Overview of the transcriptome profiles identified in hagfish, shark, and bichir: Current issues arising from some nonmodel vertebrate taxa

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 316 B, Issue 7, 2011, Pages 526-546

  Takechi, Masaki ^a   Takeuchi, Masaki ^a   Ota, Kinya G ^a   Nishimura, Osamu ^a,b   Mochii, Makoto ^c   Itomi, Kazu ^a   Adachi, Noritaka ^a,d   Takahashi, Maiko ^a   Fujimoto, Satoko ^a   Tarui, Hiroshi ^a   Okabe, Masataka ^e   Aizawa, Shinichi ^a   Kuratani, Shigeru ^a  

^a RIKEN   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c UNIVERSITY OF HYOGO   (Japan)

^d KOBE UNIVERSITY   (Japan)

^e JIKEI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL; ARTICLE; CLASSIFICATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; HAGFISH; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEIC ACID DATABASE; PHYLOGENY; SHARK;

ANIMALS; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; HAGFISHES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PHYLOGENY; SHARKS; TRANSCRIPTOME;

CHONDRICHTHYES; EPTATRETUS BURGERI; HAGFISH; MYXINIDAE; POLYPTERIDAE; POLYPTERUS SENEGALUS; POLYPTERUS SENEGALUS SENEGALUS; SCYLIORHINUS TORAZAME; VERTEBRATA;

EID: 80054963049     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.21427     Document Type: Article

References (210)

1. Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ. 2004. Bmp4 and morphological variation of beaks in Darwin's finches. Science 305:1462-1465.
2. Abzhanov A, Kuo WP, Hartmann C, Grant BR, Grant PR, Tabin CJ. 2006. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 442:563-567.
3. Albertson RC, Yan YL, Titus TA, Pisano E, Vacchi M, Yelick PC, Detrich 3rd HW, Postlethwait JH. 2010. Molecular pedomorphism underlies craniofacial skeletal evolution in Antarctic notothenioid fishes. BMC Evol Biol 10:4.
4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
5. Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711-1714.
6. Anderson CB, Meier S. 1981. The influence of the metameric pattern in the mesoderm on migration of cranial neural crest cells in the chick embryo. Dev Biol 85:385-402.
7. Balfour FM. 1878. The development of the elasmobranchial fishes. J Anat Physiol 11:405-706.
8. Ballard WW, Mellinger J, Lechenault H. 1993. A series of normal stages for development of Scyliorhinus canicula, lesser spotted dogfish (chondrichthyes: Scyliorhinidae). J Exp Zool (Mol Dev Evol) 267:318-336.
9. Bartsch P, Gemballa S, Piotrowski T. 1997. The embryonic and larval development of Polypterus senegalus cuvier, 1829: its staging with reference to external and skeletal features, behavior and locomotory habits. Acta Zool (Stockholm) 78:309-328.
10. Bennett JT, Stickney HL, Choi WY, Ciruna B, Talbot WS, Schier AF. 2007. Maternal nodal and zebrafish embryogenesis. Nature 450:E1-E2.
11. Bjerring HC. 1971. The nerve supply to the second metamere basicranial muscle in osteolepiform vertebrates, with some remarks on the basic composition of the endocranium. Act Zool (Stockholm) 52:189-225.
12. Bjerring HC. 1977. A contribution to structural analysis of the head of craniate animals. Zool Script 6:127-183.
13. Bjornson CR, Griffin KJ, Farr 3rd GH, Terashima A, Himeda C, Kikuchi Y, Kimelman D. 2005. Eomesodermin is a localized maternal determinant required for endoderm induction in zebrafish. Dev Cell 9:523-533.
14. Boguski MS, Lowe TM, Tolstoshev CM. 1993. Dbest-database for "expressed sequence tags." Nat Genet 4:332-333.
15. Bothe I, Dietrich S. 2006. The molecular setup of the avian head mesoderm and its implication for craniofacial myogenesis. Dev Dyn 235:2845-2860.
16. Carrera I, Ferreiro-Galve S, Sueiro C, Anadon R, Rodriguez-Moldes I. 2008. Tangentially migrating gabaergic cells of subpallial origin invade massively the pallium in developing sharks. Brain Res Bull 75:405-409.
17. Cataudella S, Sola L, Capanna E. 1978. Remarks on the karyotype of the polypteriformes. The chromosomes of Polypterus delhezi, P. endlicheri congicus and P. palmas. Experientia 34:999-1000.
18. Charite J, McFadden DG, Merlo G, Levi G, Clouthier DE, Yanagisawa M, Richardson JA, Olson EN. 2001. Role of dlx6 in regulation of an endothelin-1-dependent, dhand branchial arch enhancer. Genes Dev 15:3039-3049.
19. Chou HH, Holmes MH. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17:1093-1104.
20. Clouthier DE, Williams SC, Yanagisawa H, Wieduwilt M, Richardson JA, Yanagisawa M. 2000. Signaling pathways crucial for craniofacial development revealed by endothelin-a receptor-deficient mice. Dev Biol 217:10-24.
