Gene duplication and the properties of biological networks

Journal of Molecular Evolution

Volumn 61, Issue 6, 2005, Pages 758-764

  Hughes, Austin L ^a   Friedman, Robert ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Biological networks; Gene duplication; Genome evolution; Scale free networks

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; GENE DUPLICATION; GENOME ANALYSIS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; SACCHAROMYCES CEREVISIAE;

ANIMALS; CAENORHABDITIS ELEGANS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, FUNGAL; GENOME, HELMINTH; MODELS, BIOLOGICAL; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE;

CAENORHABDITIS ELEGANS; SACCHAROMYCES CEREVISIAE;

EID: 28244482030     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0037-z     Document Type: Article

References (25)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Barabási A-L, Albert R (1999) Emergence of scaling in random networks. Science 286:509-512
3. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
4. Friedman R, Hughes AL (2001a) Gene duplication and the structure of eukaryotic genomes. Genome Res 11:373-381
5. Friedman R, Hughes AL (2001b) Pattern and timing of gene duplication in animal genomes. Genome Res 11:1842-1847
6. Hughes AL, Friedman R (2003) Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Res 13:794-799
7. Hughes AL, Friedman R (2004) Differential loss of ancestral gene families as a source of genomic divergence in animals. Pro R Soc Lond B (Suppl) 271:S107-S109
8. Kanehisa M (2000) Post-genome informatics. Oxford University Press, Oxford
9. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624
10. Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275-276
11. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
12. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain P-O, Han J-D J, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual J-F, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berritz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mange SE, Saxton WM, Strome S, van den Heuvel S , Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M (2004) A map of the interactome network of the metazoan C. elegans. Science 303:540-543
13. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
14. Ravasz E, Barabási A-L (2003) Hierarchical organization in complex networks. Phys Rev E 67:026112
15. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási A-L (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555
16. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
17. Seoighe C, Wolfe KH (1999) Updated map of duplicated regions in the yeast genome. Gene 238:253-261
18. Strimmer K, van Haeseler A (1996) Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
19. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland, MA
20. Thompson JD, Higgins DG, Gibson T (1994) CLUSTALW: 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
21. Tong AHY, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesan H, Goldberg DS, Haynes J, Humphries C, He G, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu A-M, Shapiro J, Sheikh B, Suter B, Wong SL, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C (2004) Global mapping of the yeast genetic interaction network. Science 303:808-813
22. Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicated genes. Mol Biol Evol 18:1283-1292
23. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713
24. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
25. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32-43