Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data

Developmental Dynamics

Volumn 240, Issue 5, 2011, Pages 1005-1016

  Abbasi, Amir Ali ^a  

^a QUAID I AZAM UNIVERSITY   (Pakistan)

Author keywords

Evolution; Fish fin; Limb development; Vertebrates

Indexed keywords

BONE MORPHOGENETIC PROTEIN; BONE MORPHOGENETIC PROTEIN 4; FIBROBLAST GROWTH FACTOR; FIBROBLAST GROWTH FACTOR 8; HOX PROTEIN; NUCLEIC ACID BINDING PROTEIN; PROTEIN DHAND; PROTEIN EN1; PROTEIN MEIS; PROTEIN PATCHED 1; PROTEIN SAL1; SONIC HEDGEHOG PROTEIN; T BOX TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DLX5; TRANSCRIPTION FACTOR GLI3; TRANSCRIPTION FACTOR MSX1; TRANSCRIPTION FACTOR PITX1; TRANSCRIPTION FACTOR TBX4; TRANSCRIPTION FACTOR TBX5; UNCLASSIFIED DRUG; WNT PROTEIN; WNT7A PROTEIN;

ANIMAL ANATOMY; ANIMAL GENETICS; BRANCHIOSTOMA; CAENORHABDITIS ELEGANS; CARPAL BONE; CARTILAGINOUS TISSUE; CIONA INTESTINALIS; CLADISTICS; DOGFISH; DROSOPHILA; EMBRYO; EMBRYONIC STRUCTURES; ENHANCER REGION; EVOLUTION; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; EVOLUTIONARY HOMOLOGY; FIBULA; FIN (ORGAN); FINGER; FISH; FISH GENETICS; FORELIMB; FOSSIL; GENE DELETION; GENE EXPRESSION; GENE INSERTION; GENE MUTATION; GENETIC CODE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOMICS; GNATHOSTOME; HINDLIMB; HOX GENE; HUMAN; LIMB DEVELOPMENT; MESODERM; MOUSE; NUCLEOTIDE BINDING SITE; PALEONTOLOGY; PHALANX; PHYLOGENY; PRIORITY JOURNAL; RADIUS; REGULATORY SEQUENCE; REVIEW; SKELETON; SYNAPOMORPHY; TARSAL BONE; TELEOST; TIBIA; TRANSCRIPTION REGULATION; ULNA; VERTEBRATE;

ANIMAL FINS; ANIMALS; BIOLOGICAL EVOLUTION; EXTREMITIES; PALEONTOLOGY; VERTEBRATES;

TETRAPODA; VERTEBRATA;

EID: 79955016324     PISSN: 10588388     EISSN: 10970177     Source Type: Journal    
DOI: 10.1002/dvdy.22572     Document Type: Review

References (79)

