Appendix S4: List of morphological characters ...

Appendix S4: List of morphological characters. References correspond to papers in which the definition and coding of characters are based. Citations of those papers are in the main References section. Neurocranium 1. Median chondrified rostral cartilage strongly bound to premaxillary ascending process via rostropremaxillary ligament: (0) completely absent; (1) present. (Parenti, 1981; Hartel and Stiassny, 1986; Stiassny, 1986; Johnson and Patterson, 1993; Springer, 1993; Pietsch and Orr, 2007; Parenti, 2008; Ghedotti and Davis, 2013) 2. Mesethmoid: (0) present as a distinct element; (1) absent or not ossified. (Rosen, 1964; Gosline, 1970; Parenti, 1981; Dyer and Chernoff, 1996; Nelson, 2006) 3. Position of mesethmoid: (0) anterior to lateral ethmoids; (1) posterior to lateral ethmoids. (Regan, 1907; Olney et al., 1993; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 2. 4. Relative position of anterior margins of mesethmoid and vomer: (0) vomer anterior to mesethmoid; (1) mesethmoid anterior to vomer. (Fink and Fink, 1981, 1996). Inapplicable to species with state 1 of characters 2 and 9. 5. Rostral organ on mesethmoid: (0) absent; (1) present. (Nelson, 1985, 2006). Inapplicable to species with state 1 of character 2. 6. Median dorsal keel of mesethmoid: (0) absent, (1) present. (Stiassny, 1986, 1996; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 2. 7. Supraethmoid: (0) fused with mesethmoid or absent; (1) present as separate paired ossification. (Johnson and Patterson, 1996; Wiley and Johnson, 2010). 8. Kinethmoid: (0) absent; (1) present. (Fink and Fink, 1981, 1996; Britz et al., 2009; Mayden and Chen, 2010) 9. Vomer: (0) present; (1) absent. (Schaefer, 1990; Parenti, 1981; Dyer and Chernoff, 1996; Patterson and Johnson, 1997; Nelson, 2006; Pietsch and Orr, 2007; Parenti, 2008; Mayden and Chen, 2010)

10. Palato-vomerine ligament: (0) not divided; (1) divided. (Stiassny, 1986; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 9. 11. One or two pairs of pre-nasal bones: (0) absent; (1) present. (Freihofer, 1978; Forey et al., 1996; Wiley and Johnson, 2010) 12. Nasal: (0) present; (1) absent. (Gregory, 1932; Pietsch, 1981; Santini and Tyler, 2003; Tyler et al., 2003; Mayden and Chen, 2010; Nakae and Sasaki, 2010; Conway et al., 2011) 13. Fusion of nasals: (0) absent; (1) present in adults. (Allis, 1909; Pietsch, 1978; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 12. 14. Ligament between nasal and lateral ethmoid: (0) absent; (1) present. (Dyer and Chernoff, 1996). Inapplicable to species with state 1 of character 12. 15. Pseudomesial bar: (0) absent; (1) present as an autogenous bone between blind side lateral ethmoid and frontal. (Chabanaud, 1934; Chapleau, 1993; Wiley and Johnson, 2010) 16. Continuous medial cartilage below frontals running from ethmoid cartilage to parasphenoid: (0) absent; (1) present. (Johnson and Patterson, 1993; Wiley and Johnson, 2010) 17. Fusion of frontals: (0) absent; (1) present. (Tchernavin, 1947; Rosen, 1974; Weitzman, 1974; Robins, 1989; Wang et al., 2003; Nelson, 2006) 18. Tubercles on cranium: (0) absent; (1) present. (Imamura, 2004; Ishii and Imamura, 2008) 19. Paired foramina in frontal bones, posterodorsally to the orbits: (0) absent; (1) present. (Buckup, 1998) 20. Covering of frontal by epaxial muscle: (0) absent; (1) present. (Sasaki, 1989) 21. Frontal-occipital crest bearing a rostral horn: (0) absent; (1) present. (Olney et al., 1993) 22. Parietal: (0) present; (1) absent. (Rosen and Patterson, 1969; Parenti, 1981; Johnson, 1984; Kido, 1988; Tyler et al., 1989; Winterbottom, 1993; Dyer and Chernoff, 1996; Santini and Tyler, 2003; Lucinda and Reis, 2005; Britz and Conway, 2009; Mayden and Chen, 2010; Smith and Busby, 2014) 23. Fusion of parietals to supraoccipital: (0) absent; (1) present. (Fink and Fink, 1981, 1996; Wiley and

Johnson, 2010). Inapplicable to species with state 1 of character 22. 24. Orbitosphenoid: (0) present; (1) absent. (Fraser, 1972; Springer and Freihofer, 1976; Moore, 1993; Forey et al., 1996; Grande and Poyato Ariza, 1999; Hilton, 2003; Nelson, 2006; Wiley and Johnson, 2010) 25. Position of orbitosphenoid and pterosphenoid: (0) contacting each other; (1) orbitosphenoid not contacting pterosphenoid. (Albert, 2001). Inapplicable to species with state 1 of character 24. 26. Pterosphenoid: (0) present; (1) absent. (Pietsch, 1974; Yabe, 1985; Kido, 1988; Springer, 1993; Hoshino, 2001; Imamura et al., 2005; Keivany and Nelson, 2006; Nelson, 2006; Pietsch and Orr, 2007; Odani and Imamura, 2011) 27. Position of pterosphenoid and brain: (0) set posteriorly, distant to lateral ethmoid; (1) pterosphenoid, still containing brain, articulating with lateral ethmoid. (Howes, 1993; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 26. 28. Basisphenoid: (0) present; (1) absent. (Rosen and Bailey, 1963; Rosen and Patterson, 1969; Eakin, 1978; Johnson, 1982; Parenti, 1984; Tyler et al., 1989; Chapleau, 1993; Moore, 1993; Winterbottom, 1993; Ishida, 1994; Dyer and Chernoff, 1996; Imamura, 1996; Imamura, 2000; Kim, 2002; Hilton, 2003; Santini and Tyler, 2003; Tyler et al., 2003; Bergman, 2004; Imamura, 2004; Hilton and Kley, 2005; Imamura et al., 2005; Shinohara and Imamura, 2005; Nelson, 2006; Thacker and Roje, 2009; Bruner, 2011; Wiley and Johnson, 2010; Odani and Imamura, 2011; López-Arbarello, 2012) 29. Parasphenoid: (0) present; (1) absent. (Nelson, 2006) 30. Bony or cartilaginous parasphenoid apophysis, as a ventral blade along its length beneath orbits, where pharyngobranchials 3 attach: (0) absent; (1) present. (Rosen, 1984; Blum, 1988; Tyler et al, 1989; Rosen and Patterson, 1990). Inapplicable to species with state 1 of characters 29 and 110. 31. Auditory foramen on prootic: (0) absent; (1) present. (Fink and Fink, 1981, 1996) 32. Dermopterotic: (0) absent or fused to autopterotic; (1) independent from autopterotic. (Johnson and Patterson, 1996)

