What is the role of genome duplication in the evolution of complexity and diversity?

Molecular Biology and Evolution

Volumn 23, Issue 5, 2006, Pages 887-892

  Crow, Karen D ^a   Wagner, Günter P ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Extinction; Genome duplication

Indexed keywords

CONFERENCE PAPER; GENE DUPLICATION; GENE MUTATION; GENETIC DRIFT; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; MOLECULAR EVOLUTION; SPECIES DIVERSITY; SPECIES EXTINCTION; TAXONOMY; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CAENORHABDITIS ELEGANS; CELL LINEAGE; DIPLOIDY; FISH; GENOMICS; MUTATION; PHYLOGENY;

VERTEBRATA;

ANIMALS; CAENORHABDITIS ELEGANS; CELL LINEAGE; DIPLOIDY; EVOLUTION, MOLECULAR; FISHES; GENE DUPLICATION; GENOME; GENOMICS; MODELS, GENETIC; MUTATION; PHYLOGENY; VARIATION (GENETICS);

EID: 33646572856     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj083     Document Type: Conference Paper

References (60)

1. Blanc, G., and K. H. Wolfe. 2004a. Widespread paleopolyploidy in model plant species inferred from age distributions of dupli-cate genes. Plant Cell 16:1667-1678.
2. _. 2004b. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679-1691.
3. Bowers, J. E., B. A. Chapman, J. K. Rong, and A. H. Paterson. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438.
4. Carroll, S. B. 1995. Homeotic genes and the evolution of arthropods and chordates. Nature 376:479-485.
5. Conant, G. C., and A. Wagner. 2003. Asymmetric sequence divergence of duplicate genes. Genome Res. 13:2052-2058.
6. _. 2004. Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. Proc. R. Soc. Lond. B Biol. Sci. 271:89-96.
7. Crow, K. D., P. F. Stadler, V. J. Lynch, C. Amemiya, and G. P. Wagner. 2005. The "fish specific" Hox cluster duplication is coincident with the origin of teleosts. Mol. Biol. Evol. 23:121-136.
8. Donoghue, P. C. J., and M. A. Purnell. 2005. Gene duplication, extinction, and vertebrate evolution. Trends Ecol. Evol. 20:312-319.
9. Duda, T. F., and S. R. Palumbi. 1999. Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc. Natl. Acad. Sci. USA 96:6820-6823.
10. Fares, M. A., D. Bezemer, A. Moya, and I. Marin. 2003. Selection on coding regions determined Hox7 genes evolution. Mol. Biol. Evol. 20:2104-2112.
11. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
12. Fried, C., S. J. Prohaska, and P. F. Stadler. 2004. Exclusion of repetitive DNA elements from gnathostome Hox clusters. J. Exp. Zoolog. B Mol. Dev. Evol. 302:165-173.
13. Gale, M. D., and K. M. Devos. 1998. Plant comparative genetics after 10 years. Science 282:656-659.
14. Gu, Z., L. M. Steinmetz, X. Gu, C. Scharfe, R. W. Davis, and W. H. Li. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66.
15. Hoegg, S., H. Brinkmann, J. S. Taylor, and A. Meyer. 2004. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J. Mol. Evol. 59:190-203.
16. Holland, P. W., J. Garcia-Fernandez, N. A. Williams, and A. Sidow. 1994. Gene duplications and the origins of vertebrate development. Development (Suppl.):125-133.
17. Hughes, A. L. 1999. Adaptive evolution of genes and genomes. Oxford University Press, New York.
18. Hughes, A. L., J. A. Green, J. M. Garbayo, and R. M. Roberts. 2000. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc. Natl. Acad. Sci. USA 97:3319-3323.
19. Irish, V. F. 2003. The evolution of floral homeotic gene function. Bioessays 25:637-646.
20. Irish, V. F., and A. Litt. 2005. Flower development and evolution: gene duplication, diversification and redeployment. Curr. Opin. Genet. Dev. 15:454-460.
21. Jackson, R. C. 1976. Evolution and systematic significance of polyploidy. Annu. Rev. Ecol. Syst. 7:209-234.
22. Kellis, M., B. W. Birren, and E. S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624.
23. Kondrashov, F. A., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. 2002. Selection in the evolution of gene duplications. Genome Biol. 3:Research 0008.0001-0008.0009.
24. Ku, H. M., T. Vision, J. P. Liu, and S. D. Tanksley. 2000. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA 97:9121-9126.
25. Lawton-Rauh, A. 2003. Evolutionary dynamics of duplicated genes in plants. Mol. Phylogenet. Evol. 29:396-409.
