paco: implementing Procrustean Approach to Cophylogeny in R

What is it about?

Living organisms do not evolve independently, as evolutionary changes in individuals of a given species can trigger evolutionary change in individuals of other species. This is particularly so in tightly associated organisms, such as parasites and their hosts, pollinators and flowering plants, and lichenized fungi and algae, to name a few. Cophylogeny is a discipline that studies the coevolutionary relationships of associated organisms by means of comparing phylogenetic trees, which are branching diagrams that show the inferred evolutionary relationships among species. PACo (Procrustean Approach to Cophylogeny) is a statistical technique specifically devised to this end. In a first step PACo translates the relationships between species from tree space (which is hard to grasp) into Euclidean space. Then the two configurations in Euclidean space are rotated and scaled to match each other as much as possible. This allows identifying which parts of the phylogenies of both sets of organisms are more related to each other. PACo was first developed by Balbuena et al. (2013). In this paper we provide a more user friendly platform and extend its capabilities by rendering paco as a package of R, a free software environment for statistical computing and graphics, which is widely used in different biological disciplines.

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Photo by Krzysztof Niewolny on Unsplash

Photo by Krzysztof Niewolny on Unsplash

Why is it important?

We provide a robust, versatile tool capable of not only exploring cophylogenetic hypotheses in interacting clades but also the potential coevolutionary dynamics of those clades. The R package, paco formalises and extends the original R code provided by Balbuena et al. (2013) in several key areas to increase the utility of the method. As a package on the CRAN database, an immediate advantage of paco is increased accessibility for both installation and use. Furthermore, paco has the advantage that code for the analysis of phylogenetic congruence is broken into distinct functional steps providing a more user-friendly approach. Finally, paco provides a larger suite of null models than in its original inception. Although paco is intended to assess the phylogenetic congruence between groups of interacting species, the method is also directly applicable to other scenarios that may show phylogenetic congruence including historical biogeography, molecular systematics, and cultural evolution.