33. Occipital hook, used for carrying eggs on head of males: (0) absent; (1) present. (Berra, 2003) 34. Deep mediodorsal opening to posttemporal fossa: (0) absent; (1) present. (Fink and Fink, 1981, 1996) 35. Position of epiotics: (0) contacting parietal; (1) separated from parietal and meeting each other on midline posterior to supraoccipital. (Pietsch and Grobecker, 1987; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 22. 36. Subepiotic fossa: (0) absent; (1) present. (Forey et al., 1996; Wiley and Johnson, 2010) 37. Post-epiotic process: (0) absent or reduced; (1) reaching nuchal plates or vertebral column. (Curran, 1989) 38. Exoccipital: (0) present; (1) absent. (Nelson, 2006) 39. Foramen exoccipitale covered by tympanum-like membrane: (0) absent; (1) present. (Lauder and Liem, 1983; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 38. 40. Posterior extension of exoccipitals rounding vagus nerve: (0) absent; (1) present. (López-Arbarello, 2012). Inapplicable to species with state 1 of character 38. 41. Lagenar capsules: (0) absent; (1) present. (Fink and Fink, 1981, 1996) 42. Ventral cone-shaped projection of basioccipital: (0) absent; (1) present. (Acero and Betancur-R., 2007) 43. Paired articular processes of basioccipital forming diarthrosis with upper pharyngeal jaws: (0) absent; (1) present. (Wiley and Johnson, 2010) 44. Occipital condylum: (0) not tripartite, formed by basioccipital; (1), tripartite, formed by basioccipital and exoccipitals. (Johnson, 1992). Inapplicable to species with state 1 of character 38. 45. Intercalar: (0) present; (1) absent. (Ramaswami, 1948, 1952a, 1952b, 1952c, 1952d, 1955a, 1955b; Rosen and Patterson, 1969; Howes, 1978, 1980; Sawada, 1982; Nakabo, 1983; Ishida, 1994; Dyer and Chernoff, 1996; Forey et al., 1996; Albert, 2001; Hilton, 2003; Imamura et al., 2005; Zanata and Vari, 2005; Keivany and Nelson, 2006; Nelson, 2006; Britz and Conway, 2009; Britz et al., 2009; López-

Arbarello, 2012). Given its high variability, is coded as missing for most of the Cyprinidae. Infraorbital series 46. Supraorbital: (0) present; (1) absent. (Li and Wilson, 1996; Mirande, 2010; Wiley and Johnson, 2010) 47. Suborbital stay, formed by third infraorbital: (0) absent; (1) present. (Imamura, 2004; Nelson, 2006) Laterosensory system 48. Supraorbital canal in premaxillary ascending process: (0) absent; (1) present. (López-Arbarello, 2012) 49. “Anterior infraorbitals”, bones carrying infraorbital sensory canal anterior to orbit: (0) absent; (1) present. (López-Arbarello, 2012). 50. Jakubowski's organ: (0) absent; (1) present. (Jakubowski, 1974; Freihofer, 1978; Johnson and Patterson, 1993; Wiley and Johnson, 2010) 51. Recessus lateralis: (0) absent; (1) present. (Grande, 1985; di Dario, 2004; Nelson, 2006) 52. Large cavernous canals on head (as part of lateral-line system): (0) absent; (1) present. (Sasaki, 1989) 53. Supratemporal commissural sensory canal: (0) not passing through parietals and supraoccipital; (1) passing through parietals and supraoccipital. (Patterson and Rosen, 1977; Grande, 1982; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 22. Jaws and teeth 54. Median maxillo-premaxillary buccal ligament: (0) from medial face of maxilla to medial face of ascending premaxillary process of same side, when present; (1) inserting on contralateral buccal elements. (Stiassny, 1986, 1996; Wiley and Johnson, 2010) 55. Anterior expansion of maxillary alveolar arm: (0) absent; (1) present. (Costa, 1998) 56. Articulaton between maxillae and neurocranium: (0) markedly ankylosed; (1) not markedly ankylosed. (Diogo, 2008)

