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 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..., 4 biological datasets were extracted from the literature and provided as nexus files. AP - Acacia & Pseudomyrmex. This dataset was extracted from Gomez-Acevedo et al. Neotropical mutualism between Acacia and Pseudomyrmex: Phylogeny and divergence times. Molecular Phylogenetics and Evolution, 2010. It displays the interaction between Acacia plants and Pseudomyrmex, a genus of ants. The host and symbiont trees include 9 and 7 leaves, respectively. The dataset has 22 multiple-associations.MP - Myrmica & Phengaris. This dataset was extracted from Jansen et al. A phylogenetic test of the parasite-host associations between Maculinea butterflies (Lepidoptera: Lycaenidae) and Myrmica ants (Hymenoptera: Formicidae). European Journal of Entomology, 2011. It is composed of a pair of host and symbiont trees which have each 8 leaves. The dataset has 8 multiple-associations.SBL - Seabirds & Lice. This dataset was extracted from Paterson et al. Host-parasite co-speciation, host switching, ..., The java code can be found at https://github.com/sinaimeri/AmoCoala