@article {46256, title = {Jungles: a new solution to the host/parasite phylogeny reconciliation problem}, journal = {Mathematical biosciences}, volume = {149}, year = {1998}, note = {LR: 20031114; JID: 0103146; ppublish}, month = {1998}, pages = {191 - 223}, address = {UNITED STATES}, abstract = {The problem of finding least-cost reconstructions of past host/parasite associations, given the phylogenetic histories of a set of host taxa and of their associated parasites, is known to be complex. I provide in this article a new method of implicitly listing all the potentially optimal solutions to the problem, by considering each hypothesised past association individually, in a structure I have termed a Jungle. These structures are demonstrated to enable fast acquisition of globally optimal solutions under general weighting schemes, including minimisation of total number of postulated events and maximization of postulated cospeciation events. A simple example is given, and the pocket gopher/chewing louse system investigated by Hafner and Nadler [Hafner and Nadler, Nature 332 (1988) 258] is re-examined.}, keywords = {animals, host parasite, Lice Infestations/parasitology/veterinary, Likelihood Functions, Mallophaga, Models, Biological, Phylogeny, Rodent Diseases/parasitology, Rodentia/parasitology}, isbn = {0025-5564}, author = {Charleston,Michael A.} } @article {39555, title = {Trees within trees: phylogeny and historical associations}, journal = {Trends in Ecology and Evolution}, volume = {13}, year = {1998}, month = {1998}, pages = {356 - 359}, abstract = {

The association between two or more lineages over evolutionary time is a recurrent theme spanning several different fields within biology, from molecular evolution to coevolution and biogeography. In each {\textquoteleft}historical association\&$\#$39;, one lineage is associated with another, and can be thought of as tracking the other over evolutionary time with a greater or lesser degree of fidelity. Examples include genes tracking organisms, parasites tracking hosts and organisms tracking geological and geographical changes. Parallels among these problems raise the tantalizing prospect that each is a special case of a more general problem, and that a single analytical tool can be applied to all three kinds of association.

}, author = {Page,Roderic D. M. and Charleston,Michael A.} } @article {39065, title = {Reconciled trees and incongruent gene and species trees}, journal = {Discrete Mathametics and Theoretical Computer Science}, volume = {37}, year = {1997}, month = {1997}, pages = {57 - 70}, abstract = {

We present a method for visualising and quantifying the relationship between a pair of gene and species trees that constructs a third tree termed a reconciled tree. Given a gene tree and a species tree the reconciled tree represents the history of the gene tree embedded within the species tree. The reconciled tree is constructed from one or more subtrees of the species tree, and contains the gene tree as a subtree. The relationship between the gene tree and the species tree can be expressed in terns of the number of gene duplications and gene losses required to construct the reconciled tree. This number can be used as an optimality criterion for selecting the species tree that best accounts for the observed gene tree.

}, url = {https://pdfs.semanticscholar.org/be60/40228f09daddc2001254850f4b54936dc0c0.pdf}, author = {Page,Roderic D. M. and Charleston,Michael A.} } @article {38837, title = {From gene to organismal phylogeny: reconciled trees and the gene tree / species tree problem}, journal = {Molecular Phylogenetics and Evolution}, volume = {7}, year = {1997}, month = {1997}, pages = {231 - 240}, abstract = {

The process of gene duplication, loss and lineage sorting can result in incongruence between the phylogenies of genes and those of species. This incongruence complicates the task of infering the latter from the former. We describe the use of reconciled trees to reconstruct the history of a gene tree with respect to a species tree. Reconciled trees allow the history of the gene tree to be visualized and also quantify the relationship between the two trees. The cost of a reconciled tree is the total number of duplications and gene losses required to reconcile a gene tree with its species tree. We describe the use of heuristic searches to find the species tree that yields the reconciled tree with the lowest cost. This method can be used to infer species trees from one or more gene trees.

}, url = {http://www.phthiraptera.info/sites/phthiraptera.info/files/0157.pdf}, author = {Page,Roderic D. M. and Charleston,Michael A.} }