Maps between trees and cladistic analysis of historical associations among genes, organisms and areas

The concept of a reconciled tree arose indipendently in molecular systematics, parasitology and biogeography as a means of describing historical associations. Examples of historical associations include genes and organisms, hosts and parasitic organisms, and organisms and areas. A reconciled tree combines the tree for the host and its associate into a single summary of the historical association of the two entities under the assumption that no horizontal transmission of associates has occured. In this paper I define reconciled trees, describe an algorithm for their computation, and develop measures to quantify the degree of fit between trees, host parasite cospeciation and biogeography. The problem of incorporating horizontal transmission of associates (e.g., dispersal or host switching) is also addressed by introducing the concept of maximising the amount of codivergance (shared history) between the associates.