An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping
Genet. mol. res. (Online)
;
5(1): 233-241, Mar. 31, 2006. ilus, tab, graf
Article
in English
| LILACS
| ID: lil-449129
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.
Full text:
Available
Index:
LILACS (Americas)
Main subject:
Phylogeny
/
Primates
/
Evolution, Molecular
/
Models, Genetic
Type of study:
Health economic evaluation
/
Prognostic study
Limits:
Animals
/
Humans
Language:
English
Journal:
Genet. mol. res. (Online)
Journal subject:
Molecular Biology
/
Genetics
Year:
2006
Type:
Article
Affiliation country:
Brazil
Institution/Affiliation country:
Universidade Federal do Rio de Janeiro/BR
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