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  Quantifying the stationarity and time reversibility of the nucleotide substitution process

Squartini, F., & Arndt, P. F. (2008). Quantifying the stationarity and time reversibility of the nucleotide substitution process. Molecular Biology and Evolution, 25(12), 2525-2535. doi:10.1093/molbev/msn169.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7E7C-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7E7D-6
Genre: Journal Article
Alternative Title : MBE

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 Creators:
Squartini, Federico1, Author              
Arndt, Peter F.1, Author              
Affiliations:
1Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              

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Free keywords: Markov models of nucleotide substitutions • stationarity • time reversibility • maximum likelihood estimation • CpG effect
 Abstract: Markov models describing the evolution of the nucleotide substitution process, widely used in phylogeny reconstruction, usually assume the hypotheses of stationarity and time reversibility. Although these models give meaningful results when applied to biological data, it is not clear if the 2 assumptions mentioned above hold and, if not, how much sequence evolution processes deviate from them. To this aim, we introduce 2 sets of indices that can be calculated from the nucleotide distribution and the substitution rates. The stationarity indices (STIs) can be used to test the validity of the equilibrium assumption. The irreversibility indices (IRIs) are derived from the Kolmogorov cycle conditions for time reversibility and quantify the degree of nontime reversibility of a process. We have computed STIs and IRIs for the evolutionary process of 2 lineages, Drosophila simulans and Homo sapiens. In the latter case, we use a modified form of the indices that takes into account the CpG decay process. In both cases, we find statistically significant deviations from the ideal case of a process that has reached stationarity and is time reversible.

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Language(s): eng - English
 Dates: 2008-12-25
 Publication Status: Published in print
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Title: Molecular Biology and Evolution
  Alternative Title : MBE
Source Genre: Journal
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Pages: - Volume / Issue: 25 (12) Sequence Number: - Start / End Page: 2525 - 2535 Identifier: ISSN: 0737-4038