Abstract
The widely popular hypothesis that there were two rounds of genome duplication by polyploidization early in vertebrate history (the 2R hypothesis) has been difficult to test until recently. Among the lines of evidence adduced in support of this hypothesis are relative genome size, relative gene number, and the existence of genomic regions putatively duplicated during polyploidization. The availability of sequence for a substantial portion of the human genome makes possible the first rigorous tests of this hypothesis. Comparison of gene family size in the human genome and in invertebrate genomes shows no evidence of a 4:1 ratio between vertebrates and invertebrates. Furthermore, explicit phylogenetic tests for the topology expected from two rounds of polyploidization have revealed alternative topologies in a substantial majority of human gene families. Likewise, phylogenetic analyses have shown that putatively duplicated genomic regions often include genes duplicated at widely different times over the evolution of life. The 2R hypothesis thus can be decisively rejected. Rather, current evidence favors a model of genome evolution in which tandem duplication, whether of genomic segments or of individual genes, predominates.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Bork, P. and Copley, R. (2001) Filling in the gaps. Nature, 409, 818–820.
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-I interferon gene cluster determined from a YAC clone contig. Genomics, 22, 540–552.
Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.
Friedman, R. and Hughes, A.L. (2001) Pattern and timing of gene duplication in animal genomes. Genome Res., in press.
Guigo, R., Muchnik, I. and Smith, T.F. (1996) Reconstruction of ancient molecular phylogeny. Mol. Phyl. Evol., 46, 189–213.
Hughes, A.L. (1995) The evolution of the type I interferon gene family in mammals. J. Mol. Evol., 41, 539–548.
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.
Hughes, A.L. (1999a) Adaptive Evolution of Genes and Genomes, Oxford University Press, New York, NY
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.
Hughes, A.L. (1999c) Genomic catastrophism and the origin of vertebrate immunity. Arch. Immunol. Ther. Exper., 47, 347–353.
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.
Hughes, A.L. (2001) Evolution of the integrin α and β protein families. J. Mol. Evol., 52, 63–72.
Hughes, M.K. and Hughes, A.L. (1993) Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol., 10, 1360–1369.
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.
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.
International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860–891.
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.
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.
Makałowski, W. (2001) Are we polyploids? A brief history of one hypothesis. Genome Res., 11, 667–670.
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.
Ohno, S. (1970) Evolution by Gene Duplication, Springer, New York, NY.
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406–425.
Sidow, A. (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev., 6, 715–722.
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.
Sonnenberg, A. (1993) Integrins and their ligands. Curr. Top. Microbiol. Immunol., 184, 7–35.
Strimmer, K. and von Haeseler, A. (1996) Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13, 964–969.
Yeager, M. and Hughes, A.L. (1999) Evolution of the mammalian MHC: natural selkection, recombination, and convergent evolution. Immunol. Rev., 167, 45–58.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Hughes, A.L., Friedman, R. (2003). 2R or not 2R: Testing hypotheses of genome duplication in early vertebrates. In: Meyer, A., Van de Peer, Y. (eds) Genome Evolution. Springer, Dordrecht. https://doi.org/10.1007/978-94-010-0263-9_9
Download citation
DOI: https://doi.org/10.1007/978-94-010-0263-9_9
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-3957-4
Online ISBN: 978-94-010-0263-9
eBook Packages: Springer Book Archive