Novel method for discerning the action of selection during evolution
ABSTRACT
A common problem in molecular comparative geno- mics is the identification of genes that are under positive, adaptive selection [1]. Such genes are likely to be crucial for speciation, species differentiation, and func- tional specialization. However, discerning the difference between positive selection and relaxation of func- tional constraint can be difficult using current methods. Both processes generally increase the rate of ami- no acid change relative to synonymous changes within coding regions, and unless the amino acid rate is over- whelmingly high across an entire gene, the signature of positive selection can be obscured [2]. Some methodologies do not explicitly determine the difference be- tween a relaxation of functional constraint and positive selection, leaving researchers to determine via other means whether the trajectory of a gene has been specialization or creation of a new function, or removal from the genome via a process of degeneration.
A common problem in molecular comparative geno- mics is the identification of genes that are under positive, adaptive selection [1]. Such genes are likely to be crucial for speciation, species differentiation, and func- tional specialization. However, discerning the difference between positive selection and relaxation of func- tional constraint can be difficult using current methods. Both processes generally increase the rate of ami- no acid change relative to synonymous changes within coding regions, and unless the amino acid rate is over- whelmingly high across an entire gene, the signature of positive selection can be obscured [2]. Some methodologies do not explicitly determine the difference be- tween a relaxation of functional constraint and positive selection, leaving researchers to determine via other means whether the trajectory of a gene has been specialization or creation of a new function, or removal from the genome via a process of degeneration.
Cite this paper
nullYang, M. , Solidar, A. and J. Wyckoff, G. (2010) Novel method for discerning the action of selection during evolution. Journal of Biomedical Science and Engineering, 3, 109-113. doi: 10.4236/jbise.2010.32016.
nullYang, M. , Solidar, A. and J. Wyckoff, G. (2010) Novel method for discerning the action of selection during evolution. Journal of Biomedical Science and Engineering, 3, 109-113. doi: 10.4236/jbise.2010.32016.
References
[1] Graur, D. and Li, W.H. (2000) Fundamentals of molecular evolution. Sinauer Associates. [2] Fay, J.C., Wyckoff, G.J. and Wu, C.I. (2001) Positive and negative selection on the human genome. Genetics, 158, 1227-34. [3] Karlin, S. and Ghandour, G. (1985) Multiple-alphabet amino acid sequence comparisons of the immunoglobulin kappa-chain constant domain. Proc Natl Acad Sci U S A, 82, 8597-601. [4] Feng, D.F., Johnson, M.S. and Doolittle, R.F. (1985) Aligning amino acid sequences: Comparison of commonly used methods. J. Mol. Evol., 21, 112-125. [5] Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) A model of evolutionary change in proteins, in Dayhoff, M.O. Edition, Atlas of Protein Sequence and Structure. Natl. Biomed. Res. Found., Washington DC, 5(3), 345- 352. [6] Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A, 89, 10915-9. [7] Henikoff, J.G. and Henikoff, S. (1996) Blocks database and its applications. Methods Enzymol, 266, 88-105. [8] Tang, H., Wyckoff, G.J., Lu, J. and Wu, C.I. (2004) A universal evolutionary index for amino acid changes. Mol Biol Evol, 21, 1548-56. [9] Minsky, A. (2004) Information content and complexity in the high-order organization of DNA. Annu Rev Biophys Biomol Struct, 33, 317-42. [10] Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res, 18, 6097-100. [11] Smith, A.D., Sumazin, P. and Zhang, M.Q. (2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A, 102, 1560-5. [12] Nalla, V.K. and Rogan, P.K. (2008) Automated splicing mutation analysis by information theory. Hum Mutat, 29, 1168. [13] Nalla, V.K. and Rogan, P.K. (2005) Automated splicing mutation analysis by information theory. Hum Mutat, 25, 334-42. [14] Shannon, C.E. (1948) A mathematical theory of communication. Bell System Technical Journal, 27, 379-423, 623-656. [15] Hall, T.M. (2005) Multiple modes of RNA recognition by zinc finger proteins. Curr Opin Struct Biol, 15, 367-73. [16] Brown, R.S. (2005) Zinc finger proteins: Getting a grip on RNA. Curr Opin Struct Biol, 15, 94-8. [17] Klug, A. (1999) Zinc finger peptides for the regulation of gene expression. J Mol Biol, 293, 215–8. [18] Schuh, R. et al. (1986) A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Kruppel—a drosophila segmentation gene. Cell, 47, 1025-32. [19] Miller, J., McLachlan, A.D. and Klug, A. (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Embo J, 4, 1609-14. [20] Wang, Z. et al. (2006) Solution structure of a Zap1 zinc- responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae. J Mol Biol, 357, 1167-83.
[1] Graur, D. and Li, W.H. (2000) Fundamentals of molecular evolution. Sinauer Associates. [2] Fay, J.C., Wyckoff, G.J. and Wu, C.I. (2001) Positive and negative selection on the human genome. Genetics, 158, 1227-34. [3] Karlin, S. and Ghandour, G. (1985) Multiple-alphabet amino acid sequence comparisons of the immunoglobulin kappa-chain constant domain. Proc Natl Acad Sci U S A, 82, 8597-601. [4] Feng, D.F., Johnson, M.S. and Doolittle, R.F. (1985) Aligning amino acid sequences: Comparison of commonly used methods. J. Mol. Evol., 21, 112-125. [5] Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) A model of evolutionary change in proteins, in Dayhoff, M.O. Edition, Atlas of Protein Sequence and Structure. Natl. Biomed. Res. Found., Washington DC, 5(3), 345- 352. [6] Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A, 89, 10915-9. [7] Henikoff, J.G. and Henikoff, S. (1996) Blocks database and its applications. Methods Enzymol, 266, 88-105. [8] Tang, H., Wyckoff, G.J., Lu, J. and Wu, C.I. (2004) A universal evolutionary index for amino acid changes. Mol Biol Evol, 21, 1548-56. [9] Minsky, A. (2004) Information content and complexity in the high-order organization of DNA. Annu Rev Biophys Biomol Struct, 33, 317-42. [10] Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res, 18, 6097-100. [11] Smith, A.D., Sumazin, P. and Zhang, M.Q. (2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A, 102, 1560-5. [12] Nalla, V.K. and Rogan, P.K. (2008) Automated splicing mutation analysis by information theory. Hum Mutat, 29, 1168. [13] Nalla, V.K. and Rogan, P.K. (2005) Automated splicing mutation analysis by information theory. Hum Mutat, 25, 334-42. [14] Shannon, C.E. (1948) A mathematical theory of communication. Bell System Technical Journal, 27, 379-423, 623-656. [15] Hall, T.M. (2005) Multiple modes of RNA recognition by zinc finger proteins. Curr Opin Struct Biol, 15, 367-73. [16] Brown, R.S. (2005) Zinc finger proteins: Getting a grip on RNA. Curr Opin Struct Biol, 15, 94-8. [17] Klug, A. (1999) Zinc finger peptides for the regulation of gene expression. J Mol Biol, 293, 215–8. [18] Schuh, R. et al. (1986) A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Kruppel—a drosophila segmentation gene. Cell, 47, 1025-32. [19] Miller, J., McLachlan, A.D. and Klug, A. (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Embo J, 4, 1609-14. [20] Wang, Z. et al. (2006) Solution structure of a Zap1 zinc- responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae. J Mol Biol, 357, 1167-83.