Algorithms for Reconstructing Evolutionary Relationships between Phylogenies: The Multi-Valued Case

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An important contribution towards understanding host/parasite systems is the reconstruction of cophylogenies, i. e., the mapping of parasite and host phylogenies onto each other and the identification and (relative) dating of the pertinent evolutionary events: speciation of host and parasites as well as gain and loss of parasites through changes in host preferences. In nature, it is the rule rather than the exception that multiple parasite species infect the same host, while the same parasites affects a range of host species. The evolution of multi-host/multi-parasite systems is not only of academic interest but also has potential consequences for managing infectious diseases. The evolution of mobile genetic elements with efficient mechanisms for horizontal transfer, such as retroviruses and plasmids is another field of application. Nevertheless, mathematical models and computational tools so far have focused nearly exclusively on associations of single parasites with single hosts and multiple parasites with a single host. Here we propose to close this gap and develop a formal framework as well as computational tools to study co-phylogenies that describe multi-host, multi-parasite assemblages. To this end, we will extend the well-studied concept of reconciliation maps to reconciliation relations between parasite and host trees, develop suitable scoring schemes for such generalized models, and explore generalizations of the algorithmic approaches for host/parasite systems and their closely related gene/species systems. In conjunction with a rapidly increasing body of data on host/parasite associations and the deluge of genomic data, we envision that a new generation of tools capable of treating many-to-many associations will provide new insights into the evolutionary mechanisms of tightly linked, co-evolving assemblages also beyond the scope of host/parasite systems.