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MBE Advance Access published online on May 3, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl006
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted April 19, 2006

Research Article

An Improved Statistical Method for Detecting Heterotachy in Nucleotide Sequences

Guy Baele 1, Jeroen Raes 2, Yves Van de Peer 3 *, and Stijn Vansteelandt 4

1 Department of Applied Mathematics and Computer Science, Ghent University, Krijgslaan 281 S9, B-9000 Ghent, Belgium; Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium
2 Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium; Present address: Computational and Structural Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
3 Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium
4 Department of Applied Mathematics and Computer Science, Ghent University, Krijgslaan 281 S9, B-9000 Ghent, Belgium

* To whom correspondence should be addressed.
Yves Van de Peer, E-mail: yves.vandepeer{at}psb.ugent.be


  Abstract

The principle of heterotachy states that the substitution rate of sites in a gene can change through time. In this article, we propose a powerful statistical test to detect sites that evolve according to the process of heterotachy. We apply this test to an alignment of 1289 eukaryotic rRNA molecules to (1) determine how widespread the phenomenon of heterotachy is in ribosomal RNA, (2) to test whether these heterotachous sites are non-randomly distributed, i.e. linked to secondary structure features of ribosomal RNA, and (3) to determine the impact of heterotachous sites on the bootstrap support of monophyletic groupings. Our study revealed that with 21 monophyletic taxa, approximately two thirds of the sites in the considered set of sequences is heterotachous. While the detected heterotachous sites do not appear bound to specific structural features of the small subunit rRNA, their presence is shown to have a large beneficial influence on the bootstrap support of monophyletic groups. Using extensive testing, we show that this may not be due to heterotachy itself, but merely due to the increased substitution rate at the detected heterotachous sites.

Keywords: heterotachy; covarion; false discovery rate; bootstrap support; ribosomal RNA; eukaryotes.
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