21. Coolen M, Sauka-Spengler T, Nicolle D, Le-Mentec C, Lallemand Y, Da Silva C, Plouhinec JL, Robert B, Wincker P, Shi DL, Mazan S. 2007. Evolution of axis specification mechanisms in jawed vertebrates: insights from a chondrichthyan. PLoS ONE 2:e374.
22. Coolen M, Menuet A, Chassoux D, Compagnucci C, Henry S, Lévèque L, Da Silva C, Gavory F, Samain S, Wincker P, Thermes C, D'Aubenton-Carafa Y, Rodriguez-Moldes I, Naylor G, Depew M, Sourdaine P, Mazan S. 2008. The dogfish Scyliorhinus canicula: a reference in jawed vertebrates. In: Gann A, Crotty D, editors. Emerging model organisms. New York: Cold Spring Harbor Laboratory Press. p 431-446.
23. Cooper MS, Virta VC. 2007. Evolution of gastrulation in the ray-finned (actinopterygian) fishes. J Exp Zool (Mol Dev Evol) 308:591-608.
24. Dahn RD, Davis MC, Pappano WN, Shubin NH. 2007. Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning. Nature 445:311-314.
25. Dean B. 1899. On the embryology of bdellostoma stouti. A genera account of myxinoid development from the egg and segmentation to hatching. Festschrift zum 70ten Geburststag Carl von Kupffer 220-276.
26. de Beer GR. 1937. The development of the vertebrate skull. London: Oxford Univ Press.
27. Depew MJ, Simpson CA. 2006. 21st century neontology and the comparative development of the vertebrate skull. Dev Dyn 235:1256-1291.
28. Depew MJ, Lufkin T, Rubenstein JL. 2002. Specification of jaw subdivisions by dlx genes. Science 298:381-385.
29. Didier DA. 1995. Embryology of Callorhinchus milii i.: staging and early development. Am Zool 35:496.
30. Didier DA, Leclair EE, Vanbuskirk DR. 1998. Embryonic staging and external features of development of the chimaeroid fish, Callorhinchus milii (holocephali, callorhinchidae). J Morphol 236:25-47.
31. Eames BF, Schneider RA. 2008. The genesis of cartilage size and shape during development and evolution. Development 135:3947-3958.
32. Eames BF, Sharpe PT, Helms JA. 2004. Hierarchy revealed in the specification of three skeletal fates by sox9 and runx2. Dev Biol 274:188-200.
33. Eames BF, Allen N, Young J, Kaplan A, Helms JA, Schneider RA. 2007. Skeletogenesis in the swell shark Cephaloscyllium ventriosum. J Anat 210:542-554.
34. Ekblom R, Balakrishnan CN, Burke T, Slate J. 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics 11:219.
35. Engleka MJ, Craig EJ, Kessler DS. 2001. Vegt activation of sox17 at the midblastula transition alters the response to nodal signals in the vegetal endoderm domain. Dev Biol 237:159-172.
36. Evans AL, Gage PJ. 2005. Expression of the homeobox gene pitx2 in neural crest is required for optic stalk and ocular anterior segment development. Hum Mol Genet 14:3347-3359.
37. Fan X, Dougan ST. 2007. The evolutionary origin of nodal-related genes in teleosts. Dev Genes Evol 217:807-813.
38. Feldman B, Gates MA, Egan ES, Dougan ST, Rennebeck G, Sirotkin HI, Schier AF, Talbot WS. 1998. Zebrafish organizer development and germ-layer formation require nodal-related signals. Nature 395:181-185.
39. Fernholm B. 1974. Diurnal variations in behaviour of the hagfish Eptatretus burgeri. Marine Biol 27:351-356.
40. Forey P, Janvier P. 1993. Agnathans and the origin of jawed vertebrates. Nature 361:129-134.
41. Freitas R, Zhang G, Albert JS, Evans DH, Cohn MJ. 2006a. Developmental origin of shark electrosensory organs. Evol Dev 8:74-80.
42. Freitas R, Zhang G, Cohn MJ. 2006b. Evidence that mechanisms of fin development evolved in the midline of early vertebrates. Nature 442:1033-1037.
43. Freitas R, Zhang G, Cohn MJ. 2007. Biphasic hoxd gene expression in shark paired fins reveals an ancient origin of the distal limb domain. PLoS ONE 2:e754.
44. Freund R, Dorfler D, Popp W, Wachtler F. 1996. The metameric pattern of the head mesoderm-does it exist? Anat Embryol (Berl) 193:73-80.
45. Furlong RF, Holland PW. 2002. Bayesian phylogenetic analysis supports monophyly of ambulacraria and of cyclostomes. Zool Sci 19:593-599.
46. Furlong RF, Younger R, Kasahara M, Reinhardt R, Thorndyke M, Holland PW. 2007. A degenerate parahox gene cluster in a degenerate vertebrate. Mol Biol Evol 24:2681-2686.
