Skip Navigation



MBE Advance Access published online on September 13, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl116
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/12/2274    most recent
msl116v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Pie, M. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pie, M. R.
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
Accepted September 7, 2006

Letter

The Influence of Phylogenetic Uncertainty on the Detection of Positive Darwinian Selection

Marcio R. Pie 1 *

1 Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, PR 81531-990, Brazil

* To whom correspondence should be addressed.
Marcio R. Pie, E-mail: pie{at}ufpr.br


  Abstract

The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied dataset. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, three empirical datasets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.

Keywords: adaptive evolution; molecular phylogeny; likelihood ratio tests.
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
 Nucleic Acids ResHome page
A. Stern, A. Doron-Faigenboim, E. Erez, E. Martz, E. Bacharach, and T. Pupko
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W506 - W511.
[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.