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Journal Articles Systematic Biology Year : 2023

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation


Phylogenetic tree reconciliation is extensively 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 \emph{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. Here, we present a method called 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. In the initial step, we estimate the probabilities of spread events using heuristic frequencies. Subsequently, in the second step, we employ an approximate Bayesian computation (ABC) approach to infer the probabilities of the remaining 4 classical events (cospeciation, duplication, host switch, and loss) based on these values. 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. To validate our method, we conducted experiments on synthetic datasets and demonstrated its efficacy using real-world examples. Our results showcase that AmoCoala produces biologically plausible reconciliation scenarios, further emphasizing its effectiveness. The software is accessible at \url{} and supplementary material on a Dryad repository at \url{} with an associated DOI of doi:10.5061/dryad.5x69p8d6v (this last link will only be active upon publication).
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Dates and versions

hal-03673256 , version 1 (20-05-2022)
hal-03673256 , version 2 (12-10-2022)
hal-03673256 , version 3 (20-07-2023)
hal-03673256 , version 4 (29-08-2023)





Blerina Sinaimeri, Laura Urbini, Marie-France Sagot, Catherine Matias. Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation. Systematic Biology, 2023, pp.syad058. ⟨10.1093/sysbio/syad058⟩. ⟨hal-03673256v4⟩
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