Reply to Holmes and Duchêne, “Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?”: Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless

In their Letter to the Editor of mBio , written in response to our recent article on evolution of the global RNA virome (1), Holmes and Duchene submit that the extreme sequence divergence between the RNA-dependent RNA polymerases (RdRps) makes it impossible to infer deep relationships between RNA viruses from any type of sequence analysis. We certainly agree with Holmes and Duchene that extreme caution is due in the analysis and interpretation of deep phylogenies, and in particular, that alignment quality is central to our ability to resolve long-distance evolutionary relationships. If the alignment is largely wrong (i.e., does not align homologous protein sites) or noninformative (i.e., cannot be used to distinguish between alternative histories), it is of no utility for phylogenetic reconstruction. Moreover, even a correct and informative alignment does not guarantee correct phylogenetic reconstruction due to the technical limitations of the software, systematic biases of the available evolutionary models, and the fundamentally random nature of sequence divergence. Therefore, formal phylogenetic analysis should be accompanied by careful consideration of the associated biological data and examined in terms of the implications of the respective evolutionary scenarios. Where exactly lies the boundary between an alignment that is suitable for phylogenetic reconstruction and one that is “highly unlikely to be accurate” is far from being an easy question. In the ideal situation (high sequence similarity, random homoplasy), one might need as little as O (log k ) informative sites to resolve a tree of k sequences (2). With real-life data, it is critical …