SUPPLEMENTARY INFORMATION
I. Character list
1. Eye lens. 0 = absent (0); 1 = present.
2. Ribbon-shaped synaptic organelles in retina. 0 = absent; 1 = present.
3. Tabular muscles in `tongue' musculature. 0 = absent; 1 = present.
4. Lateral-line neuromasts. 0 = absent; 1 = present.
5. Nerve control of heart. 0 = absent; 1 = present.
6. Heart response to catecholamine. 0 = absent; 1 = present.
7. Blood system. 0 = open; 1 = close.
8. Spleen. 0 = absent; 1 = present.
9. Concentrated exocrine pancreas. 0 = absent; 1 = present.
10. Typhlosole in intestine. 0 = absent; 1 = present.
11. Larval stage. 0 = present; 1 = absent.
12. Compartmentalized adenohypophysis. 0 = absent; 1 = present.
13. Pituitary control of melanophores. 0 = absent; 1 = present.
14. Kidney tubules
with glomerulae. 0 = absent; 1 = present.
15. Osmoregulation. 0 = absent; 1 = present.
16. Granulocytes and neutrophils. 0 = absent; 1 = present.
17. Two types of giant Mauthner cells in the central nervous system. 0 = absent; 1 = present.
18. Electroreceptive cells. 0 = absent; 1 = present.
19. Sperm. 0 = not shed through coelomic cavity; 1 = shed through coelomic cavity.
20. Cartilaginous copula. 0 = absent; 1 = present.
21. Pancreas. 0 = absent; 1 = present.
22. Differentiated adenohypophysis. 0 = absent; 1 = present.
23. Skull. 0 = absent; 1 = present.
24. Cartilaginous or calcified braincase (neurocranium). 0 = absent; 1 = present.
25. Dorsally closed cartilaginous or calcified braincase (neurocranium). 0 = absent; 1 =
present.
26. Olfactory organ. 0 = absent; 1 = present.
27. Terminal nasohypophysial opening (inhalant or not). 0 = absent; 1 = present.
28. Dorsal nasohypophysial opening (inhalant or not). 0 = absent; 1 = present.
29. Optic capsules (exclusive of the lens): absent (0), present (1).
30. Transversely biting teeth. 0 = absent; 1 = present.
31. Heart. 0 = absent; 1 = present.
32. Closed pericardium. 0 = absent; 1 = present.
33. Trunk and tail musculature with chevron-shaped muscle blocks. 0 = absent; 1 = present.
34. Zigmoid myomeres. 0 = absent; 1 = present.
35. Radials in fin. 0 = absent; 1 = present.
36. Numerous and closely set radials in unpaired fin. 0 = absent; 1 = present.
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37. Radial muscles in fin. 0 = absent; 1 = present.
38. Dorsal fin. 0 = absent; 1 = present.
39. Separate dorsal fin. 0 = absent; 1 = present.
40. Preanal fin persisting in adult. 0 = absent; 1 = present.
41. Anal fin. 0 = absent; 1 = present.
42. Caudal fin with internal support. 0 = absent; 1 = present.
43. Tail. 0 = isoceral; 1 = hypoceral; 2 = epiceral.
44. Paired fin folds or fins. 0 = absent; 1 = present.
45. Paired fin folds or fins concentrated in the pectoral or epibranchial regions. 0 = absent; 1 =
present.
46. Muscles in paired fins. 0 = absent; 1 = present.
47. Arcualia. 0 = absent; 1 = present.
48. Gill openings arranged in posteriorly slanting line. 0 = absent; 1 = present.
49. Number of gill units. 0 = more than ten; 1 = less than ten.
50. Olfactory tract. 0 = absent; 1 = present.
51. Olfactory organ unpaired or with closely set and confluent nasal sacs. 0 = absent; 1 =
present.
52. Olfactory organ paired with entirely separated nasal sacs. 0 = absent; 1 = present.
53. Nasohypophysial duct serving branchial respiration. 0 = absent; 1 = present.
54. Nasohypophysial duct posteriorly closed and serving only as a common "nostril". 0 =
absent; 1 = present.
55. Extrinsic eye muscles. 0 = absent; 1 = present.
56. Photosensory pineal organ (or pineal foramen). 0 = absent; 1 = present.
57. Semicircular canals. 0 = absent; 1 = present.
58. Single semicircular canal. 0 = absent; 1 = present.
59. Two vertical semicircular canals. 0 = absent; 1 = present.
60. Two vertical semicircular canals forming distinct loops. 0 = absent; 1 = present.
61. Lateral lines enclosed in canals. 0 = absent; 1 = present.
62. Lateral-line grooves or canals. 0 = absent; 1 = present on head (1); 2 = present on head
and body.(ORDERED)
63. Neuromasts. 0 = absent; 1 = isolated; 2 = in grooves; 3 = in tubes. (ORDERED)
64. Cerebellum. 0 = absent; 1 = present.
65. Large and paired cerebellum. 0 = absent; 1 = present.
66. Vagus and glossopharyngeus nerves included in occipital region. 0 = absent; 1 = present.
67. Closely set atrium and ventricle. 0 = absent; 1 = present.
68. Large dorsal jugular vein. 0 = absent; 1 = present.
69. Subaponeurotic vascular system. 0 = absent; 1 = present.
70. Calcified cartilage. 0 = absent; 1 = present.
71. Perichondral bone. 0 = absent; 1 = present.
72. Endoskeletal cranial roof. 0 = absent; 1 = present.
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73. Occiput enclosing IX and X. 0 = absent; 1 = present.