1. Abbasi AA. 2008. Are we degenerate tetraploids? More genomes, new facts. Biol Direct 3: 50.
2. Abbasi AA, Paparidis Z, Malik S, Goode DK, Callaway H, Elgar G, Grzeschik KH. 2007. Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS ONE 2: e366.
3. Abbasi AA, Paparidis Z, Malik S, Bangs F, Schmidt A, Koch S, Lopez-Rios J, Grzeschik KH. 2010. Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development. BMC Dev Biol 10: 44.
4. Adamska M, MacDonald BT, Sarmast ZH, Oliver ER, Meisler MH. 2004. En1 and Wnt7a interact with Dkk1 during limb development in the mouse. Dev Biol 272: 134-144.
5. Adamska M, Billi AC, Cheek S, Meisler MH. 2005. Genetic interaction between Wnt7a and Lrp6 during patterning of dorsal and posterior structures of the mouse limb. Dev Dyn 233: 368-372.
6. Aoto K, Nishimura T, Eto K, Motoyama J. 2002. Mouse GLI3 regulates Fgf8 expression and apoptosis in the developing neural tube, face, and limb bud. Dev Biol 251: 320-332.
7. Aoyagi N, Wassarman DA. 2000. Genes encoding Drosophila melanogaster RNA polymerase II general transcription factors: diversity in TFIIA and TFIID components contributes to gene-specific transcriptional regulation. J Cell Biol 150: F45-50.
8. Barna M, Pandolfi PP, Niswander L. 2005. Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development. Nature 436: 277-281.
9. Boisvert CA, Kurik EM, Ahleberg PE. 2008. The pectoral fin of Panderichthys and the origin of digits. Nature 456: 636-638.
10. Capdevila J, Izpisua Belmonte JC. 2001. Patterning Mechanisms Controlling Vertebrate Limb Development. Annu Rev Cell Dev Biol 17: 87-132.
11. Capellini TD, Di Giacomo G, Salsi V, Brendolan A, Ferretti E, Srivastava D, Zappavigna V, Selleri L. 2006. Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution and Shh expression. Development 133: 2263-2273.
12. Carroll SB. 2001. Chance and necessity: the evolution of morphological complexity and diversity. Nature 409: 1102-1109.
13. Carroll SB. 2005. Evolution at two levels: on genes and form. PLoS Biol 3: e245.
14. Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134: 25-36.
15. Chiang C, Litingtung Y, Harris MP, Simandl BK, Li Y, Beachy PA, Fallon JF. 2001. Manifestation of the limb prepattern: limb development in the absence of sonic hedgehog function. Dev Biol 236: 421-435.
16. Coates MI. 1996. The Devonian tetrapod Acanthostega gunnari Jarvik:postcranial anatomy, basal tetrapod interrelationships and patterns of skeletal evolution. Trans R Soc Edinb Earth Sci 87: 363-421.
17. Coates MI. 2003. The evolution of paired fins. Theory in Biosciences 122: 266-287.
18. Coates MI, Clack JA. 1990. Polydactyly in the earliest tetrapod limbs. Nature 347: 66-69.
19. Coates MI, Cohn MJ. 1998. Fins, limbs, and tails: outgrowth and axial patterning in vertebrate evolution. BioEssays 20: 371-381.
20. Cohn MJ, Lovejoy CO, Wolpert L, Coates MI. 2002. Branching, segmentation and the metapterygial axis: pattern versus process in the vertebrate limb. BioEssays 24: 460-465.
21. 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.
22. Dathe K, Kjaer KW, Brehm A, Meinecke P, Nurnberg P, Neto JC, Brunoni D, Tommerup N, Ott CE, Klopocki E, Seemann P, Mundlos S. 2009. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet 84: 483-492.
23. Davis MC, Dahn RD, Shubin NH. 2007. An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature 447: 473-476.
24. Forey P, Janvier P. 1993. Agnathans and the origin of jawed vertebrates Nature 361: 129-134.
25. Fraidenraich D, Lang R, Basilico C. 1998. Distinct regulatory elements govern Fgf4 gene expression in the mouse blastocyst, myotomes, and developing limb. Dev Biol 204: 197-209.
26. 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.
