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Advances in Bioinformatics
Volume 2010 (2010), Article ID 856825, 7 pages
http://dx.doi.org/10.1155/2010/856825
Research Article

Adaptive Evolution Hotspots at the GC-Extremes of the Human Genome: Evidence for Two Functionally Distinct Pathways of Positive Selection

1Laboratory of Computational Oncology, Department of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
2Department of Medicine, Queen Mary Hospital, University of Hong Kong, Pokfulam Rd, Pokfulam, Hong Kong

Received 25 August 2009; Revised 31 December 2009; Accepted 10 February 2010

Academic Editor: Igor B. Rogozin

Copyright © 2010 Clara S. M. Tang and Richard J. Epstein. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Y. Zhao and RJ. Epstein, “Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line,” Mol Biol Evol., vol. 25, no. 8, pp. 1737–1749, 2008. View at Google Scholar
  2. A. Levasseur, L. Orlando, X. Bailly, M. C. Milinkovitch, E. G. J. Danchin, and P. Pontarotti, “Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution,” Biological Reviews, vol. 82, no. 4, pp. 551–572, 2007. View at Publisher · View at Google Scholar · View at PubMed
  3. M. Camps, A. Herman, E. R. N. Loh, and L. A. Loeb, “Genetic constraints on protein evolution,” Critical Reviews in Biochemistry and Molecular Biology, vol. 42, no. 5, pp. 313–326, 2007. View at Publisher · View at Google Scholar · View at PubMed
  4. T. L. O'Loughlin, W. M. Patrick, and I. Matsumura, “Natural history as a predictor of protein evolvability,” Protein Engineering, Design and Selection, vol. 19, no. 10, pp. 439–442, 2006. View at Publisher · View at Google Scholar · View at PubMed
  5. A. R. Templeton, “The reality and importance of founder speciation in evolution,” BioEssays, vol. 30, no. 5, pp. 470–479, 2008. View at Publisher · View at Google Scholar · View at PubMed
  6. J. C. Fay and P. J. Wittkopp, “Evaluating the role of natural selection in the evolution of gene regulation,” Heredity, vol. 100, no. 2, pp. 191–199, 2008. View at Publisher · View at Google Scholar · View at PubMed
  7. J. D. Jensen, A. Wong, and C. F. Aquadro, “Approaches for identifying targets of positive selection,” Trends in Genetics, vol. 23, no. 11, pp. 568–577, 2007. View at Publisher · View at Google Scholar · View at PubMed
  8. A. L. Hughes, “Near neutrality: leading edge of the neutral theory of molecular evolution,” Annals of the New York Academy of Sciences, vol. 1133, pp. 162–179, 2008. View at Publisher · View at Google Scholar · View at PubMed
  9. H. Kokko and I. Ots, “When not to avoid inbreeding,” Evolution, vol. 60, no. 3, pp. 467–475, 2006. View at Publisher · View at Google Scholar
  10. N. L. Clark and W. J. Swanson, “Pervasive adaptive evolution in primate seminal proteins,” PLoS Genetics, vol. 1, no. 3, article no. e35, 2005. View at Publisher · View at Google Scholar · View at PubMed
  11. L. Horth, “Sensory genes and mate choice: evidence that duplications, mutations, and adaptive evolution alter variation in mating cue genes and their receptors,” Genomics, vol. 90, no. 2, pp. 159–175, 2007. View at Publisher · View at Google Scholar · View at PubMed
  12. N. L. Clark, G. D. Findlay, X. Yi, M. J. MacCoss, and W. J. Swanson, “Duplication and selection on abalone sperm lysin in an allopatric population,” Molecular Biology and Evolution, vol. 24, no. 9, pp. 2081–2090, 2007. View at Publisher · View at Google Scholar · View at PubMed
  13. J. Zhang, “On the evolution of codon volatility,” Genetics, vol. 169, no. 1, pp. 495–501, 2005. View at Publisher · View at Google Scholar · View at PubMed
  14. A. L. Hughes, “Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level,” Heredity, vol. 99, no. 4, pp. 364–373, 2007. View at Publisher · View at Google Scholar · View at PubMed
  15. D. L. Stern and V. Orgogozo, “Is genetic evolution predictable?” Science, vol. 323, no. 5915, pp. 746–751, 2009. View at Publisher · View at Google Scholar · View at PubMed
  16. C. S. Tang and R. J. Epstein, “A structural split in the human genome,” PLoS ONE, vol. 2, no. 7, article no. e603, 2007. View at Google Scholar
  17. C. S. Tang, Y. Z. Zhao, D. K. Smith, and R. J. Epstein, “Intron length and accelerated 3' gene evolution,” Genomics, vol. 88, no. 6, pp. 682–689, 2006. View at Publisher · View at Google Scholar · View at PubMed
  18. D. Karolchik, AS Hinrichs, TS Furey et al., “The UCSC Table Browser data retrieval tool,” Nucleic Acids Res., 2004, 32(Database issue):D493-6, PMID: 14681465. View at Google Scholar
  19. A. E. Vinogradov, “‘Genome design’ model and multicellular complexity: golden middle,” Nucleic Acids Research, vol. 34, no. 20, pp. 5906–5914, 2006. View at Publisher · View at Google Scholar · View at PubMed
  20. A. Wagner, “Robustness, evolvability, and neutrality,” FEBS Letters, vol. 579, no. 8, pp. 1772–1778, 2005. View at Publisher · View at Google Scholar · View at PubMed
