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Robust inference of positive selection from recombining coding sequences.

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dc.contributor.authorScheffler, Konrad.
dc.contributor.authorMartin, Darren Patrick.
dc.contributor.authorSeoighe, Cathal.
dc.date.accessioned2013-05-13T11:00:41Z
dc.date.available2013-05-13T11:00:41Z
dc.date.created2006
dc.date.issued2006
dc.description.abstractMotivation: 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 >90%, the proposed method decreases the false positive rate to acceptable levels while retaining high power. We applied the method to two HIV-1 datasets for which we have previously found that inference of positive selection is invalid owing 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 datasets 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.en
dc.description.notesThis study was supported by the South African National Bioinformatics Network and by the National Institute of Allergy and Infectious Disease and the National Institutes of Health through the Centre for the AIDS Programme of Research in South Africa (grant no. 1U19AI51794). Funding to pay the Open Access publication charges was provided by the South African National Bioinformatics Network.en
dc.identifier.citationScheffler, K., Martin, D.P., Seoighe, C. 2006. Robust inference of positive selection from recombining coding sequences. Bioinformatics 22(20) pp. 2493-2499.en
dc.identifier.issn1367-4803
dc.identifier.urihttp://dx.doi.org/10.1093/bioinformatics/btl427en
dc.identifier.urihttp://hdl.handle.net/10413/8866
dc.language.isoenen
dc.publisherOxford University Press.en
dc.subjectVirus diseases--Pathogenesis.en
dc.subjectGenetic recombination.en
dc.subjectGenetic recombination--Research.en
dc.subjectMolecular evolution.en
dc.titleRobust inference of positive selection from recombining coding sequences.en
dc.typePeer reviewed journal articleen

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