27. Galli A, Robay D, Osterwalder M, Bao X, Benazet JD, Tariq M, Paro R, Mackem S, Zeller R. 2010. Distinct roles of Hand2 in initiating polarity and posterior Shh expression during the onset of mouse limb bud development. PLoS Genet 6: e1000901.
28. Harafuji N, Keys DN, Levine M. 2002. Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. Proc Natl Acad Sci USA 99: 6802-6805.
29. Harfe BD, Scherz PJ, Nissim S, Tian H, McMahon AP, Tabin CJ. 2004. Evidence for an expansion-based temporal Shh gradient in specifying vertebrate digit identities. Cell 118: 517-528.
30. Hinchliffe JR. 2002. Developmental basis of limb evolution. Int J Dev Biol 46: 835-845.
31. Horton AC, Mahadevan NR, Minguillon C, Osoegawa K, Rokhsar DS, Ruvinsky I, de Jong PJ, Logon MP, Gibson-Brown JJ. 2008. Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Dev Genes Evol 218: 613-628.
32. Johanson Z, Joss J, Biosvert CA, Ericsson R, Sutija M, Ahleberg P. 2007. Fish fingers: digit homologues in Sarcopterygian fish fins. 308: 757-768.
33. Khokha MK, Hsu D, Brunet LJ, Dionne MS, Harland RM. 2003. Gremlin is the BMP antagonist required for maintenance of Shh and Fgf signals during limb patterning. Nat Genet 34: 303-307.
34. Kmita M, Fraudeau N, Herault Y, Duboule D. 2002. Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs. Nature 420: 145-150.
35. Kuijper S, Feitsma H, Sheth R, Korving J, Reijnen M, Meijlink F. 2005. Function and regulation of Alx4 in limb development: complex genetic interactions with Gli3 and Shh. Dev Biol 285: 533-544.
36. Lettice LA, Heaney SJ, Purdie LA, Li L, de Beer P, Oostra BA, Goode D, Elgar G, Hill RE, de Graaff E. 2003. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 12: 1725-1735.
37. Levine M, Tjian R. 2003. Transcription regulation and animal diversity. Nature 424: 147-151.
38. Litingtung Y, Dahn RD, Li Y, Fallon JF, Chiang C. 2002. Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity. Nature 418: 979-983.
39. Logan M. 2003. Finger or toe: the molecular basis of limb identity. Development 130: 6401-6410.
40. Lopez-Martinez A, Chang DT, Chiang C, Porter JA, Ros MA, Simandl BK, Beachy PA, Fallon JF. 1995. Limb-patterning activity and restricted posterior localization of the amino-terminal product of Sonic hedgehog cleavage. Curr Biol 5: 791-796.
41. Maas SA, Fallon JF. 2005. Single base pair change in the long-range Sonic hedgehog limb-specific enhancer is a genetic basis for preaxial polydactyly. Dev Dyn 232: 345-348.
42. Maatouk DM, Choi KS, Bouldin CM, Harfe BD. 2009. In the limb AER Bmp2 and Bmp4 are required for dorsal-ventral patterning and interdigital cell death but not limb outgrowth. Dev Biol 327: 516-523.
43. Mabee PM. 2000. Developmental data and phylogenetic systematics: evolution of the vertebrate limb. Am Zool 40: 789-800.
44. Maston GA, Evans SK, Green MR. 2006. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 7: 29-59.
45. Morrissey LB, Janvier P, Braddy SJ, Bennett JP, Marriott SB, Tarrant PR. 2006. Swimming with...Devonian fish. Geol Today 22: 66-67.
46. Nelson CE, Morgan BA, Burke AC, Laufer E, DiMambro E, Murtaugh LC, Gonzales E, Tessarollo L, Parada LF, Tabin C. 1996. Analysis of Hox gene expression in the chick limb bud. Development 122: 1449-1466.
47. Niswander L. 2003. Pattern formation: old models out on a limb. Nat Rev Genet 4: 133-143.
48. Panman L, Drenth T, Tewelscher P, Zuniga A, Zeller R. 2005. Genetic interaction of Gli3 and Alx4 during limb development. Int J Dev Biol 49: 443-448.
49. Paparidis Z, Abbasi AA, Malik S, Goode DK, Callaway H, Elgar G, deGraaff E, Lopez-Rios J, Zeller R, Grzeschik KH. 2007. Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Dev Growth Differ 49: 543-553.
50. Qu S, Niswender KD, Ji Q, van der Meer R, Keeney D, Magnuson MA, Wisdom R. 1997. Polydactyly and ectopic ZPA formation in Alx-4 mutant mice. Development 124: 3999-4008.
