Biological applications of reticulation analysis

This paper describes phylogenetic and ecological problems where mechanisms other than lateral gene transfer create, in the data, complexities that can be resolved by reticulation analysis. One such mechanism is homoplasy, whi ch is the portion of phylogenetic similarity resulting from convergence. In the study of host-parasite relationships, reticulations provide a way of r epresenting the putative historical events that may have led to a lack of f it between host and parasite trees. In historical biogeography (vicariance or dispersal), different processes may act concomitantly, producing data th at can partly be represented by a tree and partly by additional edges (reti culations).