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Licensed Unlicensed Requires Authentication Published by De Gruyter June 10, 2015

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination

  • Peter B. Chi , Sujay Chattopadhyay , Philippe Lemey , Evgeni V. Sokurenko and Vladimir N. Minin EMAIL logo


When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because different segments of the sequence alignment support different phylogenies. Similarly, convergent selective pressures at the molecular level can also lead to phylogenetic tree incongruence across the sequence alignment. Current methods for detection of phylogenetic incongruence are not equipped to distinguish between these two different mechanisms and assume that the incongruence is a result of recombination or other horizontal transfer of genetic information. We propose a new recombination detection method that can make this distinction, based on synonymous codon substitution distances. Although some power is lost by discarding the information contained in the nonsynonymous substitutions, our new method has lower false positive probabilities than the comparable recombination detection method when the phylogenetic incongruence signal is due to convergent evolution. We apply our method to three empirical examples, where we analyze: (1) sequences from a transmission network of the human immunodeficiency virus, (2) tlpB gene sequences from a geographically diverse set of 38 Helicobacter pylori strains, and (3) hepatitis C virus sequences sampled longitudinally from one patient.

Corresponding author: Vladimir N. Minin, Departments of Statistics and Biology, University of Washington, Seattle, WA, 98195, USA, e-mail:


We thank Adam Leaché and Ken Rice for helpful comments and discussions. VNM was supported by the National Science Foundation grant DMS-0856099 and the National Institutes of Health grants R01-AI107034 and U54-GM111274. VNM and EVS were supported by the NIH ARRA award 1RC4AI092828. PL acknowledges funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013) under ERC Grant agreement no. 260864.


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Supplemental Material:

The online version of this article (DOI: 10.1515/sagmb-2014-0078) offers supplementary material, available to authorized users.

Published Online: 2015-6-10
Published in Print: 2015-8-1

©2015 by De Gruyter

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