Rh: Reconciled Trees Maps between Trees and Cladistic Analysis of Historical Associations among Genes, Organisms, and Areas

The concept of a reconciled tree arose independently in molecular systematics, parasitology, and biogeography as a means of describing "historical associations." Examples of historical associations include genes and organisms, host and parasitic organisms, and organisms and areas. A reconciled tree combines the tree for a host and its associate into a single summary of the historical association between the two entities under the assumption that no horizontal transmission of associates has occurred. This paper defines reconciled trees, describes an algorithm for their computation, and develops measures to quantify the degree of fit between host and associate trees. Examples are given of applying the method to gene trees and species 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 maximizing the amount of codivergence (shared history) between the associates. What about the nonideal data, which like Lincoln's common men God must have loved, for He made so many of them. This is the real problem in biogeography, where our efforts must come together in the long run. Recently workers in molecular systematics, parasitology, and biogeography have recognised that their disciplines may all be attempting to solve a common problem, namely reconstructing the history of an association between an "associate" (such as a gene, a parasite, or an organism) and its "host" (such as an organism, a parasite's host, or an area) (e. is a general problem raises the possibility of a general solution, a methodology that can be used to examine associations at all levels among genes, organisms, and areas. My purpose in this paper is to describe one candidate for a general method. This method emerged independently (and in various stages of development) in molecular motivated by the realisation that some incongruence between host and associate cladograms might be more apparent than real. Fundamental to any study of historical association is the relationship between the genealogies of members of the association. In one sense this is analogous to the problem in systematics of inferring the history of character change on a tree. Given a character whose states varying among a group of taxa, together with some hypothesis of the relative weight or cost of changes between those character states (such as a character state tree or a step matrix) then the goal is to find the assignment(s) of character states to internal nodes …