The application of cophylogenic tools to gene sets

Several studies of host-parasite evolution have used gene trees developed for each partner as a means to detect the influence of one on the evolution of the other, a process known as cophylogeny. We now extend this concept and present a process to test whether two genes or gene regions within the same species have coevolved in order to assess their further utility in the same phylogenetic analysis. The process entails well-established methods; firstly based upon a given set of sequence data, inference of best-fit evolutionary models and associated parameters through to gene tree building by maximum likelihood. This is followed by a "ParaFit" analysis of pairwise combination of genes or gene regions. The pairwise combinations that pass the test of cophylogeny may then be horizontally concatenated for phylogenetic inference of the set of taxa under study. The complete mathematical properties of this process presently remain unexplored; however, we demonstrate the utility of such an analysis prior to phylogenetic inference using examples from available datasets.