51. Rallis C, Del Buono J, Logan MP. 2005. Tbx3 can alter limb position along the rostrocaudal axis of the developing embryo. Development 132: 1961-1970.
52. Remenyi A, Scholer HR, Wilmanns M. 2004. Combinatorial control of gene expression. Nat Struct Mol Biol 11: 812-815.
53. Ruvinsky I, Gibson-Brown JJ. 2000. Genetic and developmental bases of serial homology in vertebrate limb evolution Development 127: 5233-5244.
54. Ruvkun G, Hobert O. 1998. The taxonomy of developmental control in Caenorhabditis elegans. Science 282: 2033-2041.
55. Shubin NH, Alberch P. 1986. A morphogenetic approach to the origin and basic organisation of the tetrapod limb. Evol Biol 1: 319-387.
56. Shubin N, Tabin C, Carroll S. 1997. Fossils, genes and the evolution of animal limbs. Nature 388: 639-648.
57. Shubin N, Tabin C, Carroll S. 2009. Deep homology and the origins of evolutionary novelty. 457: 818-823.
58. Shubin NH, Daeschler EB, Jenkins FA, Jr. 2006. The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440: 764-771.
59. Sordino P, van der Hoeven F, Duboule D. 1995. Hox gene expression in teleost fins and the origin of vertebrate digits. Nature 375: 678-681.
60. Spitz F, Gonzalez F, Duboule D. 2003. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113: 405-417.
61. Sun X, Mariani FV, Martin GR. 2002. Functions of FGF signalling from the apical ectodermal ridge in limb development. Nature 418: 501-508.
62. Suzuki T, Takeuchi J, Koshiba-Takeuchi K, Ogura T. 2004. Tbx genes specify posterior digit identity through Shh and BMP signaling. Dev Cell 6: 43-53.
63. Tabin CJ. 1992. Why we have (only) five fingers per hand: hox genes and the evolution of paired limbs. Development 116: 289-296.
64. 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.
65. Tarchini B, Duboule D. 2006. Control of Hoxd genes' collinearity during early limb development. Dev Cell 10: 93-103.
66. Tarchini B, Duboule D, Kmita M. 2006. Regulatory constraints in the evolution of the tetrapod limb anterior-posterior polarity. Nature 443: 985-988.
67. te Welscher P, Zuniga A, Kuijper S, Drenth T, Goedemans HJ, Meijlink F, Zeller R. 2002. Progression of vertebrate limb development through SHH-mediated counteraction of GLI3. Science 298: 827-830.
68. Tickle C. 2006. Making digit patterns in the vertebrate limb. Nature Rev Mol Cell Biol 7: 45-53.
69. Towers M, Mahood R, Yin Y, Tickle C. 2008. Integration of growth and specification in chick wing digit-patterning. Nature 452: 882-886.
70. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. 2009. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10: 252-263.
71. Vokes SA, Ji H, Wong WH, McMahon AP. 2008. A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. Genes Dev 22: 2651-2663.
72. Wagner GP, Pavlicev M, Cheverud JM. 2007. The road to modularity Nature Rev Genet 8: 921-931.
73. Wang B, Fallon JF, Beachy PA. 2000. Hedgehog-regulated processing of Gli3 produces an anterior/posterior repressor gradient in the developing vertebrate limb. Cell 100: 423-434.
74. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
75. White IE. 1946. Jamoytius kerwoodi, a new chordate from Silurian of Lanarkshire (Scotland). Geol Mag 83: 89-97.
76. Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nature Rev Genet 8: 206-216.
77. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20: 1377-1419.
78. Zakany J, Kmita M, Duboule D. 2004. A dual role for Hox genes in limb anterior-posterior asymmetry. Science 304: 1669-1672.
79. Zuniga A, Michos O, Spitz F, Haramis AP, Panman L, Galli A, Vintersten K, Klasen C, Mansfield W, Kuc S, Duboule D, Dono R, Zeller R. 2004. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev 18: 1553-1564.