47. Gage PJ, Suh H, Camper SA. 1999. Dosage requirement of pitx2 for development of multiple organs. Development 126:4643-4651.
48. Galtier N, Daubin V. 2008. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci 363:4023-4029.
49. Gee H. 1996. Before the backbone: views on the origin of the vertebrates. London: Chapman & Hall.
50. Gess RW, Coates MI, Rubidge BS. 2006. A lamprey from the Devonian period of South Africa. Nature 443:981-984.
51. Gillis JA, Shubin NH. 2009. The evolution of gnathostome development: insight from chondrichthyan embryology. Genesis 47:825-841.
52. Gillis JA, Dahn RD, Shubin NH. 2009. Shared developmental mechanisms pattern the vertebrate gill arch and paired fin skeletons. Proc Natl Acad Sci USA 106:5720-5724.
53. Goodrich ES. 1930. Studies on the structure and development of vertebrates. New York: MacMillan.
54. Gore AV, Sampath K. 2002. Localization of transcripts of the zebrafish morphogen squint is dependent on egg activation and the microtubule cytoskeleton. Mech Dev 112:153-156.
55. Gore AV, Maegawa S, Cheong A, Gilligan PC, Weinberg ES, Sampath K. 2005. The zebrafish dorsal axis is apparent at the four-cell stage. Nature 438:1030-1035.
56. Griffin KJ, Amacher SL, Kimmel CB, Kimelman D. 1998. Molecular identification of spadetail: regulation of zebrafish trunk and tail mesoderm formation by t-box genes. Development 125:3379-3388.
57. Grigoriou M, Tucker AS, Sharpe PT, Pachnis V. 1998. Expression and regulation of lhx6 and lhx7, a novel subfamily of lim homeodomain encoding genes, suggests a role in mammalian head development. Development 125:2063-2074.
58. Hall BK. 1998. Evolutionary developmental biology. London: Chapman & Hall.
59. Hall BK, Olson WM. 2003. Keywards and concepts in evolutionary developmental biology. London: Harvard university press.
60. Hallstrom BM, Janke A. 2009. Gnathostome phylogenomics utilizing lungfish est sequences. Mol Biol Evol 26:463-471.
61. Hardisty MW, Potter IC. 1971. The general biology of adult lampreys. In: Hardisty MW, Potter IC, editors. The biology of lampreys. London: Academic Press Inc. p 128-206.
62. Hedges SB. 2009. Vertebrates (vertebrata). In: Hedges SB, Kumar S, editors. The timetree of life. Oxford university press. p 309-314.
63. Hedges SB, Kumar S. 2009. The timetree of life. New York: Oxford University Press.
64. Heinicke M, Naylor G, Hedges SB. 2009. Cartilaginous fishes (chondrichthyes). The timetree of life. New York: Oxford university press.
65. Ho RK, Kane DA. 1990. Cell-autonomous action of zebrafish spt-1 mutation in specific mesodermal precursors. Nature 348:728-730.
66. Holland LZ, Holland ND, Gilland E. 2008. Amphioxus and the evolution of head segmentation. Integr Comp Biol 48:630-646.
67. Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res 9:868-877.
68. Hudson C, Clements D, Friday RV, Stott D, Woodland HR. 1997. Xsox17alpha and -beta mediate endoderm formation in xenopus. Cell 91:397-405.
69. Hurley IA, Mueller RL, Dunn KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG, Coates MI. 2007. A new time-scale for ray-finned fish evolution. Proc Biol Sci 274:489-498.
70. Inoue JG, Miya M, Tsukamoto K, Nishida M. 2003. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish." Mol Phylogenet Evol 26:110-120.
71. Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh B. 2010. Evolutionary origin and phylogeny of the modern holocephalans (chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol Biol Evol 27:2576-2586.
72. Ivory P, Jeal F, Nolan CP. 2005. Age determination, growth and reproduction in the lesser-spotted dogfish, Scyliorhinus canicula (L.). J Northw Atl Fish Sci 35.
73. Jacobson AG. 1988. Somitomeres: mesodermal segments of vertebrate embryos. Development 104:209-220.
74. Janvier P. 1996. Early vertebrates. Oxford: Clarendon Press.
75. Jarvik E. 1980. Basic structure and evolution of vertebrates. New York: Academic press.
76. Jefferies RPS. 1986. The ancestry of the vertebrates. London: British Museum (Natural History).
77. Jørgensen J, Lomholt JP, Weber RE, Malte H. 1998. The biology of hagfishes. Cambrige: Chapman and Hall Ltd.
78. Jouve C, Iimura T, Pourquie O. 2002. Onset of the segmentation clock in the chick embryo: evidence for oscillations in the somite precursors in the primitive streak. Development 129:1107-1117.
79. Kasamatsu J, Suzuki T, Ishijima J, Matsuda Y, Kasahara M. 2007. Two variable lymphocyte receptor genes of the inshore hagfish are located far apart on the same chromosome. Immunogenetics 59:329-331.
80. Kessel M. 1992. Respecification of vertebral identities by retinoic acid. Development 115:487-501.
81. Kessel M, Gruss P. 1991. Homeotic transformations of murine vertebrae and concomitant alteration of hox codes induced by retinoic acid. Cell 67:89-104.
82. Kessel M, Balling R, Gruss P. 1990. Variations of cervical vertebrae after expression of a hox-1.1 transgene in mice. Cell 61:301-308.
83. Kikugawa K, Katoh K, Kuraku S, Sakurai H, Ishida O, Iwabe N, Miyata T. 2004. Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biol 2:3.
84. Kimelman D. 2006. Squinting at the zebrafish axis. Dev Cell 10:6-7.
85. Kimmel CB, Warga RM. 1987. Indeterminate cell lineage of the zebrafish embryo. Dev Biol 124:269-280.
86. Kitamura K, Miura H, Miyagawa-Tomita S, Yanazawa M, Katoh-Fukui Y, Suzuki R, Ohuchi H, Suehiro A, Motegi Y, Nakahara Y, Kondo S, Yokoyama M. 1999. Mouse pitx2 deficiency leads to anomalies of the ventral body wall, heart, extra- and periocular mesoderm and right pulmonary isomerism. Development 126:5749-5758.
87. Klein SL. 1987. The first cleavage furrow demarcates the dorsal-ventral axis in xenopus embryos. Dev Biol 120:299-304.
88. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, Robb A, Beetz-Sargent M, Holt RA, Moore R, Brahmbhatt S, Rosner J, Rexroad 3rd CE, McGowan CR, Davidson WS. 2008. A salmonid est genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics 9:545.
89. Kubota S, Kuro-o M, Mizuno S, Kohno S. 1993. Germ line-restricted, highly repeated DNA sequences and their chromosomal localization in a japanese hagfish (Eptatretus okinoseanus). Chromosoma 102:163-173.
90. Kubota S, Takano J, Tsuneishi R, Kobayakawa S, Fujikawa N, Nabeyama M, Kohno S. 2001. Highly repetitive DNA families restricted to germ cells in a japanese hagfish (Eptatretus burgeri): a hierarchical and mosaic structure in eliminated chromosomes. Genetica 111:319-328.
91. Kuraku S. 2008. Insights into cyclostome phylogenomics: pre-2R or post-2R? Zool Sci 25:960-968.
92. Kuraku S. 2010. Palaeophylogenomics of the vertebrate ancestor- impact of hidden paralogy on hagfish and lamprey gene phylogeny. Integr Comp Biol 50:124-129.
93. Kuraku S, Kuratani S. 2006. Timescale for cyclostome evolution inferred with a phylogenetic diagnosis of hagfish and lamprey cDNA sequences. Zool Sci 23:1053-1064.
94. Kuraku S, Meyer A. 2009. The evolution and maintenance of hox gene clusters in vertebrates and the teleost-specific genome duplication. Int J Dev Biol 53:765-773.
95. Kuraku S, Hoshiyama D, Katoh K, Suga H, Miyata T. 1999. Monophyly of lampreys and hagfishes supported by nuclear DNA-coded genes. J Mol Evol 49:729-735.
96. Kuraku S, Takio Y, Tamura K, Aono H, Meyer A, Kuratani S. 2008. Noncanonical role of hox14 revealed by its expression patterns in lamprey and shark. Proc Natl Acad Sci USA 105:6679-6683.
97. Kuraku S, Meyer A, Kuratani S. 2009a. Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol 26:47-59.
98. Kuraku S, Ota KG, Kuratani S. 2009b. Jawless fishes (cyclostomata). In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford university press. p 317-319.
99. Kuratani S. 2003. Evolutionary developmental biology and vertebrate head segmentation: a perspective from developmental constraint. Theory Biosci 122:230-251.
100. Kuratani S. 2005. Craniofacial development and the evolution of the vertebrates: the old problems on a new background. Zool Sci 22:1-19.
101. Kuratani S. 2008. Is the vertebrate head segmented?-evolutionary and developmental considerations. Integr Comp Biol 48:647-657.
102. Kuratani S, Horigome N. 2000. Developmental morphology of branchiomeric nerves in a cat shark, Scyliorhinus torazame, with special reference to rhombomeres, cephalic mesoderm, and distribution patterns of cephalic crest cells. Zool Sci 17:893-909.
103. Kuratani S, Ota KG. 2008a. Hagfish (cyclostomata, vertebrata): searching for the ancestral developmental plan of vertebrates. Bioessays 30:167-172.
104. Kuratani S, Ota KG. 2008b. Primitive versus derived traits in the developmental program of the vertebrate head: views from cyclostome developmental studies. J Exp Zool (Mol Dev Evol) 310:294-314.
