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Bioinformatics Advance Access published online on August 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl427
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© 2006 The Author(s)
Received June 26, 2006
Revised July 31, 2006
Accepted August 1, 2006

Article

Robust inference of positive selection from recombining coding sequences

Konrad Scheffler 1 *, Darren P. Martin 1, and Cathal Seoighe 1

1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Private Bag, Rondebosch 7701, South Africa

* To whom correspondence should be addressed.
Konrad Scheffler, E-mail: konrad{at}cbio.uct.ac.za


  Abstract

Motivation: Accurate detection of positive Darwinian selection can provide important insights to researchers investigating the evolution of pathogens. However, many pathogens (particularly viruses) undergo frequent recombination and the phylogenetic methods commonly applied to detect positive selection have been shown to give misleading results when applied to recombining sequences. We propose a method that makes maximum likelihood inference of positive selection robust to the presence of recombination. This is achieved by allowing tree topologies and branch lengths to change across detected recombination breakpoints. Further improvements are obtained by allowing synonymous substitution rates to vary across sites.

Results: Using simulation we show that, even for extreme cases where recombination causes standard methods to reach false positive rates above 90%, the proposed method decreases the false positive rate to acceptable levels while retaining high power. We applied the method to two HIV-1 data sets for which we have previously found that inference of positive selection is invalid due to high rates of recombination. In one of these (env gene) we still detected positive selection using the proposed method, while in the other (gag gene) we found no significant evidence of positive selection.

Availability: A HyPhy batch language implementation of the proposed methods and the HIV-1 data sets analysed are available at http://www.cbio.uct.ac.za/pub_support/bioinf06. The HyPhy package is available at http://www.hyphy.org, and it is planned that the proposed methods will be included in the next distribution. RDP2 is available at http://darwin.uvigo.es/rdp/rdp.html.

Associate Editor: Keith A Crandall
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