An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping
- PMID: 16755514
An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping
Abstract
The molecular clock theory has greatly enlightened our understanding of macroevolutionary events. Maximum likelihood (ML) estimation of divergence times involves the adoption of fixed calibration points, and the confidence intervals associated with the estimates are generally very narrow. The credibility intervals are inferred assuming that the estimates are normally distributed, which may not be the case. Moreover, calculation of standard errors is usually carried out by the curvature method and is complicated by the difficulty in approximating second derivatives of the likelihood function. In this study, a standard primate phylogeny was used to examine the standard errors of ML estimates via the bootstrap method. Confidence intervals were also assessed from the posterior distribution of divergence times inferred via Bayesian Markov Chain Monte Carlo. For the primate topology under evaluation, no significant differences were found between the bootstrap and the curvature methods. Also, Bayesian confidence intervals were always wider than those obtained by ML.
Similar articles
-
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.Mol Biol Evol. 2011 Jul;28(7):2161-72. doi: 10.1093/molbev/msr045. Epub 2011 Feb 10. Mol Biol Evol. 2011. PMID: 21310946
-
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.Mol Biol Evol. 2006 Jan;23(1):212-26. doi: 10.1093/molbev/msj024. Epub 2005 Sep 21. Mol Biol Evol. 2006. PMID: 16177230
-
Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches.Syst Biol. 2004 Apr;53(2):244-64. doi: 10.1080/10635150490423458. Syst Biol. 2004. PMID: 15205051
-
Phylogeny estimation: traditional and Bayesian approaches.Nat Rev Genet. 2003 Apr;4(4):275-84. doi: 10.1038/nrg1044. Nat Rev Genet. 2003. PMID: 12671658 Review.
-
Using models of nucleotide evolution to build phylogenetic trees.Dev Comp Immunol. 2005;29(3):211-27. doi: 10.1016/j.dci.2004.07.007. Dev Comp Immunol. 2005. PMID: 15572070 Review.
Cited by
-
Suppressors of RNAi from plant viruses are subject to episodic positive selection.Proc Biol Sci. 2013 Jun 26;280(1765):20130965. doi: 10.1098/rspb.2013.0965. Print 2013 Aug 22. Proc Biol Sci. 2013. PMID: 23804618 Free PMC article.
-
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4. Mol Biol Evol. 2011. PMID: 21546353 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