105. Kuratani S, Horigome N, Hirano S. 1999. Developmental morphology of the head mesoderm and reevaluation of segmental theories of the vertebrate head: evidence from embryos of an agnathan vertebrate, Lampetra japonica. Dev Biol 210:381-400.
106. Kusakabe R, Kuratani S. 2005. Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Dev Dyn 234:824-834.
107. Kusakabe R, Takechi M, Tochinai S, Kuratani S. 2004. Lamprey contractile protein genes mark different populations of skeletal muscles during development. J Exp Zool (Mol Dev Evol) 302:121-133.
108. Lee SH, Bedard O, Buchtova M, Fu K, Richman JM. 2004. A new origin for the maxillary jaw. Dev Biol 276:207-224.
109. Lefebvre V, Li P, de Crombrugghe B. 1998. A new long form of sox5 (l-sox5), sox6 and sox9 are coexpressed in chondrogenesis and cooperatively activate the type ii collagen gene. EMBO J 17:5718-5733.
110. Løvtrup S. 1977. The phylogeny of vertebrata. New York: Wiley.
111. Luer CA, Walsh CJ, Bodine AB, Wyffels JT. 2007. Normal embryonic development in the clearnose skete, Raja eglanteria, with experimental observations on artificial insemination. Environ Biol Fish 80:239-255.
112. Mallatt J. 2008. The origin of the vertebrate jaw: neoclassical ideas versus newer, development-based ideas. Zool Sci 25:990-998.
113. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczcki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. 2009. CDD: specific functional annotation with the conserved domain database. Nucleic Acids Res 37:D205-D210.
114. Marshall AM. 1881. On the head cavities and associated nerves of elasmobranchs. Q J Microsc Sci 21:72-97.
115. Martin BL, Kimelman D. 2008. Regulation of canonical wnt signaling by brachyury is essential for posterior mesoderm formation. Dev Cell 15:121-133.
116. McCauley DW, Bronner-Fraser M. 2004. Conservation and divergence of bmp2/4 genes in the lamprey: expression and phylogenetic analysis suggest a single ancestral vertebrate gene. Evol Dev 6:411-422.
117. McCauley DW, Bronner-Fraser M. 2006. Importance of soxe in neural crest development and the evolution of the pharynx. Nature 441:750-752.
118. Meier S. 1979. Development of the chick embryo mesoblast. Formation of the embryonic axis and establishment of the metameric pattern. Dev Biol 73:24-45.
119. Meier S, Packard Jr DS. 1984. Morphogenesis of the cranial segments and distribution of neural crest in the embryos of the snapping turtle, Chelydra serpentina. Dev Biol 102:309-323.
120. Meier S, Tam PP. 1982. Metameric pattern development in the embryonic axis of the mouse. I. Differentiation of the cranial segments. Differentiation 21:95-108.
121. Mellinger J, Wrisez F, Alluchon-Gerard MJ. 1984. Recherches en vue de letablissement dune table du developpment de la petite roussette, Scyirhinus canicula (l.), poisson selacien. Bull Soc Zool, Fr 109:3-18.
122. Mellinger J, Wrisez F, Alluchon-Gerard MJ. 1986. Developmental biology of an oviparous shark, Scyliorhinus canicula. In: Uyeno T, Arai R, Taniuchi T, Matsuura K, editors. Proceedings of the second international conference on Indo-Pacific fishes. Tokyo: Ichthyological Society of Japan. p 310-332.
123. Merrill AE, Eames BF, Weston SJ, Heath T, Schneider RA. 2008. Mesenchyme-dependent bmp signaling directs the timing of mandibular osteogenesis. Development 135:1223-1234.
124. Miller CT, Yelon D, Stainier DY, Kimmel CB. 2003. Two endothelin 1 effectors, hand2 and bapx1, pattern ventral pharyngeal cartilage and the jaw joint. Development 130:1353-1365.
125. Minoux M, Rijli FM. 2010. Molecular mechanisms of cranial neural crest cell migration and patterning in craniofacial development. Development 137:2605-2621.
126. Miura S, Hanaoka K, Togashi S. 2008. Skeletogenesis in Xenopus tropicalis: characteristic bone development in an anuran amphibian. Bone 43:901-909.
127. Mootoosamy RC, Dietrich S. 2002. Distinct regulatory cascades for head and trunk myogenesis. Development 129:573-583.
128. Nair S, Li W, Cornell R, Schilling TF. 2007. Requirements for endothelin type-a receptors and endothelin-1 signaling in the facial ectoderm for the patterning of skeletogenic neural crest cells in zebrafish. Development 134:335-345.
129. Nakai Y, Kubota S, Kohno S. 1991. Chromatin diminution and chromosome elimination in four japanese hagfish species. Cytogenet Cell Genet 56:196-198.
130. Nakai Y, Kubota S, Goto Y, Ishibashi T, Davison W, Kohno S. 1995. Chromosome elimination in three Baltic, South Pacific and North-East Pacific hagfish species. Chromosome Res 3:321-330.
