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Statistical methods for testing functional divergence after gene duplication
Abstract
Functional innovations after gene duplication may result in altered functional constraints between member gene clusters of a gene family. This type (type I) of functional divergence is measured by the coefficient of functional divergence (theta lambda), which can be interpreted as the decrease in rate correlation between gene clusters, or the probability that the evolutionary rate at a site is statistically independent between two gene clusters. A simple stochastic model has been developed for estimating theta lambda and testing its statistical significance. The current model includes the model of rate variation among sites as a special case when theta lambda = 0. Moreover, we have developed a site-specific profile based on the hidden Markov model to identify critical amino acid residues that are responsible for these functional differences between two gene clusters, which may have great potential in functional genomics.
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Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Cited by
Evolution by gene duplication: An update
Zhang, J. (2003) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(03)00033-8 · Cited by 2,201
Yang, Z., & Nielsen, R. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004148 · Cited by 1,374
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution[W]
Blanc, G., & Wolfe, K. H. (2004) · The Plant Cell · doi:10.1105/tpc.021410 · Cited by 1,076
Evolutionary microbial genomics: insights into bacterial host adaptation
Toft, C., & Andersson, S. G. E. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2798 · Cited by 432
Causes of evolutionary rate variation among protein sites
Echave, J., Spielman, S. J., & Wilke, C. O. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.18 · Cited by 328
Metadata
- Authors
- Gu, X.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-12-01
- Volume
- 16
- Issue
- 12
- Pages
- 1664-1674
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2092414509
- Cited by
- 457
- References
- 1
- FWCI
- 4.13
- Type
- journal article
- Language
- en
- Open access
- closed
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