57. Infraorbital branch of buccal VII: (0) not piercing premaxilla: (1) piercing premaxilla. (Forey et al., 1996; Wiley and Johnson, 2010) 58. Paradentary: (0) absent; (1) present. (Parenti, 1984) 59. Coronoid bones: (0) present; (1) absent. (Nelson, 1973; Wiley and Johnson, 2010) 60. Angular and articular: (0) not fused; (1) fused. (Nelson, 1973; Patterson and Rosen, 1977; Arratia, 1997; Wilson and Murray, 2008; Wiley and Johnson, 2010) 61. Position of retroarticular: (0) forming part of joint surface of quadrate; (1) excluded from joint surface of quadrate. (Nelson, 1973; Patterson and Rosen, 1977; Arratia, 1997; Wilson and Murray, 2008; Wiley and Johnson, 2010) 62. Acrodin cap on teeth: (0) absent; (1) present. (Gardiner, 1984; Gayet et al., 2002) 63. Development of dentary and premaxillary teeth: (0) completely extraosseus; (1) some or all developed in crypts. (Fink and Fink, 1981, 1996) Suspensorium 64. Articulation of palatoquadrate with neurocranium: (0) with a single condylum; (1) articulating in two places, as in an amphistylic jaw suspension. (Nelson, 2006) 65. Contact between maxilla and preopercle with palatoquadrate or homologous structures: (0) present; (1) absent. (Gardiner and Schaeffer, 1989) 66. Dermal portion of palatine: (0) present; (1) absent. (Fink and Fink, 1981, 1996; Johnson and Brothers, 1993; Baldwin and Johnson, 1996; Johnson and Patterson, 1996; Wiley and Johnson, 2010; Johnson et al., 2012) 67. Dorsomedial process of palatine contacting mesethmoid: (0) absent; (1) present. (Fink and Fink, 1981, 1996). Inapplicable to species with state 1 of character 2. 68. Median palato-maxillary ligament: (0) present; (1) absent. (Stiassny, 1986; Wiley and Johnson, 2010) 69. Entopterygoid: (0) present; (1) absent. (Johnson, 1984, 1993; Yabe, 1985; Mooi and Johnson, 1997;

Imamura, 2003; Santini and Tyler, 2001, 2003; Keivany and Nelson, 2006; Pietsch and Orr, 2007; Wiley and Johnson, 2010; Johnson et al., 2012; Keivany, 2014) 70. Assymetrical loss of entopterygoid: (0) either present or absent in both sides; (1) absent in blind side. (Hoshino, 2001). Inapplicable to species with state 1 of character 69. 71. Ectopterygoid: (0) present; (1) absent as a separate ossification. (Johnson, 1984, 1993; Albert, 2001; Mayden and Chen, 2010; Wiley and Johnson, 2010; Conway et al., 2011; Birindelli, 2014; Keivany, 2014). Coded as absent in all the Siluriformes according to Diogo (2004). 72. Position of ectopterygoid: (0) not forming part of skull roof; (1) forming part of skull roof. (LópezArbarello, 2012). Inapplicable to species with state 1 of character 71. 73. Metapterygoid: (0) present; (1) absent. (Gosline, 1970; Costa, 1998; Parenti, 2008; Britz et al., 2009; Johnson et al., 2011) 74. Fenestra between hyomandibular and metapterygoid for passage of levator arcus palatini: (0) absent; (1) present. (Forey et al., 1996). Inapplicable to species with state 1 of character 73. 75. Preopercle: (0) present; (1) absent. (Nelson, 2006) 76. Subopercle: (0) present; (1) absent. (Nelson, 2006) 77. Interopercle as an independent element: (0) absent; (1) present. (Lauder and Liem, 1983; Armbruster, 2004; Diogo, 2008; Rocha et al., 2012) 78. Symplectic: (0) absent as a free element; (1) present, autogenous (Gardiner and Schaeffer, 1989; Johnson et al., 2012) Branchial and hyoid arches 79. Gill slit: (0) a single, more or less developed, slit; (1) two small slits. (Nelson, 2006) 80. Number of gill arches: (0) four or five; (1) three and one-half (seven hemibranchs). (Tyler et al., 2003). 81. Gill arches and neurocranium: (0) articulated; (1) free from neurocranium. (Forey et al., 1996) 82. Toothed saccular outgrowths posterior to last gill arch: (0) absent; (1) present. (Haedrich, 1967)

83. Ossified basihyal: (0) absent; (1) present. (Shinohara, 1994; de Pinna, 1996a; Imamura, 1996; Endo, 2002; Wiley and Jonhson, 2010; Grande et al., 2013). 84. Form of basihyal: (0) flat or, in general, without dorsal groove; (1) with dorsal groove. (Albert, 2001). Inapplicable to species with state 0 of character 83. 85. Dorsal hypohyal: (0) present; (1) absent. (Rosen and Parenti, 1981; Costa, 1998; Reis, 1998; Diogo et al., 2003; Rodiles-Hernández et al., 2005; Birindelli, 2014) 86. Foramen between hypohyals for passage of hyoidean artery: (0) absent; (1) present. (de Pinna, 1996a). Inapplicable to species with state 1 of character 85. 87. Ceratohyals: (0) absent or a single ossified ceratohyal on each side; (1) two independent ossified ceratohyals on each side. (Diogo, 2008) 88. Interhyal: (0) present; (1) absent. (Rosen and Parenti, 1981; de Pinna, 1992; Diogo et al., 2003; Parenti, 2005, 2008; Britz and Moritz, 2007; Britz and Conway, 2009; Johnson et al., 2011; Birindelli, 2014) 89. Medial process on interhyal contacting with preopercle: (0) absent; (1) present. (Pietsch and Grobecker, 1987; Wiley and Johnson, 2010). Inapplicable to species with state 1 of characters 75 and 88. 90. Urohyal formed by a medial tendon bone: (0) absent; (1) present. (de Pinna, 1996a; Santini and Tyler, 2003; Britz et al., 2009) 91. Distinct sciatic portion of urohyal: (0) absent; (1) present. (Chapleau, 1993). Inapplicable to species with state 0 of character 90. 92. Fusion of urohyal and basibranchial 1: (0) not fused; (1) fused. (Imamura, 1996). Inapplicable to species with state 0 of character 90 and state 1 of character 96. 93. Basket-like structure (jugostegalia) formed by branchiostegal rays: (0) absent; (1) present. 94. Articulation of branchiostegal rays: (0) only with ceratohyals; (1) some rays articulating with ventral hypohyal. (Fink and Weitzman, 1982; Wiley and Johnson, 2010)