131. Nath K, Elinson RP. 2007. Rna of amvegt, the axolotl orthologue of the xenopus meso-endodermal determinant, is not localized in the oocyte. Gene Expr Patterns 7:197-201.
132. Nath K, Boorech JL, Beckham YM, Burns MM, Elinson RP. 2005. Status of rnas, localized in Xenopus laevis oocytes, in the frogs Rana pipiens and Eleutherodactylus coqui. J Exp Zool (Mol Dev Evol) 304:28-39.
133. Noack K, Zardoya R, Meyer A. 1996. The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: ancient establishment of the consensus vertebrate gene order. Genetics 144:1165-1180.
134. Noden DM, Francis-West P. 2006. The differentiation and morphogenesis of craniofacial muscles. Dev Dyn 235:1194-1218.
135. Northcutt RG. 2008. Historical hypotheses regarding segmentation of the vertebrate head. Integr Comp Biol 48:611-619.
136. Okabe M, Graham A. 2004. The origin of the parathyroid gland. Proc Natl Acad Sci USA 101:17716-17719.
137. O'Neill P, McCole RB, Baker CV. 2007. A molecular analysis of neurogenic placode and cranial sensory ganglion development in the shark, Scyliorhinus canicula. Dev Biol 304:156-181.
138. Ota KG, Kuratani S. 2006. The history of scientific endeavors towards understanding hagfish embryology. Zool Sci 23:403-418.
139. Ota KG, Kuratani S. 2008. Developmental biology of hagfishes, with a report on newly obtained embryos of the japanese inshore hagfish, Eptatretus burgeri. Zool Sci 25:999-1011.
140. Ota KG, Kuratani S. 2010. Expression pattern of two collagen type 2 alpha1 genes in the japanese inshore hagfish (Eptatretus burgeri) with special reference to the evolution of cartilaginous tissue. J Exp Zool (Mol Dev Evol) 314:157-165.
141. Ota KG, Kuraku S, Kuratani S. 2007. Hagfish embryology with reference to the evolution of the neural crest. Nature 446:672-675.
142. Oulion S, Debiais-Thibaud M, Aubenton-Carafa YD, Thermes C, Da Silva C, Bernard-Samain S, Gavory F, Wincker P, Mazan S, Casane D. 2010. Evolution of hox gene clusters in gnathostomes: insights from a survey of a shark (Scyliorhinus canicula) transcriptome. Mol Biol Evol 27:2829-2838.
143. Ozeki H, Kurihara Y, Tonami K, Watatani S, Kurihara H. 2004. Endothelin-1 regulates the dorsoventral branchial arch patterning in mice. Mech Dev 121:387-395.
144. Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL, Cooper MD. 2004a. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430:174-180.
145. Pancer Z, Mayer WE, Klein J, Cooper MD. 2004b. Prototypic t cell receptor and cd4-like coreceptor are expressed by lymphocytes in the agnathan sea lamprey. Proc Natl Acad Sci USA 101:13273-13278.
146. Pancer Z, Saha NR, Kasamatsu J, Suzuki T, Amemiya CT, Kasahara M, Cooper MD. 2005. Variable lymphocyte receptors in hagfish. Proc Natl Acad Sci USA 102:9224-9229.
147. Parton A, Bayne CJ, Barnes DW. 2010. Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea). Comp Biochem Physiol D Genom Proteom 5:199-206.
148. Perez O, Benitez MS, Nath K, Heasman J, Del Pino EM, Elinson RP. 2007. Comparative analysis of Xenopus vegt, the meso-endodermal determinant, identifies an unusual conserved sequence. Differentiation 75:559-565.
149. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J. 2002. TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651-652.
150. Platt JB. 1891. A contribution to the morphology of the vertebrate head, based on a study of acanthias vulgaris. J Morphol 5:79-106.
151. Potter IC, Rothwell B. 1970. The mitotic chromosomes of the lamprey, petromyzon marinus l. Cell Mol Life Sci 26:429-430.
152. Potter IC, Robinson ES, Walton SM. 1968. The mitotic chromosomes of the lamprey Mordacia mordax (agnatha: Petromyzonidae). Experientia 24:966-967.
153. Raff RA. 2000. Evo-devo: the evolution of a new discipline. Nat Rev Genet 1:74-79.
154. Reiter JF, Alexander J, Rodaway A, Yelon D, Patient R, Holder N, Stainier DY. 1999. Gata5 is required for the development of the heart and endoderm in zebrafish. Genes Dev 13:2983-2995.
155. Richman JM, Lee SH. 2003. About face: signals and genes controlling jaw patterning and identity in vertebrates. Bioessays 25:554-568.
156. Robson P, Wright GM, Youson JH, Keeley FW. 2000. The structure and organization of lamprin genes: multiple-copy genes with alternative splicing and convergent evolution with insect structural proteins. Mol Biol Evol 17:1739-1752.
157. Rodriguez-Moldes I, Ferreiro-Galve S, Carrera I, Sueiro C, Candal E, Mazan S, Anadon R. 2008. Development of the cerebellar body in sharks: spatiotemporal relations of pax6 expression, cell proliferation and differentiation. Neurosci Lett 432:105-110.
158. Romer AS. 1966. Vertebrate paleontology. Chicago: University of Chicago Press.
159. Romer AS, Parsons TS. 1977. The veretrate body. Philadelphia: Saunders.
160. Ruvinsky I, Silver LM, Ho RK. 1998. Characterization of the zebrafish tbx16 gene and evolution of the vertebrate t-box family. Dev Genes Evol 208:94-99.
161. Ryan K, Garrett N, Mitchell A, Gurdon JB. 1996. Eomesodermin, a key early gene in xenopus mesoderm differentiation. Cell 87:989-1000.
162. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
163. Sambasivan R, Gayraud-Morel B, Dumas G, Cimper C, Paisant S, Kelly RG, Tajbakhsh S. 2009. Distinct regulatory cascades govern extraocular and pharyngeal arch muscle progenitor cell fates. Dev cell 16:810-821.
164. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual, 2nd edition. Cold spring harbour, NY: Cold spring harbour laboratory.
165. Santagati F, Rijli FM. 2003. Cranial neural crest and the building of the vertebrate head. Nat Rev Neurosci 4:806-818.
166. Sato T, Kurihara Y, Asai R, Kawamura Y, Tonami K, Uchijima Y, Heude E, Ekker M, Levi G, Kurihara H. 2008. An endothelin-1 switch specifies maxillomandibular identity. Proc Natl Acad Sci USA 105:18806-18811.
167. Scammon RE. 1911. Nomal plates on the development of Squalus acanthias. In: Keibel F, editor. Normentafeln zur entwickelungsgeschichte der wirbeltiere. Jena: Verlag von Gustav Fischer.
168. Schulte-Merker S, Ho RK, Herrmann BG, Nusslein-Volhard C. 1992. The protein product of the zebrafish homologue of the mouse t gene is expressed in nuclei of the germ ring and the notochord of the early embryo. Development 116:1021-1032.
169. Sewertzoff AN. 1911. Die kiemenbogennerven der fische. Anat Anz 38:487-495.
170. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26:1135-1145.
171. Shigetani Y, Nobusada Y, Kuratani S. 2000. Ectodermally derived fgf8 defines the maxillomandibular region in the early chick embryo: epithelial-mesenchymal interactions in the specification of the craniofacial ectomesenchyme. Dev Biol 228:73-85.
172. Shigetani Y, Sugahara F, Kawakami Y, Murakami Y, Hirano S, Kuratani S. 2002. Heterotopic shift of epithelial-mesenchymal interactions in vertebrate jaw evolution. Science 296:1316-1319.
173. Shigetani Y, Sugahara F, Kuratani S. 2005. A new evolutionary scenario for the vertebrate jaw. Bioessays 27:331-338.
174. Smith JJ, Antonacci F, Eichler EE, Amemiya CT. 2009. Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci USA 106:11212-11217.
175. Snel B, Huynen MA, Dutilh BE. 2005. Genome trees and the nature of genome evolution. Annu Rev Microbiol 59:191-209.
176. Stottmann RW, Anderson RM, Klingensmith J. 2001. The bmp antagonists chordin and noggin have essential but redundant roles in mouse mandibular outgrowth. Dev Biol 240:457-473.
177. Suda Y, Kurokawa D, Takeuchi M, Kajikawa E, Kuratani S, Amemiya C, Aizawa S. 2009. Evolution of otx paralogue usages in early patterning of the vertebrate head. Dev Biol 325:282-295.
178. Suzuki T, Ota T, Fujiyama A, Kasahara M. 2004a. Construction of a bacterial artificial chromosome library from the inshore hagfish, Eptatretus burgeri: a resource for the analysis of the agnathan genome. Genes Genet Syst 79:251-253.
179. Suzuki T, Shin IT, Kohara Y, Kasahara M. 2004b. Transcriptome analysis of hagfish leukocytes: a framework for understanding the immune system of jawless fishes. Dev Comp Immunol 28:993-1003.
180. Takechi M, Kuratani S. 2010. History of studies on mammalian middle ear evolution: a comparative morphological and developmental biology perspective. J Exp Zool (Mol Dev Evol) 314:417-433.
181. Takeuchi M, Okabe M, Aizawa S. 2008. The genus polypterus (bichirs): a fish group diverged at the stem of ray-finned fishes (actinopterygii). In: Gann A, Crotty D, editors. Emerging model organisms. Cold Spring Harbor Laboratory Press. p 447-469.
182. Takeuchi M, Okabe M, Aizawa S. 2009a. The genus polypterus (bichirs): a fish group diverged at the stem of ray-finned fishes (actinopterygii). Cold Spring Harb Protoc 2009:pdb emo117.
183. Takeuchi M, Okabe M, Aizawa S. 2009b. Microinjection of bichir (polypterus) embryos. Cold Spring Harb Protoc 2009:pdb prot5157.