  21. A. B. Reams and E. L. Neidle, “Selection for gene clustering by tandem duplication,” Annual Review of Microbiology, vol. 58, pp. 119–142, 2004. View at Publisher · View at Google Scholar · View at PubMed
  22. H. Philippe, D. Casane, S. Gribaldo, P. Lopez, and J. Meunier, “Heterotachy and functional shift in protein evolution,” IUBMB Life, vol. 55, no. 4-5, pp. 257–265, 2003. View at Publisher · View at Google Scholar · View at PubMed
  23. M. Lynch and J. S. Conery, “The evolutionary demography of duplicate genes,” Journal of Structural and Functional Genomics, vol. 3, no. 1–4, pp. 35–44, 2003. View at Publisher · View at Google Scholar
  24. R. Frankham, “Stress and adaptation in conservation genetics,” Journal of Evolutionary Biology, vol. 18, no. 4, pp. 750–755, 2005. View at Publisher · View at Google Scholar · View at PubMed
  25. R. R. Copley, L. E. O. Goodstadt, and C. Ponting, “Eukaryotic domain evolution inferred from genome comparisons,” Current Opinion in Genetics and Development, vol. 13, no. 6, pp. 623–628, 2003. View at Publisher · View at Google Scholar
  26. J. S. Mattick and M. J. Gagen, “The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms,” Molecular Biology and Evolution, vol. 18, no. 9, pp. 1611–1630, 2001. View at Google Scholar
  27. E. Beutler, T. Gelbart, J. Han, J. A. Koziol, and B. Beutler, “Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 1, pp. 192–196, 1989. View at Google Scholar
  28. N. G. C. Smith and L. D. Hurst, “Molecular evolution of an imprinted gene: repeatability of patterns evolution within the mammalian insulin-like growth factor type II receptor,” Genetics, vol. 150, no. 2, pp. 823–833, 1998. View at Google Scholar
  29. J. W. Drake, “Mutations in clusters and showers,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 20, pp. 8203–8204, 2007. View at Publisher · View at Google Scholar · View at PubMed
  30. E. V. Koonin and Y. I. Wolf, “Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world,” Nucleic Acids Research, vol. 36, no. 21, pp. 6688–6719, 2008. View at Publisher · View at Google Scholar · View at PubMed
  31. M. Lynch and J. S. Conery, “The evolutionary fate and consequences of duplicate genes,” Science, vol. 290, no. 5494, pp. 1151–1155, 2000. View at Publisher · View at Google Scholar
  32. X. He and J. Zhang, “Gene complexity and gene duplicability,” Current Biology, vol. 15, no. 11, pp. 1016–1021, 2005. View at Publisher · View at Google Scholar · View at PubMed
  33. R. P. Sugino and H. Innan, “Selection for more of the same product as a force to enhance concerted evolution of duplicated genes,” Trends in Genetics, vol. 22, no. 12, pp. 642–644, 2006. View at Publisher · View at Google Scholar · View at PubMed
  34. U. Bergthorsson, D. A. N. I. Andersson, and J. R. Roth, “Ohno's dilemma: evolution of new genes under continuous selection,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 43, pp. 17004–17009, 2007. View at Publisher · View at Google Scholar · View at PubMed
  35. Z. Jiang, H. Tang, M. Ventura et al., “Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution,” Nature Genetics, vol. 39, no. 11, pp. 1361–1368, 2007. View at Publisher · View at Google Scholar · View at PubMed
  36. G. H. Perry, F. Yang, T. Marques-Bonet et al., “Copy number variation and evolution in humans and chimpanzees,” Genome Research, vol. 18, no. 11, pp. 1698–1710, 2008. View at Publisher · View at Google Scholar · View at PubMed
  37. P. J. Hastings, A. Slack, J. F. Petrosino, and S. M. Rosenberg, “Adaptive amplification and point mutation are independent mechanisms: evidence for various stress-inducible mutation mechanisms,” PLoS Biology, vol. 2, no. 12, article no. e399, 2004. View at Publisher · View at Google Scholar · View at PubMed
  38. E. S. Slechta, K. I. M. L. Bunny, E. Kugelberg, E. Kofoid, D. A. N. I. Andersson, and J. R. Roth, “Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 22, pp. 12847–12852, 2003. View at Publisher · View at Google Scholar · View at PubMed
  39. S. N. Rodin and D. V. Parkhomchuk, “Position-associated GC asymmetry of gene duplicates,” Journal of Molecular Evolution, vol. 59, no. 3, pp. 372–384, 2004. View at Publisher · View at Google Scholar · View at PubMed
  40. D. A. Drummond and C. O. Wilke, “Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution,” Cell, vol. 134, no. 2, pp. 341–352, 2008. View at Publisher · View at Google Scholar · View at PubMed
  41. I. K. Jordan, I. B. Rogozin, Y. I. Wolf, and E. V. Koonin, “Essential genes are more evolutionarily conserved than are nonessential genes in bacteria,” Genome Research, vol. 12, no. 6, pp. 962–968, 2002. View at Publisher · View at Google Scholar · View at PubMed
  42. G. V. Glazko, V. N. Babenko, E. V. Koonin, and I. B. Rogozin, “Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection,” Biology Direct, vol. 1, p. 4, 2006. View at Publisher · View at Google Scholar · View at PubMed