Gen(om)e duplications in the evolution of early vertebrates

Current Opinion in Genetics and Development

Volumn 6, Issue 6, 1996, Pages 715-722

  Sidow, Arend ^a  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEVELOPMENTAL GENETICS; EVOLUTION; GENE DUPLICATION; GENOME; MULTIGENE FAMILY; NATURAL SELECTION; PHYLOGENY; PRIORITY JOURNAL; REGULATOR GENE; SHORT SURVEY; VERTEBRATE;

VERTEBRATA;

EID: 0030473920     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(96)80026-8     Document Type: Article

References (39)

1. 1. Atchley WR, Fitch WM, Bronner-Fraser M: Molecular evolution of the MyoD family of transcription factors. Proc Natl Acad Sci USA 1994, 91:11522-11526.
2. 2. Duboule D: Guidebook to the Homeobox Genes. Oxford, UK: Oxford University Press; 1994.
3. 3. Gamer LW, Wright CVE: Murine Cdx-4 bears striking similarities to the Drosophila caudal gene in its homeodomain sequence and early expression pattern. Mech Dev 1994, 43:71-81.
4. 4. Good PJ: A conserved family of elav-like genes in vertebrates. Proc Natl Acad Sci USA 1995, 92:4557-4561.
5. 5. Kingsley C, Winoto A: Cloning of GT box-binding proteins: a novel Sp1 multigene family regulating T-cell receptor gene expression. Mol Cell Biol 1992, 12:4251-4261.
6. 6. Kingsley DM: The TGF-β superfamily: new members, new receptors, and new genetic tests of function in different organisms. Genes Dev 1994, 8:133-146.
7. 7. Uyttendaele H, Marazzi G, Wu G, Van Q, Sassoon D, Kitajewski J: Notch4/int3, a mammary proto-oncogene, is an endothelial cell-specific mammalian Notch gene. Development 1996, 122:2251-2259.
8. 8. D'Esposito M, Morelli F, Acampora D, Migliaccio E, Simeone A, Boncinelli E: Evx2, a human homeobox gene homologous to the even-skipped homeotic gene, is localized at the 5′ end of the Hox4 locus on chromosome 2. Genomics 1991, 10:43-50.
9. 9. Sidow A: Diversification of the Wnt gene family on the ancestral lineage of vertebrates. Proc Natl Acad Sci USA 1992, 89:5098-5102.
10. 10. Davidson D: The function and evolution of Msx genes: pointers and paradoxes. Trends Genet 1995, 11:405-411.
11. 11. Echelard Y, Epstein DJ, St-Jacques B, Shen L, Mohler J, McMahon JA, McMahon AP: Sonic hedgehog, a member of a family of putative signaling molecules, is implicated in the regulation of CNS and limb polarity. Cell 1993, 75:1417-1430.
12. 12. Miklos GLG, Rubin GM: The role of the genome project in determining gene function: insight from model organisms. Cell 1996, 86:521-529.
13. 13. Becak ML, Becak W, Rabello MN: Cytological evidence of constant tetrapoloidy in the bisexual South American frog, Odontophrynus americanus. Chromosoma 1966, 19:188-193.
14. 14. Ohno S, Wolf U, Atkin NB: Evolution from fish to mammals by gene duplication. Hereditas 1968, 59:169-187.
15. 15. Ohno S: Evolution by Gene Duplication. New York: Springer Verlag; 1970.
16. 16. Holland PWH, Garcia-Fernandez JG: Hox genes and chordate evolution. Dev Biol 1996, 173:382-395. A comprehensive review of Hox cluster evolution from the authors who showed that amphioxus has a single cluster. Expression patterns of the AmphiHox genes in development indicates that the conserved and perhaps ancestral expression domain of the chordate Hox genes is in the neurectoderm and not in the mesoderm. Furthermore, the authors convincingly make the point that expression of orthologous marker genes - in this case, expression of amphihox 3 in the amphioxus nerve cord and expression of its vertebrate orthologs in the developing hindbrain - can be used to establish homology of developing tissues in the absence of obvious morphological similarity.
17. 17. Holland PWH, Garcia-Fernandez JG, Williams N, Sidow A: Gene duplications and the origins of vertebrate development Development 1994, (Suppl):125-133.
18. 18. Sharman AC, Holland PWH: Conservation, duplication, and divergence of developmental genes during chordate evolution. Netherlands J Zool 1996, 46:1-21.
19. 19. Elgar G, Sandford R, Aparicio S, Macrae A, Venkatesh B, Brenner S: Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes). Trends Genet 1996, 12:145-150. A succinct summary of the results from the first few years of genomics research on the pufferfish. The puffer's genome is small but other than in size there are no fundamental differences in genome organization between it and mammals. My own take-home message here is that large-scale gene duplications must have preceded the divergence of bony fish and tetrapods.
20. 20. Lundin LG: Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 1993, 16:1-19.
21. 21. Chan SJ, Cao QP, Steiner DF: Evolution of the insulin superfamily: cloning of a hybrid insulin/insulin-like growth factor cDNA from amphioxus. Proc Natl Acad Sci USA 1990, 87:9319-9323.
