Although there is an increasingly vaster literature on co-phylogenetic reconstructions for studying host-parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Many of the algorithms do the host-parasite reconciliation analysis using an event-based model, where the events include in general (a subset of) co-speciation, duplication, loss, and host-switch. All known event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. A crucial issue in this method is that from a biological point of view, reasonable cost values for an event-based parsimonious reconciliation are not easily chosen. Different approaches have been developed to infer such cost values for a given pair of host and symbiont trees. However, a major limitation of these approaches is their inability to model the invasion of different host species by a same symbiont species (referred to as a spread event), which is thought to happen in symbiotic relations. To mention one example, the same species of insects may pollinate different species of plants. This results in multiple associations observed between the symbionts and their hosts (meaning that a symbiont is no longer specific to a host), that are not compatible with the current methods of coevolution.
To deal with this problem, we developed an algorithm, called AmoCoala, a more realistic version of a previous tool called Coala, which for a given pair of host and symbiont trees, estimates the probabilities of the cophylogeny events, in presence of spread events, relying on an approximate Bayesian computation (ABC) approach.
AmoCoala may be downloaded here.
Contacts: Blerina Sinaimeri, Marie-France Sagot, and Catherine Matias
References:
- Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation, B.Sinaimeri, L.Urbini, M. -F. Sagot and C. Matias, submitted.
