Ancient genome duplications did not structure the human hox-bearing chromosomes

Genome Research

Volumn 11, Issue 5, 2001, Pages 771-780

  Hughes, Austin L ^a   Da Silva, Jack ^b   Friedman, Robert ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

^b EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HOMEODOMAIN PROTEIN;

ANIMAL CELL; CHICKEN; CHROMOSOME 12; CHROMOSOME 17; CHROMOSOME 2; CHROMOSOME 7; CHROMOSOME STRUCTURE; DROSOPHILA; FROG; GENE CLUSTER; GENE DUPLICATION; GENE LOCATION; GENETIC ANALYSIS; GOLDFISH; HISTORY; HOMEOBOX; HUMAN; HUMAN CELL; HYPOTHESIS; INVERTEBRATE; KLUYVEROMYCES; LETTER; MAMMAL; MOUSE; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; POLYPLOIDY; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE; UNINDEXED SEQUENCE; VERTEBRATE; XENOPUS;

ANIMALS; CHROMOSOMES, HUMAN; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, HOMEOBOX; GENOME; HUMANS; MULTIGENE FAMILY; PHYLOGENY; TIME;

ANIMALIA; ANURA; CARASSIUS AURATUS; GALLUS GALLUS; INVERTEBRATA; KLUYVEROMYCES; MAMMALIA; SCHIZOSACCHAROMYCES POMBE; VERTEBRATA;

EID: 0035010738     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.GR-1600R     Document Type: Letter

References (31)

1. Amores, A.A., Force, Y.L., Van, L., Joly, C., Amemiya, A., Fritz, R.K., Ho, J., Langeland, V., Prince, Y.L., Wang, M., et al. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-1714.
2. Bailey, W.J., Kim, J., Wagner, G., and Ruddle, F.H. 1997. Phylogenetic reconstruction of the vertebrate Hox cluster duplication. Mol. Biol. Evol. 14: 843-853.
3. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 95-105.
4. Friedman, R. and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11: 373-381.
5. Gellner, K. and Brenner, S. 1999. Analysis of 148 kb of genomic DNA around the wnt locus of Fugu rubripes. Genome Res. 9: 251-258.
6. Hughes, A.L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B 256: 119-124.
7. _. 1998a. 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. _. 1998b. Protein phylogenies provide evidence of a radical discontinuity between arthropod and vertebrate immune systems, Immunogenetics 47: 283-296.
9. _. 1999a. 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. _. 1999b. Adaptive evolution of genes and genome. Oxford University Press, New York.
11. _. 2001. Evolution of the integrin α and β protein families. J. mol. Evol. 52: 63-72.
12. Kasahara, M., Nayaka, J., Satta, Y., and Takahata, N. 1997. Chromosomal duplication and the emergence of the adaptive immune system. Trends Genet. 13: 90-92.
13. Kumar, S. and Hedges, S.B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-920.
14. Kumar, S., Tamura, K., and Nei, M. 1993. MEGA: Molecular Evolutionary Genetics Analysis, Version 1.01. Pennsylvania State University, University Park, PA.
15. 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.
16. Miklos, G.L.G. and Rubin, G.M. 1996. The role of the genome project in determining gene function: Insight from model organisms. Cell 86: 521-529.
17. Nei, M. 1991. Relative efficiencies of different tree-making methods for molecular data. In Phylogenetic analysis of DNA sequences (eds. M.M. Miyamoto and J.L. Cracraft), pp. 90-128. Oxford University Press, Oxford.
18. Nei, M. and Gojobori, T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
19. Ohno, S. 1970. Evolution by gene duplication. Springer Verlag, New York.
20. Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 405-425.
21. Seoighe, C. and Wolfe, K.H. 1999. Updated map of duplicated regions in the yeast genome. Gene 238: 253-261.
22. Sidow, A. 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6: 715-722.
23. Simmen, M.W., Leitgeb, S., Clark, V.H., Jones, S.J.M., and Bird, A. 1998. Gene number in an invertebrate chordate, Ciona intestinalis. Proc. Natl. Acad. Sci. 95: 4437-4440.
24. Skrabanek, L. and Wolfe, K.H. 1998. Eukaryotic gene duplication - where's the evidence? Curr. Opin. Genet. Dev. 8: 694-700.
25. Swofford, D.L. 1990. PAUP: Phylogenetic Analysis Using Parsimony, Version 3.0. Illinois Natural History Survey, Champaign, IL.
26. Takezaki, N., Rzhetsky, A., and Nei, M. 1995. Phylogenetic test of the molecular clock and linearized tree. Mol. Bio. Evol. 12: 823-833.
27. Thompson, J.D., Higgins, D.G., and Gibson, J.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
28. Wolfe, K.H. and Shields, D.C. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
29. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
30. Yeager, M. and Hughes, A.L. 1999. Evolution of the mammalian MHC: Natural selection, recombination, and convergent evolution. Immunol. Rev. 167: 45-58.
31. Zhang, J. and Nei, M. 1996. Evolution of Antennapedia-class homeobox genes. Genetics 142: 295-303.