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arXiv · 2205.11084

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

Blerina Sinaimeri·Laura Urbini·Marie-France Sagot·Catherine Matias
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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

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Blerina Sinaimeri, Laura Urbini, Marie-France Sagot, Catherine Matias. 2022-05-23. Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation. https://arxiv.org/abs/2205.11084

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