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When estimating a phylogeny from a multiple sequence alignment, researchersoften assume the absence of recombination. However, if recombination ispresent, then tree estimation and all downstream analyses will be impacted,because different segments of the sequence alignment support differentphylogenies. Similarly, convergent selective pressures at the molecular levelcan also lead to phylogenetic tree incongruence across the sequence alignment.Current methods for detection of phylogenetic incongruence are not equipped todistinguish between these two different mechanisms and assume that theincongruence is a result of recombination or other horizontal transfer ofgenetic information. We propose a new recombination detection method that canmake this distinction, based on synonymous codon substitution distances.Although some power is lost by discarding the information contained in thenonsynonymous substitutions, our new method has lower false positiveprobabilities than the comparable recombination detection method when thephylogenetic incongruence signal is due to convergent evolution. We apply ourmethod to three empirical examples, where we analyze: 1) sequences from atransmission network of the human immunodeficiency virus, 2) tlpB genesequences from a geographically diverse set of 38 Helicobacter pylori strains,and 3) Hepatitis C virus sequences sampled longitudinally from one patient.

Synonymous and Nonsynonymous Distances Help Untangle Convergent Evolution and Recombination