95. Chin barbel supported by anterior branchiostegal rays: (0) absent; (1) present. (Wiley and Johnson, 2010) 96. Basibranchial 1: (0) present; (1) absent or not ossified. (Vari, 1983; Springer, 1983; Winterbottom, 1993; de Pinna and Vari, 1995; Costa, 1998) 97. Hypobranchial 3: (0) present; (1) absent. (Bertelsen et al., 1981; Bertelsen and Kreft, 1988; Pietsch and Orr, 2007) 98. Ceratobranchial 1: (0) present; (1) absent. (Pietsch and Orr, 2007) 99. Teeth on ceratobranchial 3: (0) absent; (1) present. (Costa, 1998) 100. Blade-like keel on lower pharyngeal jaw correlated with shift in insertion of part to all of transversus ventralis onto that keel: (0) absent; (1) present. (Stiassny and Jensen, 1987; Wiley and Johnson, 2010) 101. Rounded cartilage articulating ceratobranchials 5: (0) absent; (1) present. (Costa, 1998) 102. Teeth on ceratobranchial 5: (0) absent or not ankylosed to bone; (1) ankylosed to bone. (Fink and Fink, 1981, 1996) 103. Dorsal margin of epibranchial 2: (0) not particularly expanded; (1) broad and articulating extensively with pharyngobranchials 2 and 3. (Rosen, 1973; Wiley and Johnson, 2010) 104. Sac-like muscular epibranchial organ: (0) absent; (1) present. (Vari, 1983) 105. Crumenal organ: (0) absent; (1) present. (Begle, 1992; Johnson and Patterson, 1996; Wiley and Johnson, 2010, Carvalho et al., 2013) 106. Suprabranchial organ (= accessory air-breathing organ) comprising suprabranchial chamber housing expanded, modified first epibranchial (labyrinth): (0) absent; (1) present. (Cuvier and Valenciennes, 1831; Wiley and Johnson, 2010) 107. Suprabranchial air chamber: (0) absent as separate from buccal cavity; (1) present, clearly separated from buccal cavity, with respiratory air confined to suprabranchial cavity. (Lauder and Liem, 1983; Wiley and Johnson, 2010)

108. Pharyngobranchial 1: (0) present; (1) absent or not ossified. (Rosen and Greenwood, 1976; Johnson, 1984, 1993; Johnson and Brothers, 1993; Yabe, 1985; Springer, 1993; Ishida, 1994; Mooi and Johnson, 1997; Imamura, 2003; Santini and Tyler, 2003; Imamura, 2004; Springer and Orrell, 2004; Keivany and Nelson, 2006; Sarmento-Soares et al., 2006; de Pinna et al., 2007; Marceniuk and Menezes, 2007; Pietsch and Orr, 2007; Bockmann and Miquelarena, 2008; Sarmento-Soares and Martins-Pinheiro, 2008; Wiley and Johnson, 2010; Johnson et al., 2011; Odani and Imamura, 2011; Birindelli, 2014). Coded as polymorphic in the Amphiliidae, Bagridae, Heptapteridae, Ictaluridae, and Pimelodidae. 109. Pharyngobranchial 2: (0) present; (1) absent or not ossified. (Yabe, 1985; Chapleau, 1993; Springer, 1993; Springer and Orrell, 2004; Wiley and Johnson, 2010; Birindelli, 2014). Coded as polymorphic in most members of the Cottidae. 110. Pharyngobranchial 3: (0) present; (1) absent. (Albert, 2001) 111. Fusion of contralateral pharyngobranchials 3: (0) absent; (1) fused in a plate. (Dasilao and Sasaki, 1998). Inapplicable to species with state 1 of character 110. 112. Pharyngobranchial 4: (0) present; (1) absent. (Rosen and Parenti, 1981; Yabe, 1985; Johnson and Patterson, 1993; Springer, 1993; Santini and Tyler, 2003; Wiley and Johnson, 2010; Gill & Mooi, 2012) Pectoral girdle and fin 113. Articulation of pectoral girdle with cranium: (0) present; (1) absent. (Forey et al., 1996; Wiley and Johnson, 2010) 114. Posttemporal: (0) present; (1) absent. (McDowell, 1973; Sawada, 1982; Robins, 1989; Santini and Tyler, 2003; Britz et al., 2009; Mayden and Chen, 2010; Wiley and Johnson, 2010) 115. Posterior margin of posttemporal: (0) smooth; (1) serrated. (Day, 2002). Inapplicable to species with state 1 of character 114. 116. Articulation of dorsal limb of posttemporal with epioccipital: (0) absent or loose; (1) firmly bound to epioccipital. (Stiassny, 1986; Johnson and Patterson, 1993; Wiley and Johnson, 2010). Inapplicable

to species with state 1 of character 114. 117. Supracleithrum: (0) present; (1) absent. (Fink, 1985; McLennan and Mattern, 2001; Parenti, 2008) 118. Columnar coronoid process on cleithrum: (0) absent; (1) present. (Johnson and Patterson, 1996; Wiley and Johnson, 2010) 119. Humerovertebral ligament: (0) absent; (1) present. (de Pinna, 1996b). Inapplicable to species with state 1 of character 129. 120. Pelvic and ventral intercleithral cartilages: (0) absent; (1) present. (Springer, 1983; Winterbottom, 1993; Wiley and Johnson, 2010) 121. Mesocoracoid: (0) present; (1) absent. (Forey et al., 1996; Diogo et al., 2001; Nelson, 2006; Britz et al., 2009; Britz and Conway, 2009; Wiley and Johnson, 2010; Birindelli, 2014; pers. obs.) 122. Ectocoracoid: (0) absent; (1) present. (Keivany and Nelson, 2006) 123. Pectoral radials: (0) present as separate units; (1) absent as separate units, with pectoral radial plate fusing with scapulocoracoid during development. (Britz and Johnson, 2002; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 125. 124. Endoskeletal elements articulating with pectoral girdle: (0) whether a proto, meso and metapterygia, or pectoral radials directly articulated with scapula and coracoid; (1) a single “humerus”. (Diogo, 2008). Inapplicable to species with state 1 of character 125. 125. Pectoral fin: (0) present; (1) absent. (Nelson, 2006) 126. Pectoral-fin rays: (0) some of them branched; (1) all unbranched. (Ishida, 1994; Santini and Tyler, 2003; Tyler et al., 2003; Imamura, 2004). Inapplicable to species with state 1 of character 125. 127. Division of pectoral fin: (0) absent, if free rays are present, contiguous with rays attached by membrane; (1) present, a dorsal section with connnected rays and a separate ventral section with 3-15 free rays. (Nelson, 2006). Inapplicable to species with state 1 of character 125. 128. Free rays on pectoral fin: (0) absent; (1) present in variable number and used for locomotion. (Imamura, 1996; Imamura, 2004; Nelson, 2006). Inapplicable to species with state 1 of character 125.