74. Head endoskeleton expanded into a massive shield covering the gills. 0 = absent; 1 =
present.
75. Endoskeletal scleral ossification or calcification. 0 = absent; 1 = present.
76. Orthodentine or metadentine. 0 = absent; 1 = present.
77. Mesodentine. 0 = absent; 1 = present.
78. Enameloid or enamel. 0 = absent; 1 = present.
79. Dermal skeleton. 0 = absent; 1 = present.
80. Acellular dermal bone. 0 = absent; 1 = present.
81. Cellular dermal bone. 0 = absent; 1 = present.
82. Honeycomb-like middle layer of exoskeleton. 0 = absent; 1 = present.
83. Three-layered dermal skeleton. 0 = absent; 1 = present.
84. Oakleaf-shaped tubercles or odontodes in ornamentation. 0 = absent; 1 = present.
85. Large median dorsal and ventral dermal shields in head. 0 = absent; 1 = present.
86. External opening of endolymphatic duct. 0 = absent; 1 = present.
87. Opercular flaps on external branchial openings. 0 = absent; 1 = present.
88. Preanal skin fold or scale ridge. 0 = absent; 1 = present.
89. Sclerotic ring. 0 = absent; 1 = present.
90. Scales made up by a single odontodes (microsquamose). 0 = absent; 1 = present.
91. Scales made up by several odontodes (macrosquamose) and diamond-shaped. 0 = absent;
1 = present.
92. Scales made up by several odontodes (macrosquamose) and rod-shaped. 0 = absent; 1 =
present.
93. Pharyngeal dermal denticles. 0 = absent; 1 = present.
94. Elongate oral plate. 0 = absent; 1 = present.
95. Scales. 0 = absent; 1 = non-overlapping; 2 = overlapping. (ORDERED)
96. Head armour differentiated from trunk armour. 0 = absent; 1 = present.
97. Dorsal/ventral growing plates. 0 = absent; 1 = present.
98. Dorsal/ventral scutes. 0 = absent; 1 = present.
99. Scale-covered zones on tail. 0 = absent; 1 = present.
100. Horny teeth. 0 = absent; 1 = present.
101. Piston cartilage. 0 = absent; 1 = present.
102. Dentigerous cartilage. 0 = absent; 1 = present.
103. Tentacles strengthened by cartilage. 0 = absent; 1 = present.
104. Sucking disc with an annular cartilage around mouth. 0 = absent; 1 = present.
105. Mouth ventral. 0 = absent; 1 = present.
106. Tongue protractor/retractor musculature. 0 = absent; 1 = present.
107. Pouch-shaped gill. 0 = absent; 1 = present.
108. Trematic rings. 0 = absent; 1 = present.
109. Gill arterial supply. 0 = absent; 1 = pretrematic; 2 = pre- and post-trematic.
3
110. Gills ventral. 0 = absent; 1 = present.
111. Gills transversely elongated. 0 = absent; 1 = present.
112. Gills crowded posteriorly. 0 = absent; 1 = present.
113. Branchial basket. 0 = absent; 1 = present.
114. Visceral skeleton attached to head. 0 = absent; 1 = present.
115. Optic tectum. 0 = absent; 1 = present.
116. Eye dorsal. 0 = absent; 1 = present.
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II. Data set with 116 characters for 16 taxa. Note: a majority of characters are compiled from
Forey (1995) and Janvier (1996). 0 = plesiomorphic state; 1, 2,3 = apomorphic states; ? =
unavailable characters or logical impossibility; (01) = polymorphic states (0 and 1).
II. Data set with 116 characters for 16 taxa. Note: a majority of characters are compiled from Forey (1995) and
Janvier (1996). 0 = plesiomorphic state; 1, 2,3 = apomorphic states; ? = unavailable characters or logical
impossibility; (01) = polymorphic states (0 and 1).
