar in width to crown 1 neck greatly constricted, resulting in anvil-like shape

495. GFB25 Basal pore in scales 0 absent 1 present

496. Scales 0 macromeric 1 micromeric Swartz (2009) character 44.

497. Scales with well-developed pores on ganoine surface 0 absent 1 present Swartz (2009) character 45.

64

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