Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

Abstract: Phylogenetic tree reconciliation is employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation. Although certain approaches deduce event probabilities unique to each pair of host and symbiont trees, which can subsequently be converted into cost values, a significant limitation lies in their inability to model the invasion of diverse host species by the same symbiont species (termed as a spread event), which is believed to occur in symbiotic relationships. Invasions lead to the observation of multiple associations between symbionts and their hosts (indicating that a symbiont is no longer exclusive to a single host), which are incompatible with the existing methods of coevolution. We present AmoCoala, an enhanced version of the tool Coala, that provides a more realistic estimation of cophylogeny event probabilities for a given pair of host and symbiont trees, even in the presence of spread events. We expand the classical 4-event coevolutionary model to include 2 additional spread events (vertical and horizontal spreads) that lead to multiple associations. By incorporating spread events, our reconciliation model enables a more accurate consideration of multiple associations. This improvement enhances the precision of estimated cost sets, paving the way to a more reliable reconciliation of host and symbiont trees. Our results showcase that AmoCoala produces biologically plausible reconciliation scenarios, further emphasizing its effectiveness. The software is accessible at https://github.com/sinaimeri/AmoCoala