22. 22. Garcia-Fernandez JG, Holland PWH: Archetypal organization of the amphioxus Hox gene cluster. Nature 1994, 370:563-566.
23. 23. Holland PWH: Cloning and evolutionary analysis of msh-like homeobox genes from mouse, zebrafish, and ascidian. Gene 1991, 98:253-257.
24. 24. Pendleton JW, Nagai BK, Murtha MT, Ruddle FH: Expansion of the Hox gene family and the evolution of chordates. Proc Natl Acad Sci USA 1993, 90:6300-6304.
25. 25. Sharman AC, Hay-Schmidt A, Holland PWH: Cloning and analysis of an HMG gene from the lamprey Lampetra fluviatilis: gene duplication in vertebrate evolution. Gene 1996, in press.
26. 26. Sidow A, Thomas WK: An evolutionary framework for eukaryotic model organisms. Curr Biol 1994, 4:596-603.
27. 27. Ohta T: Role of gene duplication in evolution. Genome 1989, 31:304-310.
28. 28. Palopoli MF, Patel NH: Neo-Darwinian developmental evolution: can we bridge the gap between pattern and process? Curr Opin Genet Dev 1996, 6:502-508. A different perspective on developmental evolution, this one mostly from changes in regulation of genes without prior duplication. Shifts in expression boundaries of Hox genes as well as the beautiful work on butterfly wing spots are reviewed and lead the authors to suggest that large-effect genes drive developmental evolution.
29. 29. Crossley PH, Minowada G, MacArthur CA, Martin GR: Roles for FGF8 in the induction, initiation, and maintenance of chick limb development Cell 1996, 84:127-136.
30. 30. MacArthur CA, Lawshe A, Xu J, Santos-Ocampo S, Heikinheimo M, Chellaiah AT, Ornitz DM: FGF8 isoforms activate receptor splice forms that are expressed in mesenchymal regions of mouse development Development 1995, 121:3603-3613.
31. 31. Parr BA, McMahon AP: Dorsalizing signal Wnt-7a required for normal polarity of D-V and A-P axes of mouse limb. Nature 1995, 374:350-353.
32. 32. Storm EE, Huynh TV, Copeland NG, Jenkins NA, Kingsley DM, Lee S-J: Limb alterations in brachypodism mice due to mutations in a new member of the TGFβ-superfamily. Nature 1994, 368:639-643.
33. 33. Laufer E, Nelson CE, Johnson RL, Morgan BA, Tabin C: Sonic hedgehog and Fgf-4 act through a signaling cascade and feedback loop to integrate growth and patterning of the developing limb bud. Cell 1994, 79:993-1003.
34. 34. Eldredge N, Gould SJ: Punctuated equilibria: an alternative to phyletic gradualism. In Models in Paleobiology. Edited by Schopf TJM. San Francisco: Freeman: 1972:82-115.
35. 35. Holland PWH, Holland LZ, Williams NA, Holland ND: An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution. Development 1992, 116:653-661.
36. 36. Holland PWH: Molecular biology of lancelets: insights into development and evolution. Israel J Zool 1996, in press. If you can't get this paper in your library, call the author for a reprint. A wonderful summary of everything that amphioxus is good for and everything that has been learnt from expression analyses and developmental gene cloning, most of which was done in the author's lab. Amphioxus seems to have retained a number of ancestral chordate characters without much modification so it provides a window into early vertebrate evolution like no other animal. Most regulator genes identified from it to date come as single homologs (despite extensive searches), which narrows considerably the time frame in which early-vertebrate genome duplications could have happened (i.e. after amphioxus and the ancestral vertebrate lineages diverged). In addition, it is amenable to in situ analysis; comparative studies of homeobox gene expression patterns have already yielded significant insights into the conservation of chordate developmental characters.
37. 37. Williams NA, Holland PWH: Old head on young shoulders. Nature 1996, 383:490. An amphioxus Otx gene is shown to be expressed early in development in the presumptive head region of the embryo, like its vertebrate homologs. The details are fascinating; coordinated expression changes in Otx are conserved between amphioxus and vertebrates. Furthermore, AmphiOtx is expressed in a region that later gives rise to the primitive light receptor organ, whereas vertebrate Otx genes are expressed in the eye and the Drosophila homolog, orthodenticle, is required for eye development. This surprising degree of conservation indicates that neural cephalization had begun in the chordate ancestor and that the extent of elaboration in vertebrates could have been facilitated, in part, by duplications in the Otx gene family.
38. 38. Iwabe N, Kuma K, Miyata T: Evolution of gene famlies and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates. Mol Biol Evol 1996, 13:483-493.
39. 39. Kimura M: The Neutral Theory of Molecular Evolution. Cambridge, UK: Cambridge University Press; 1983.