26. Le Comber, S. C., and C. Smith. 2004. Polyploidy in fishes: patterns and processes. Biol. J. Linn. Soc. 82:431-442.
27. Levin, D. A. 1983. Polyploidy and novelty in flowering plants. Am. Nat. 122:1-25.
28. Lumaret, R. 1988. Adaptive strategies and ploidy Levels. Acta Oecol. Oecol. Plant. 9:83-93.
29. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
30. Lynch, M., and A. Force. 2000. The origin of interspecific genomic incompatibility via gene duplication. Am. Nat. 156: 590-605.
31. Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20:544-549.
32. Malaga-Trillo, E., and A. Meyer. 2001. Genome duplication and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am. Zool. 41:676-686.
33. Merritt, T. J., and J. M. Quattro. 2001. Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase. Genetics 159:689-697.
34. Metz, C. W. 1947. The American society of naturalists - duplication of chromosome parts as a factor in evolution. Am. Nat. 81:81-103.
35. Meyer, A., and M. Schartl. 1999. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11:699-704.
36. Nelson, J. S. 1994. Fishes of the world. J. Wiley, New York.
37. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, New York.
38. Otto, S. P., and J. Whitton. 2000. Polyploid incidence and evolution. Annu. Rev. Genet. 34:401-437.
39. Patterson, C. 1993. Osteichichthyes: Teleostei. Pp. 621-656 in M. J. Benton, ed. The fossil record 2. Chapman & Hall, London.
40. Postlethwait, J. H., I. G. Woods, P. Ngo-Hazelett, Y. L. Yan, P. D. Kelly, F. Chu, H. Huang, A. Hill-Force, and W. S. Talbot. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10:1890-1902.
41. Prince, V. E., and F. B. Pickett. 2002. Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3:827-837.
42. Prohaska, S. J., and P. F. Stadler. 2004. The duplication of the Hox gene clusters in teleost fishes. Theory Biosci. 123:89-110.
43. Robinson-Rechavi, M., B. Boussau, and V. Laudet. 2004. Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Mol. Biol. Evol. 21:580-586.
44. Seoighe, C., C. R. Johnston, and D. C. Shields. 2003. Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Mol. Biol. Evol. 20:484-490.
45. Soltis, D. E., and P. S. Soltis. 1999. Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14:348-352.
46. Soltis, P. S. 2005. Ancient and recent polyploidy in angiosperms. New Phytol. 166:5-8.
47. Song, K. M., P. Lu, K. L. Tang, and T. C. Osborn. 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 92:7719-7723.
48. Tanaka, T., and M. Nei. 1989. Positive Darwinian selection observed at the variable-region genes of immunoglobulins. Mol. Biol. Evol. 6:447-459.
49. Taylor, J. S., and J. Raes. 2004. Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38:615-643.
50. Thompson, J. D., and R. Lumaret. 1992. The evolutionary dynamics of polyploid plants - origins, establishment and persistence. Trends Ecol. Evol. 7:302-307.
51. Vision, T. J., D. G. Brown, and S. D. Tanksley. 2000. The origins of genomic duplications in Arabidopsis. Science 290:2114-2117.
52. Wagner, G. P., C. Amemiya, and F. Ruddle. 2003. Hox cluster duplications and the opportunity for evolutionary novelties. Proc. Natl. Acad. Sci. USA 100:14603-14606.
53. Wagner, G. P., K. Takahashi, V. Lynch, S. J. Prohaska, C. Fried, P. F. Stadler, and C. Amemiya. 2005. Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences. J. Mol. Evol. 60:665-676.
54. Walsh, J. B. 1995. How often do duplicated genes evolve new functions. Genetics 139:421-428.
55. Wendel, J. F. 2000. Genome evolution in polyploids. Plant Mol. Biol. 42:225-249.
56. Zhang, J. Z. 2003. Evolution by gene duplication: an update. Trends Ecol. Evol. 18:292-298.
57. Zhang, J. Z., K. D. Dyer, and H. F. Rosenberg. 2000. Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proc. Natl. Acad. Sci. USA 97:4701-4706.
58. Zhang, J. Z., H. F. Rosenberg, and M. Nei. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95:3708-3713.
59. Zhang, J. Z., Y. P. Zhang, and H. F. Rosenberg. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30:411-415.
60. Zhou, R. J., H. H. Cheng, and T. R. Tiersch. 2001. Differential genome duplication and fish diversity. Rev. Fish Biol. Fish. 11:331-337.