Pelvic girdle and fin 129. Pelvic girdle and fins: (0) present; (1) absent. (Johnson and Patterson, 1993; Santini and Tyler, 2003; Nelson, 2006) 130. Ligament between pelvic bone and pleural ribs: (0) absent; (1) present. (Dyer, 1998). Inapplicable to species with state 1 of character 129. 131. Lateral margin of pelvic bones: (0) not articulating each other; (1) convex and articulated each other dorsal, anterior, and posteriorly. (Springer, 1993; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 129. 132. Articulation of pelvic-fin ray with pelvic bone: (0) not interlocked through a foramen and a flange; (1) fully interlocked. (Mok and Chang, 1986). Inapplicable to species with state 1 of character 129. 133. Pelvic ventral spine: (0) absent; (1) present. (Dyer and Chernoff, 1996). Inapplicable to species with state 1 of character 129. 134. Pelvic radials: (0) one series; (1) two series. (Gardiner et al., 2005). Inapplicable to species with state 1 of character 129. 135. Form of pelvic fins: (0) paired, separate each other and not forming a sucking disc; (1) modified into a thoracic sucking disc. (Gosline, 1970; Springer and Fraser, 1976; Parenti and Song, 1996; Nelson, 2006; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 129. Median pterygiophores and fins 136. True spines in median fins: (0) absent; (1) present. (Chapleau, 1993; Nelson, 2006; Wiley and Johnson, 2010) 137. Dorsal and anal-fin stays: (0) present; (1) absent. (Johnson, 1984; Blum, 1988; Tyler et al., 1989; Imamura, 2000; Imamura and Yabe, 2002; Imamura, 2005; Gray et al., 2009; Odani and Imamura, 2011; Smith and Busby, 2014) 138. Proximal and middle anal- and dorsal-fin pterygiophores: (0) not expanded as externally visible bony plates; (1) expanded to form a dorsal and a ventral series of bony plates covering body. (Britz and

Johnson, 2002; Wiley and Johnson, 2010) 139. Anterior nuchal plate, derived from supraneural: (0) absent; (1) present. (Birindelli, 2014) 140. Sucking disc on head derived from spinous dorsal fin: (0) absent; (1) present. (Nelson, 2006) 141. Dorsal-fin rays: (0) some of them branched; (1) all unbranched. (Ishida, 1994; Santini and Tyler, 2003; Tyler et al., 2003) 142. Base of first dorsal-fin ray: (0) not projected anteriorly; (1) projected anteriorly as a spine. (Reis, 1989) 143. Chain-link articulation of dorsal spines: (0) absent; (1) present. (Gosline, 1961; Rosen and Patterson, 1969; Johnson and Patterson, 1993; Wiley and Johnson, 2010). 144. First dorsal-fin ray: (0) not modified as a luring apparatus; (1) modified as a luring apparatus. (Pietsch and Grobecker, 1987) 145. Cirri on interspinous dorsal-fin membrane: (0) absent; (1) present. (Nelson, 2006) 146. Two pseudospines articulated with first dorsal pterygiophore: (0) absent; (1) present. (Endo, 2002; Wiley and Johnson, 2010) 147. Articulation of first proximal dorsal-fin radial with lateral ethmoid: (0) absent; (1) firmly wedged in a notch of a lateral ethmoid (blind side). (Hoshino, 2001) 148. Dorsal pterygiophores between first two neural spines: (0) just one, when present; (1) more than one. (O'Toole, 2002; Little et al., 2010). 149. Contact facets in ventral tip of first dorsal-fin pterygophore and corresponding neural spine: (0) absent; (1) present. (de Pinna, 1996b) 150. Adipose fin supports: (0) absent; (1) present, either of hyaline cartilage or chondroid tissue, penetrating supracarinalis posterior. (Stiassny, 1986, 1996; Wiley and Johnson, 2010) 151. Anal fins: (0) a single anal fin; (1) two anal fins. (Nelson, 2006) 152. Anal-fin rays: (0) some of them branched; (1) all unbranched. (Santini and Tyler, 2003; Imamura, 2004; Grande et al., 2013)

153. Position of urogenital opening in males: (0) near anus or at base of anal fin; (1) at tip of anterior anal-fin rays. (Birindelli, 2014) 154. Anal-fin origin: (0) ventral in a point posterior to head; (1) at isthmus. (Albert, 2001) 155. Form of first anal-fin pterygiophore in cross section: (0) cylindrical or with lateral and/or anterior and posterior projections; (1) star-shaped. (Liu, 1997) 156. Caudal-fin rays: (0) some of them branched; (1) all unbranched. (Imamura, 2004) 157. Proportional number of dorsal and ventral caudal-fin rays: (0) equal or more rays in dorsal lobe; (1) lower lobe with more principal rays. (Parenti, 2005) 158. Form of caudal fin: (0) with two lobes or, if reduced, dorso-ventrally symmetrical; (1) restricted to upper lobe, with lower lobe completely absent. (Nelson, 2006) 159. General form of caudal-fin skeleton: (0) dorsoventrally asymmetrical; (1) dorsoventrally symmetrical. (Costa, 1998) 160. Spur on posterior margin of neural spine of preural vertebra 2: (0) absent; (1) present. (Dasilao and Sasaki, 1998) 161. Epurals: (0) present, in variable number; (1) completely absent. (Nelson, 1969; Johnson and Brothers, 1993; Santini and Tyler, 2003; Thacker, 2003; Mayden and Chen, 2010; Wiley and Johnson, 2010) 162. Uroneurals: (0) completely absent; (1) present, as one or two pairs. (Eakin, 1978; Springer, 1993; de Pinna, 1996a; Tyler et al., 2003; Imamura, 2004; Imamura et al., 2005; Odani and Imamura, 2011; Pethiyagoda et al., 2012) 163. Pleurostyle: (0) absent; (1) present. (Lecointre and Nelson, 1996; Arratia, 1999; di Dario, 2004). 164. Caudal median cartilages together supporting lowermost ray of upper caudal lobe: (0) absent; (1) present. (Johnson and Patterson, 1996; Wiley and Johnson, 2010) 165. Fusion of hypurals: (0) some of them autogenous; (1) all of them fused to form a single plate. (Costa, 1998)

