Performance of a divergence time estimation method under a probabilistic model of rate evolution - PubMed (original) (raw)
Performance of a divergence time estimation method under a probabilistic model of rate evolution
H Kishino et al. Mol Biol Evol. 2001 Mar.
Abstract
Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.
Similar articles
- Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.
Yang Z, Rannala B. Yang Z, et al. Mol Biol Evol. 2006 Jan;23(1):212-26. doi: 10.1093/molbev/msj024. Epub 2005 Sep 21. Mol Biol Evol. 2006. PMID: 16177230 - Bayesian relaxed clock estimation of divergence times in foraminifera.
Groussin M, Pawlowski J, Yang Z. Groussin M, et al. Mol Phylogenet Evol. 2011 Oct;61(1):157-66. doi: 10.1016/j.ympev.2011.06.008. Epub 2011 Jun 23. Mol Phylogenet Evol. 2011. PMID: 21723398 - Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution.
Hasegawa M, Thorne JL, Kishino H. Hasegawa M, et al. Genes Genet Syst. 2003 Aug;78(4):267-83. doi: 10.1266/ggs.78.267. Genes Genet Syst. 2003. PMID: 14532706 Review. - Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.
Warnock RCM, Yang Z, Donoghue PCJ. Warnock RCM, et al. Proc Biol Sci. 2017 Jun 28;284(1857):20170227. doi: 10.1098/rspb.2017.0227. Proc Biol Sci. 2017. PMID: 28637852 Free PMC article. - Divergence time and evolutionary rate estimation with multilocus data.
Thorne JL, Kishino H. Thorne JL, et al. Syst Biol. 2002 Oct;51(5):689-702. doi: 10.1080/10635150290102456. Syst Biol. 2002. PMID: 12396584
Cited by
- A hierarchical Bayesian model for calibrating estimates of species divergence times.
Heath TA. Heath TA. Syst Biol. 2012 Oct;61(5):793-809. doi: 10.1093/sysbio/sys032. Epub 2012 Feb 14. Syst Biol. 2012. PMID: 22334343 Free PMC article. - An examination of phylogenetic models of substitution rate variation among lineages.
Ho SY. Ho SY. Biol Lett. 2009 Jun 23;5(3):421-4. doi: 10.1098/rsbl.2008.0729. Epub 2009 Feb 25. Biol Lett. 2009. PMID: 19324651 Free PMC article. - Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.
Zhu T, Dos Reis M, Yang Z. Zhu T, et al. Syst Biol. 2015 Mar;64(2):267-80. doi: 10.1093/sysbio/syu109. Epub 2014 Dec 11. Syst Biol. 2015. PMID: 25503979 Free PMC article. - The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.
Roger AJ, Hug LA. Roger AJ, et al. Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29;361(1470):1039-54. doi: 10.1098/rstb.2006.1845. Philos Trans R Soc Lond B Biol Sci. 2006. PMID: 16754613 Free PMC article. Review. - Evolution of the army ant syndrome: the origin and long-term evolutionary stasis of a complex of behavioral and reproductive adaptations.
Brady SG. Brady SG. Proc Natl Acad Sci U S A. 2003 May 27;100(11):6575-9. doi: 10.1073/pnas.1137809100. Epub 2003 May 15. Proc Natl Acad Sci U S A. 2003. PMID: 12750466 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources