Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation.

The article focuses on AmoCoala, a novel method for phylogenetic tree reconciliation that improves the analysis of host-symbiont coevolution by incorporating spread events—vertical and horizontal spreads—that account for multiple associations where a symbiont species invades multiple host species. AmoCoala extends the classical four-event coevolutionary model (cospeciation, duplication, host switch, and loss) by estimating spread event probabilities heuristically and inferring classical event probabilities via an approximate Bayesian computation (ABC) approach. A new distance metric, Maximum Agreement Set-labeled SubTree (MASST), is introduced to compare set-labeled trees reflecting multiple associations. Tested on synthetic and real biological datasets, AmoCoala produces biologically plausible event probability estimates and better accommodates multiple associations than previous methods, although direct parsimonious reconciliation including spread events remains a future challenge. The software and datasets are publicly available for further research.