166. Fusion of hypural two and ural centrum one: (0) absent; (1) present. (Lecointre and Nelson, 1996; Britz and Moritz, 2007) 167. Form of lower hypural plate: (0) not projected posteriorly; (1) strongly extended posteriorly. (Dasilao and Sasaki, 1998) 168. “Day's bone”, an autogenous elongated bone between hemal spines of PU2 and PU3: (0) absent; (1) present. (Day, 1914; Wiley and Johnson, 2010) Axial skeleton 169. Body covering by expansions of vertebral column: (0) absent or by scales or plates not derived from vertebral column; (1) encased by thin bony plates that are expansions of vertebral column. (Nelson, 2006) 170. Form of vertebrae: (0) amphicelous; (1) opisthocelous. (Nelson, 2006) 171. Parapophyses of first vertebra: (0) absent or oriented laterally; (1) oriented ventrally and contacting each other at midline. (Stiassny, 1986, 1996; Wiley and Johnson, 2010) 172. Vertebral centra 2-4: (0) not fused each other; (1) fused into “complex centrum” (Fink and Fink, 1981, 1996) 173. Scaphium on Weberian apparatus: (0) absent; (1) present (Fink and Fink, 1981, 1996) 174. Tripus on Weberian apparatus: (0) absent; (1) present (Fink and Fink, 1981, 1996) 175. Os suspensorium on Weberian apparatus: (0) absent; (1) present (Fink and Fink, 1981, 1996) 176. Elastic spring apparatus: (0) absent; (1) present. (Howes, 1985; Curran, 1989) 177. Supraneurals: (0) present; (1) absent. (Johnson, 1981; Blum, 1988; Stiassny, 1990; Chapleau, 1993; Johnson and Patterson, 1993; Parenti, 1993; Winterbottom, 1993; Ishida, 1994; Shinohara, 1994; Gill, 1996; Mooi and Johnson, 1997; Wiley et al., 2000; Imamura, 2002; Tyler et al., 2003; Friedman, 2008; Springer and Smith-Vaniz, 2008; Wiley and Johnson, 2010; Odani and Imamura, 2011; Grande et al., 2013; Birindelli, 2014) 178. Development of supraneurals: (0) “pattern 1”, first supraneural not diferentiated from second and

developed cephalocaudally; (1) “pattern 2”, first supraneural becomes clearly differentiated from second and formed indepedently than them, which develop cephalic and caudally from a focus. (Johnson and Patterson 1996; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 177. 179. Third and fourth neural arches: (0) free from each other; (1) fused together and to “complex centrum”. (Fink and Fink, 1981, 1996) 180. Dorsomedial portions of anterior neural arches: (0) not forming a continuous roof over neural canal; (1) expanded and abutting each other and posterior margin of exoccipital, when present, forming roof over neural canal. (Fink and Fink, 1981, 1996; Wiley and Johnson, 2010) 181. Articulation of first neural arch with exoccipital: (0) absent; (1) present. (Grande and Poyato Ariza, 1999). Inapplicable to species with state 1 of character 38. 182. Articulation of first neural arch with exoccipital and supraoccipital: (0) absent; (1) present. (Grande, 1994). Inapplicable to species with state 1 of character 38. 183. Peg-and-socket arrangement of posterior haemal arches in caudal region: (0) absent, with haemal arches fused to vertebrae; (1) present. (Rosen, 1974; Sanford, 1990; Wiley and Johnson, 2010) 184. First epineural: (0) absent or restricted to epaxial musculature; (1) displaced ventrally into horizontal septum. (Johnson and Patterson, 1993; Patterson and Johnson, 1995; Gemballa and Britz, 1998; Wiley and Johnson, 2010). 185. Bony epipleurals: (0) present; (1) absent. (Nelson, 1969; Patterson and Johnson, 1995; Arratia, 1999; Hilton, 2003; Britz et al., 2009; Wiley and Johnson, 2010) 186. Pleural ribs: (0) present; (1) absent. (Eakin, 1978; Moore, 1993; Ishida, 1994; Mooi and Johnson, 1997; Santini and Tyler, 2003; Odani and Imamura, 2011; Smith and Busby, 2014) 187. Anterior pleural ribs: (0) articulated with vertebral centra; (1) inserted on epineurals. (Gosline, 1970; Johnson and Patterson, 1993; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 186.