184. Takeuchi M, Okabe M, Aizawa S. 2009c. Whole-mount in situ hybridization of bichir (polypterus) embryos. Cold Spring Harb Protoc 2009:pdb prot5158.
185. Takeuchi M, Takahashi M, Okabe M, Aizawa S. 2009d. Germ layer patterning in bichir and lamprey; an insight into its evolution in vertebrates. Dev Biol 332:90-102.
186. Takezaki N, Figueroa F, Zaleska-Rutczynska Z, Klein J. 2003. Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes. Mol Biol Evol 20:287-292.
187. Tanaka M, Munsterberg A, Anderson WG, Prescott AR, Hazon N, Tickle C. 2002. Fin development in a cartilaginous fish and the origin of vertebrate limbs. Nature 416:527-531.
188. Thomas T, Kurihara H, Yamagishi H, Kurihara Y, Yazaki Y, Olson EN, Srivastava D. 1998. A signaling cascade involving endothelin-1, dhand and msx1 regulates development of neural-crest-derived branchial arch mesenchyme. Development 125:3005-3014.
189. Tucker AS, Yamada G, Grigoriou M, Pachnis V, Sharpe PT. 1999. Fgf-8 determines rostral-caudal polarity in the first branchial arch. Development 126:51-61.
190. van Wijhe JW. 1882. Über die mesodermsegmente und die entwicklung der nerven des selachierkopfes. Amsterdam: Ver. Akad. Wiss. p 1-50.
191. Veit O. 1947. Uber das problem wirbeltiekopf.
192. Venkatesh B, Tay A, Dandona N, Patil JG, Brenner S. 2005. A compact cartilaginous fish model genome. Curr Biol 15:R82-R83.
193. Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S. 2006. Ancient noncoding elements conserved in the human genome. Science 314:1892.
194. Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S. 2007. Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol 5:e101.
195. Vervoort A. 1980. Karyotypes and nuclear DNA contents of polypteridae (osteichthyes). Experientia 36:646-647.
196. Wang J, Lee AP, Kodzius R, Brenner S, Venkatesh B. 2009. Large number of ultraconserved elements were already present in the jawed vertebrate ancestor. Mol Biol Evol 26:487-490.
197. White JA, Heasman J. 2008. Maternal control of pattern formation in Xenopus laevis. J Exp Zool (Mol Dev Evol) 310:73-84.
198. Wourms JP. 1997. The rise of fish embryology in the nineteenth century. Am Zool 17:269-310.
199. Wright GM, Keeley FW, Youson JH, Babineau DL. 1984. Cartilage in the atlantic hagfish, Myxine glutinosa. Am J Anat 169:407-424.
200. Wright GM, Keeley FW, Robson P. 2001. The unusual cartilaginous tissues of jawless craniates, cephalochordates and invertebrates. Cell Tissue Res 304:165-174.
201. Wu P, Jiang TX, Suksaweang S, Widelitz RB, Chuong CM. 2004. Molecular shaping of the beak. Science 305:1465-1466.
202. Wu P, Jiang TX, Shen JY, Widelitz RB, Chuong CM. 2006. Morphoregulation of avian beaks: comparative mapping of growth zone activities and morphological evolution. Dev Dyn 235:1400-1412.
203. Wyffels. 2009. Embryonic development of chondrichthyan fishes-a review. In: Kunz YW, Luer CA, Kapoor BG, editors. Development of non-teleost fishes. Enfield: Scinence Publishers. p 1-103.
204. Xanthos JB, Kofron M, Wylie C, Heasman J. 2001. Maternal vegt is the initiator of a molecular network specifying endoderm in Xenopus laevis. Development 128:167-180.
205. Yanagisawa H, Clouthier DE, Richardson JA, Charite J, Olson EN. 2003. Targeted deletion of a branchial arch-specific enhancer reveals a role of dhand in craniofacial development. Development 130:1069-1078.
206. Yi SE, Daluiski A, Pederson R, Rosen V, Lyons KM. 2000. The type i bmp receptor bmprib is required for chondrogenesis in the mouse limb. Development 127:621-630.
207. Yonei-Tamura S, Abe G, Tanaka Y, Anno H, Noro M, Ide H, Aono H, Kuraishi R, Osumi N, Kuratani S, Tamura K. 2008. Competent stripes for diverse positions of limbs/fins in gnathostome embryos. Evol Dev 10:737-745.
208. Yong JZ. 1981. The life of vertebrates. Oxford: Clareondon press.
209. Zhang J, Houston DW, King ML, Payne C, Wylie C, Heasman J. 1998. The role of maternal vegt in establishing the primary germ layers in xenopus embryos. Cell 94:515-524.
210. Zhao S, Shao C, Goropashnaya AV, Stewart NC, Xu Y, Toien O, Barnes BM, Fedorov VB, Yan J. 2010. Genomic analysis of expressed sequence tags in American black bear Ursus americanus. BMC Genomics 11:201.