Skip Navigation


MBE Advance Access originally published online on May 3, 2006
Molecular Biology and Evolution 2006 23(7):1397-1405; doi:10.1093/molbev/msl006
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
23/7/1397    most recent
msl006v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (8)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Baele, G.
Right arrow Articles by Vansteelandt, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Baele, G.
Right arrow Articles by Vansteelandt, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

Research Article

An Improved Statistical Method for Detecting Heterotachy in Nucleotide Sequences

Guy Baele*,{dagger}, Jeroen Raes{dagger},1, Yves Van de Peer{dagger} and Stijn Vansteelandt*

* Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium; and {dagger} Department of Plant Systems Biology, Ghent University, Ghent, Belgium

E-mail: yves.vandepeer{at}psb.ugent.be.

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 nonrandomly distributed, that is, 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. Although 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.

Key Words: heterotachy • covarion • false discovery rate • bootstrap support • ribosomal RNA • eukaryotes


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
N. Gruenheit, P. J. Lockhart, M. Steel, and W. Martin
Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites
Mol. Biol. Evol., July 1, 2008; 25(7): 1512 - 1520.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B. Kolaczkowski and J. W. Thornton
A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy
Mol. Biol. Evol., June 1, 2008; 25(6): 1054 - 1066.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.