Musculature and tendons 188. Lachrimal tendon of A1 section of adductor mandibulae: (0) absent; (1) present. (Dyer and Chernoff, 1996) 189. Levator operculi: (0) a single element; (1) two elements, originated in pterotic and posttemporal. (Sasaki, 1989; Imamura, 2000; Imamura, 2002; Imamura and Matsuura, 2003; Shinohara and Imamura, 2005). Inapplicable to species with state 1 of character 114. 190. Adductor hyohyoidei: (0) not dorsolaterally expanded and not reducing opercular opening; (1) dorsolaterally expanded, sealing operculum to body wall and causing restricted opercular opening. (Travers, 1984; Wiley and Johnson, 2010) 191. Extension of posterior myodome: (0) not reaching basioccipital; (1) extending into basioccipital. (de Pinna, 1996a) 192. Posterior myodome: (0) not deep, without eye muscles attaching to trunk muscles; (1) deep, with eye muscles passing through myodome and attaching to trunk muscles. (Sanford, 1990; Wiley and Johnson, 2010) 193. Craniotemporalis muscle, from epaxial musculature to posttemporal: (0) present; (1) absent. (Stiassny, 1986; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 114. 194. Arrector dorsalis: (0) absent; (1) present. (Diogo, 2008) 195. Arrector ventralis: (0) absent; (1) present. (Diogo, 2008) 196. Distinct arrector 3: (0) absent; (1) present. (Diogo, 2008) 197. Extension of pectoral muscles: (0) reaching only to radials; (1) extending to pectoral fin. (Diogo, 2008). Inapplicable to species with state 1 of character 125. 198. Retractor dorsalis muscle: (0) absent; (1) present. (Rosen, 1973; Johnson, 1992; Nelson, 2006; Wiley and Johnson, 2010) 199. Sonic muscles from skull or posttemporal and inserting on surface of swim bladder or bony structures associated to it: (0) absent; (1) present. (Nelson, 2006; Birindelli, 2014). Inapplicable to

species with state 1 of character 248. 200. Extrinsic swim bladder muscle derived from epaxialis: (0) absent; (1) present. (Imamura, 1996). Inapplicable to species with state 1 of character 248. 201. Extrinsic swim bladder muscle derived from obliquus superioris: (0) absent; (1) present. (Imamura, 1996). Inapplicable to species with state 1 of character 248. Miscelanea 202. Connection between nasal tube and buccal cavity (internal choana): (0) absent; (1) present. (Nelson, 2006) 203. Bilaterally asymmetry in adults, with one eye migrating during growth: (0) absent; (1) present. (Nelson, 2006) 204. Anterior nasal barbels: (0) absent; (1) present. (Rodiles-Hernández et al., 2005; Nelson, 2006) 205. Posterior nasal barbels: (0) absent; (1) present. (Rodiles-Hernández et al., 2005; Nelson, 2006; Thomson and Page, 2006; Birindelli, 2014) 206. Elongate primordia in sagittae and lapilli: (0) absent; (1) present. (Brothers, 1984; Wiley and Johnson, 2010) 207. Pince-nez-shaped sulcus and central collicular in otholit: (0) absent; (1) present. (Endo, 2002) 208. Accessory breathing organs with respiratory nodules on first and second epibranchials, hyomandibular, and parasphenoid: (0) absent; (1) present. (Wiley and Johnson, 2010) 209. Otophysic connection with otic bullae invading otic capsule: (0) absent; (1) present. (Rosen and Patterson, 1977; Grande, 1982; Wiley and Johnson, 2010) 210. Floor of mouth: (0) present; (1) absent. (Nelson, 2006) 211. Bill formed by upper jaw: (0) absent; (1) present. (Nelson, 2006) 212. Form of mouth: (0) not forming a suctorial disc; (1) suctorial disc. (Armbruster, 2004; Nelson, 2006) 213. Fringe of small flaps extending around lower jaw and along sides of head onto body: (0) absent;

(1) present. (Nelson, 2006) 214. Fingerlike elements on upper edge of gill cover: (0) absent; (1) present. (Nelson, 2006) 215. Cirri on upper lip: (0) absent; (1) present. (Odani and Imamura, 2011) 216. Cirri on lower lip: (0) absent; (1) present. (Odani and Imamura, 2011) 217. Nostrils: (0) one pair on each side of snout; (1) one nostril on each side of snout. (Burne, 1909; Imamura et al., 2005; Nelson, 2006; Rosen and Parenti, 1981; Wiley and Johson, 2010) 218. Position of anterior nostrils: (0) on dorsum of snout; (1) entirely within gape. (Albert, 2001) 219. Groove holding maxillary barbel under eye: (0) absent; (1) present. (Curran, 1989; Birindelli, 2014) 220. Distal end of Baudelot's ligament: (0) not bifurcated; (1) bifurcated. (Fink and Fink, 1981, 1996) 221. Ink sac discharging to cloaca: (0) absent; (1) present. (Nelson, 2006) 222. Caudal regeneration: (0) absent; (1) present. (Albert, 2001) 223. Caudal peduncle plates or spines: (0) absent; (1) present. (Nelson, 2006) 224. Lateral keel on caudal peduncle: (0) absent; (1) one or two keels present. (Nelson, 2006) 225. Lateral keel on caudal peduncle: (0) absent or just one keel; (1) two keels present. (Nelson, 2006) 226. Hydrostatic balance via air breathing: (0) absent; (1) present. (Reis, 1998) 227. Venom gland in dorsal, anal, and pelvic spines: (0) absent, at least simultaneously in three spines, when present; (1) present. (Nelson, 2006). 228. Double grooved poison spines associated with venom glands just above pectoral fin, when present, and behind opercle: (0) absent or not double grooved; (1) present. (Nelson, 2006) 229. Bioluminescent hyoid barbel: (0) absent; (1) present. (Pietsch and Orr, 2007) 230. Branchiostegal photophores: (0) absent; (1) present. (Nelson, 2006) 231. Caruncles (light organs associated with dorsal-fin rays): (0) absent; (1) present. (Pietsch and Orr, 2007) 232. Bacterial bioluminescent esca: (0) absent; (1) present. (Pietsch and Orr, 2007)

