Change search
ReferencesLink to record
Permanent link

Direct link
Evaluation of Bayesian Models of Substitution Rate Evolution-Parental Guidance versus Mutual Independence
Stockholm University, Faculty of Science, Department of Mathematics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2011 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 3, 329-342 p.Article in journal (Refereed) Published
Abstract [en]

We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent and identically distributed (i.i.d.) stochastic variables. Three versions with respect to the underlying distribution (Gamma, Inverse Gaussian, and LogNormal) are considered. The i.i.d. models are compared with the autocorrelated (AC) model, where rates of adjacent nodes in the tree are AC, so that a node rate is LogNormal distributed around the rate of the parent node. The performance of different models is evaluated using three empirical data sets. For all data sets, it was clear that all tested models extracted substantial knowledge from data when posterior divergence time distributions were compared with the prior distributions and, furthermore, that they clearly outperformed a molecular clock. Moreover, the descriptive power of the i.i.d. models, as evaluated by Bayes factors, was either equal to or clearly better than that of the AC model. The latter effect increased with extended taxon sampling. Likewise, under none of the models could we find compelling evidence, in any of the data sets, for rate correlation between adjacent branches/nodes. These findings challenge previous suggestions of universality of autocorrelation in sequence evolution. We also performed an additional comparison with a divergence time prior including calibration information from fossil evidence. Adding fossil information to the prior had negligible effect on Bayes factors and mainly affected the width of the posterior distribution of the divergence times, whereas the relative position of the mean divergence times were largely unaffected.

Place, publisher, year, edition, pages
2011. Vol. 60, no 3, 329-342 p.
Keyword [en]
Bayesian statistics, divergence times, fossil calibration, phylogenetics, probabilistic modeling, substitution rates
National Category
Mathematics Biological Sciences
URN: urn:nbn:se:su:diva-68513DOI: 10.1093/sysbio/syr009ISI: 000289805600007OAI: diva2:473430
authorCount :3Available from: 2012-01-05 Created: 2012-01-04 Last updated: 2012-01-05Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Britton, Tom
By organisation
Department of MathematicsDepartment of Biochemistry and Biophysics
In the same journal
Systematic Biology
MathematicsBiological Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 49 hits
ReferencesLink to record
Permanent link

Direct link