--------------------------------------------------------------------------------------------- ---------1 1111111112 2222222223 3333333334
1234567890 1234567890 1234567890 1234567890
-------------------------------------------------------------------------------------------------------anaspids
?????????? ?????????? ??1??1011? ??1110?000
arandaspids
?????????? ?????????? ??1??1?01? ??1?????00
astraspids
?????????? ?????????? ??1????01? ???????000
cephalochordes
0000000000 0000000000 0000000000 0010000001
galeaspids
???1?????? ?????????? ??1111011? ??1?100?00
gnathostomes
1101111111 0111111100 1111110010 1111111110
hagfishes
0010000000 1000000011 0010011011 1011100001
Haikouichthys
?????????? ?????????? ?????????? 1?1111?1?0
Heterostracans
???1?????? ?????????? ??1??1?01? ??1110?000
Jamoytius
?????????? ?????????? ??1?????1? ??1?11?1?0
Lampreys
1111111111 1111111111 1111010111 1111111110
Myllokunmingia
?????????? ?????????? ?????????? 1?110001?0
Osteostracans
???1?????? ?????????? ??1111011? 1111111110
pituriaspids
?????????? ?????????? ??1111??1? ??????1??0
thelodonts
???1?????? ?????????? ??1??1101? ???110?110
tunicates
0000000001 0000000000 0000000000 0000000000
----------------------------------------------------------------------------4444444445 5555555556 6666666667 7777777778
1234567890 1234567890 1234567890 1234567890
----------------------------------------------------------------------------anaspids
1111?0?10? ?????1???? 02???????? 0??0000011
arandaspids
0??000?10? ?????1???? 022??????? ????100011
astraspids
0??000?01? ?????0???? 0?2??????? ?????00111
cephalochordes
0000000000 0000000000 0000000000 0000000000
Galeaspids
?1?000?011 0110111011 123111?11? 1111000111
gnathostomes
1121111011 0101111011 1231111111 1100111110
5
hagfishes
0100000000 1010001100 0100000000 0000000000
Haikouichthys
???100?01? ?????????? ?????????0 0??0000000
heterostracans
0110001011 01??011011 12311???10 0???010011
Jamoytius
1111?0??0? ?????????? ?????????0 0??0000000
lampreys
0110001110 1001111010 0011001111 0100000000
Myllokunmingia
0??100001? ?????????? ?????????0 0??0000000
osteostracans
012111101? 1001111011 1231111111 1111101110
pituriaspids
???111?0?? ?????????? ???11????? 11?1????1?
thelodonts
11111??01? 01?0?????? 123??????0 0??00(01)(01)011
tunicates
0000000000 0000000000 0000000000 0000000000
-----------------------------------------------------------------------------------------------1 1111111111 111111
8888888889 9999999990 0000000001 111111
1234567890 1234567890 1234567890 123456
------------------------------------------------------------------------------------------------anaspids
00000?0100 010010011? ??00001??0 ?0???1
arandaspids
0111100010 01011110?? ??00001??0 ?00??0
astraspids
00101000?0 10?02001?? ????0?1??0 10???0
cephalochordes
0000000000 0000000000 0000000000 000000
galeaspids
0000010101 00?021101? ??001?1??1 100110
gnathostomes
1010011111 1010210000 0000000020 000010
hagfishes
0000000000 0000000001 0110011110 000100
Haikouichthys
00000???00 000000000? ??0?0????0 001???
heterostracans
0111100000 100121111? ??00001??0 100??0
Jamoytius
00000???00 0000000000 ??010?11?0 ?01??0
lampreys
0000000100 0000000001 1101011120 001110
Myllokunmingia
00000???00 000000000? ??0?0?1??0 000???
osteostracans
1010011110 100011010? ??00101?21 100111
pituriaspids
???00??1?? ???0?10??? ??000?1??1 ?????1
thelodonts
00000?1?01 001020001? ??0?0?1??0 10???0
tunicates
0000000000 0000000000 0000000000 000000
III. Clades & supporting characters in Fig.3b. The category "uniquely shared derived
characters" lists all characters with a C.I. equal to 1.
Node
Node 1
Uniquely shared derived characters
23, 26, 29, 31, 34, 42, 57, 109(1)
Node 2
1, 2, 4, 5, 6, 7, 8, 9, 12, 13, 14, 15,
16, 17, 18, 21, 22, 24, 32, 43(1), 59,
64, 67, 68, 69, 72, 109(2), 115
Reversals
6
Homoplasies
3, 11, 19, 20, 30, 35, 51,
62(1), 102, 106, 107, 108,
114
10, 28, 38, 39, 44, 49, 55,
56, 63(1), 88
Node 3
Node 4
Node 5
Node 6
Node 7
Node 8
Node 9
Node 10
Node 11
Node 12
Node 13
47
101, 104, 113
25, 50, 60, 65, 66, 79
85
82, 84, 94
86
43(2), 71
46, 77, 81
62
3, 11, 19, 20, 30, 51,
102, 106, 108
38, 39, 55
28, 41, 44, 88
80, 99
41, 52, 90, 93, 95(1)
7
37, 41
36, 54
48
52, 62(2), 63(2), 73, 80,
95(2), 99, 111
98
83, 91
96, 97
45, 61, 63(3), 87, 90, 93
70, 74, 78, 96, 110
36, 54, 75, 83, 89, 91
51, 98, 116