233. Luminous organ beneath eye with rotational and shutter mechanism for controlling light emission: (0) absent; (1) present. (Nelson, 2006) 234. Circumesophageal light organ with bacterial luminiscense: (0) absent; (1) present. (Nelson, 2006) 235. Serial photophores with a lumen and a duct: (0) absent or not disposed serially and having a duct; (1) present. (Nelson, 2006) 236. Distribution of ampullary organs: (0) distributed individually in integument; (1) organized into rosettes. (Albert, 2001) 237. Scales: (0) present; (1) completely absent in adult specimens. (Nelson, 2006; Greenfield et al., 2008; Britz et al., 2009; Britz and Conway, 2009) 238. Scale-like hexagonal pattern of pigment: (0) absent; (1) present. (Harold, 1999) 239. Position of scales: (0) imbricated, when present; (1) not imbricated. (Robins, 1989; Forey et al., 1996). Inapplicable to species with state 1 of character 237. 240. Sharp spines completely covering body: (0) absent; (1) present. (Nelson, 2006) 241. Alarm substance in epidermis: (0) absent; (1) present. (Fink and Fink, 1981, 1996; Wiley and Johnson, 2010) 242. Black shoulder sac apparatus: (0) absent; (1) present, located under shoulder girdle produces bluegreen luminous fluid and opening through tubular papilla just below lateral line. (Nelson, 2006) 243. Extensive subdermal canal system communicating to the surface through small pores scattered over body: (0) absent; (1) present. (Haedrich, 1967, 1969) 244. Row of thorny scutes along lateral line: (0) absent; (1) present. (Moyer et al., 2004) 245. Odontodes on outside of body: (0) absent or restricted in distribution; (1) present on almost entire body (Armbruster, 2004) 246. Two series of plates covering completely body sides and dorsum: (0) absent; (1) present. (Reis, 1998) 247. Snout: (0) not gelatinous; (1) gelatinous. (Wiley and Johnson, 2010)

248. Swim bladder: (0) present; (1) absent. (Nishimura, 1963; Pietsch, 1981; Ishida, 1994; Imamura, 1996; Tominaga et al., 1996; Nelson, 2006) 249. Swim bladder covering: (0) not encased in bone; (1) encased in bone. (Nelson, 2006). Inapplicable to species with state 1 of character 248. 250. Peritoneal tunic of anterior region of swim bladder: (0) not attached to pleural ribs; (1) attached to anterior two pleural ribs. (Fink and Fink, 1981, 1996). Inapplicable to species with state 1 of character 248. 251. Division of swim bladder in anterior and posterior chambers: (0) absent; (1) present. (di Dario, 2004; Diogo, 2008). Inapplicable to species with state 1 of character 248. 252. Silvery peritoneum over swim bladder: (0) absent; (1) present. (di Dario, 2004). Inapplicable to species with state 1 of character 248. 253. Distal end of swin bladder: (0) not or moderately bifurcated; (1) deeply bifurcated. (Nelson, 2006). Inapplicable to species with state 1 of character 248. 254. Posterior extension and position of swim bladder: (0) not extending into haemal canal; (1) extending into haemal canal. (Dasilao and Sasaki, 1998). Inapplicable to species with state 1 of character 248. 255. Posterior extension of swim bladder: (0) not reaching parhypural; (1) extending posteriorly to parhypural. (Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 248. 256. Inflatable diverticulum of gut: (0) absent; (1) present. (Santini and Tyler, 2003) 257. Intestine position: (0) it coils to right of stomach; (1) it coils to left of stomach. (Patterson and Rosen, 1977; Li and Wilson, 1996) 258. Recessus orbitalis: (0) absent; (1) present. (Chapleau, 1993) 259. Aphakic (lensless) space on pupil: (0) absent; (1) present, with pupil in form of keyhole. (Baldwin and Johnson, 1996; Wiley and Johnson, 2010). Coded as inapplicable to the Ipnopidae, following Baldwin and Johnson (1996).

260. Priapum: (0) absent; (1) present in males. (Parenti, 1984) 261. Testis type: (0) tubular; (1) lobular. (Parenti and Grier, 2004). Coded as unknown in the Aulopiformes, Myctophiformes and Stomiatiformes, following Parenti and Grier (2004). 262. Distribution of spermatogonia in testis: (0) distributed along lobular or tubular testis; (1) restricted to distal termini of lobule. (Parenti and Grier, 2004; Parenti, 2005) 263. Flagellum in spermatozoa: (0) present; (1) absent. (Jamieson, 1991) 264. Flagellum of spermatozoa: (0) typical 9+2 axoneme arrangement; (1) 9+0 axoneme arrangement. (Matthei and Matthei, 1974; Forey et al., 1996; Wiley and Johnson, 2010). Inapplicable to species with state 1 of character 263. 265. Adhesive filaments extending from egg surface: (0) absent; (1) present. (Breder and Rosen, 1966; Semple, 1985; Mooi, 1990; Britz, 1997; Breining and Britz, 2000; Parenti, 2005; Wainright et al., 2012) 266. Extreme sexual dimorphism, with dwarf males: (0) absent; (1) present. (Regan, 1925; Wiley and Johnson, 2010) 267. Parasitic males: (0) absent or not parasiting females; (1) parasiting food of females. (Nelson, 2006) 268. Yolk sac in larvae bearing adhesive disc on its ventral surface: (0) absent; (1) present. (Breder and Rosen 1966; Wiley and Rosen, 2010) 269. Leptocephalus larva: (0) absent; (1) present. (Greenwood et al., 1966; Forey et al., 1996; Diogo, 2008) 270. Vexillum, a long, deciduous first dorsal-fin ray, in larvae: (0) absent; (1) present. (Nelson, 2006) 271. Bilateral pair of oil vesicles as floating device in larvae; (0) absent; (1) present. (Peters, 1947; Wiley and Johnson, 2010) 272. Electric organ derived from nervous system: (0) absent; (1) present. (Nelson, 2006) 273. Electric organ derived from superficial region of obliquus inferioris, just medial to pectoral-fin

origin, when present: (0) absent; (1) present. (Howes, 1985; Nelson, 2006) 274. Electric organs in hypaxial muscles just dorsal to anal fin: (0) absent; (1) present. (Bennett and Grundfest, 1959; Albert, 2001)

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