Markov-modulated Markov chains and the covarion process of molecular evolution
- PMID: 15579241
- DOI: 10.1089/cmb.2004.11.727
Markov-modulated Markov chains and the covarion process of molecular evolution
Abstract
The covarion (or site specific rate variation, SSRV) process of biological sequence evolution is a process by which the evolutionary rate of a nucleotide/amino acid/codon position can change in time. In this paper, we introduce time-continuous, space-discrete, Markov-modulated Markov chains as a model for representing SSRV processes, generalizing existing theory to any model of rate change. We propose a fast algorithm for diagonalizing the generator matrix of relevant Markov-modulated Markov processes. This algorithm makes phylogeny likelihood calculation tractable even for a large number of rate classes and a large number of states, so that SSRV models become applicable to amino acid or codon sequence datasets. Using this algorithm, we investigate the accuracy of the discrete approximation to the Gamma distribution of evolutionary rates, widely used in molecular phylogeny. We show that a relatively large number of classes is required to achieve accurate approximation of the exact likelihood when the number of analyzed sequences exceeds 20, both under the SSRV and among site rate variation (ASRV) models.
Similar articles
-
Testing for covarion-like evolution in protein sequences.Mol Biol Evol. 2007 Jan;24(1):294-305. doi: 10.1093/molbev/msl155. Epub 2006 Oct 20. Mol Biol Evol. 2007. PMID: 17056642
-
Taking variation of evolutionary rates between sites into account in inferring phylogenies.J Mol Evol. 2001 Oct-Nov;53(4-5):447-55. doi: 10.1007/s002390010234. J Mol Evol. 2001. PMID: 11675604
-
The identifiability of covarion models in phylogenetics.IEEE/ACM Trans Comput Biol Bioinform. 2009 Jan-Mar;6(1):76-88. doi: 10.1109/TCBB.2008.52. IEEE/ACM Trans Comput Biol Bioinform. 2009. PMID: 19179700
-
Computational advances in maximum likelihood methods for molecular phylogeny.Genome Res. 1998 Mar;8(3):222-33. doi: 10.1101/gr.8.3.222. Genome Res. 1998. PMID: 9521926 Review.
-
Two fundamental questions about protein evolution.Biochimie. 2015 Dec;119:278-83. doi: 10.1016/j.biochi.2014.10.020. Epub 2014 Oct 30. Biochimie. 2015. PMID: 25447137 Review.
Cited by
-
Identifying dramatic selection shifts in phylogenetic trees.BMC Evol Biol. 2007 Feb 8;7 Suppl 1(Suppl 1):S10. doi: 10.1186/1471-2148-7-S1-S10. BMC Evol Biol. 2007. PMID: 17288568 Free PMC article.
-
An empirical test of the concomitantly variable codon hypothesis.Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):10938-43. doi: 10.1073/pnas.0701900104. Epub 2007 Jun 19. Proc Natl Acad Sci U S A. 2007. PMID: 17578921 Free PMC article.
-
FastTree 2--approximately maximum-likelihood trees for large alignments.PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490. PLoS One. 2010. PMID: 20224823 Free PMC article.
-
Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.BMC Evol Biol. 2015 May 1;15:76. doi: 10.1186/s12862-015-0352-y. BMC Evol Biol. 2015. PMID: 25928234 Free PMC article.
-
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage.PLoS Biol. 2015 Aug 7;13(8):e1002220. doi: 10.1371/journal.pbio.1002220. eCollection 2015 Aug. PLoS Biol. 2015. PMID: 26252497 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
