2R or not 2R: Testing hypotheses of genome duplication in early vertebrates

Journal of Structural and Functional Genomics

Volumn 3, Issue 1-4, 2003, Pages 85-93

  Hughes, Austin L ^a   Friedman, Robert ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Gene duplication; Gene number; Genome size; Polyploidy; Vertebrate evolution

Indexed keywords

DROSOPHILA; EVOLUTION; GENE DUPLICATION; GENE NUMBER; GENE SEQUENCE; GENETIC ANALYSIS; GENOME SIZE; HUMAN; HUMAN GENOME; HYPOTHESIS; INVERTEBRATE; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; POLYPLOIDY; PRIORITY JOURNAL; REVIEW; SPECIES COMPARISON; VERTEBRATE;

ANIMALS; DROSOPHILA; EVOLUTION; GENE DUPLICATION; GENOME; HUMANS; PHYLOGENY; VERTEBRATES;

INVERTEBRATA; VERTEBRATA;

EID: 0037266536     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1022681600462     Document Type: Review

References (27)

1. Bork, P. and Copley, R. (2001) Filling in the gaps. Nature, 409, 818-820.
2. Diaz, M.O., Pomykala, H.M., Bohlander, S.K., Maltepe, E., Malik, K., Brownsein, B. and Olapede, O.I. (1994) Structure of the human type-1 interferon gene cluster determined from a YAC clone contig. Genomics, 22, 540-552.
3. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
4. Friedman, R. and Hughes, A.L. (2001) Pattern and timing of gene duplication in animal genomes. Genome Res., in press.
5. Guigo, R., Muchnik, I. and Smith, T.F. (1996) Reconstruction of ancient molecular phylogeny. Mol. Phyl. Evol., 46, 189-213.
6. Hughes, A.L. (1995) The evolution of the type I interferon gene family in mammals. J. Mol. Evol., 41, 539-548.
7. Hughes, A.L. (1998) Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. Mol. Biol. Evol., 15, 854-870.
8. Hughes, A.L. (1999a) Adaptive Evolution of Genes and Genomes. Oxford University Press, New York, NY.
9. Hughes, A.L. (1999b) Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J. Mol. Evol., 48, 565-576.
10. Hughes, A.L. (1999c) Genomic catastrophism and the origin of vertebrate immunity. Arch. Immunol. Ther. Exper., 47, 347-353.
11. Hughes, A.L. (2000) Polyploidization and vertebrate origins: a review of the evidence. In Comparative Genomics (Eds., Sankoff, S. and Nadeau, J.H.). Kluwer, Dordrecht, pp. 493-502.
12. Hughes, A.L. (2001) Evolution of the integrin α and β protein families. J. Mol. Evol., 52, 63-72.
13. Hughes, M.K. and Hughes, A.L. (1993) Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol., 10, 1360-1369.
14. Hughes, A.L. and Roberts, R.H. (2000) Independent origin of IFN-α and IFN-β in birds and mammals. J. Interferon Cytokine Res., 20, 737-739.
15. Hughes, A.L., da Silva, J. and Friedman, R. (2001) Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res., 11, 771-780.
16. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-891.
17. Kasahara, M., Nayaka, Y., Satta, Y. and Takahata, N. (1997) Chromosomal duplication and the emergence of the adaptive immune system. Trends Genet., 13, 90-92.
18. Lundin, L.G. (1993) Evolution of the vertebrate genome as reflected in paralogous chromosome regions in man and the house mouse. Genomics, 16, 1-19.
19. Makałowski, W. (2001) Are we polyploids? A brief history of one hypothesis. Genome Res., 11, 667-670.
20. Meyer, A. and Schartl, M. (1999) Gene and genome duplication 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.
21. Ohno, S. (1970) Evolution by Gene Duplication, Springer, New York, NY.
22. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
23. Sidow, A. (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev., 6, 715-722.
24. Simmen, M.W., Leitger, S., Clark, V.H., Jones, S.J.M. and Bird, A. (1998) Gene number in an invertebrate chordate, Ciona intestinalis. Proc. Natl. Acad. Sci. USA, 95, 4437-4440.
25. Sonnenberg, A. (1993) Integrins and their ligands. Curr. Top. Microbiol. Immunol. 184, 7-35.
26. Strimmer, K. and von Haeseler, A. (1996) Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13, 964-969.
27. Yeager, M. and Hughes, A.L. (1999) Evolution of the mammalian MHC: natural selkection, recombination, and convergent evolution. Immunol. Rev., 167, 45-58.