Principles of cophylogenetic maps

Abstract

Cophylogeny is the study of the relationships between phylogenies of ecologically related groups (taxa, geographical areas, genes etc.), where one, the “host” phylogeny, is independent and the other, the “associate” phylogeny, is hypothesized to be dependent to some degree on the host. Given two such phylogenies our aim is to estimate the past associations between the host and associate taxa. This chapter describes cophylogeny and discusses some of its basic principles. The necessary properties of any cophylogenetic method are described. Charleston [5] created a graph which contains all the potential solutions to a given cophylogenetic problem. The vertices of this graph are associations, either observed or hypothetical, between “host” and associated taxonomic units, and the arcs correspond to the associate phylogeny. A new and more general method of constructing the Jungle is presented, which will correctly account for reticulate host and/or parasite phylogenies.