Trends in Ecology & Evolution
Trees within trees: phylogeny and historical associations
Section snippets
Types of historical association
Historical associations can be divided into three basic categories (Table 1): genes and organisms, organisms and organisms, and organisms and areas. At the molecular level, each gene has a phylogenetic history that is intimately connected with, but not necessarily identical to, the history of the organisms in which the gene resides5, 6. Processes such as gene duplication, lineage sorting and horizontal transfer can produce complex gene trees that differ from organismal trees3, 7, 8.
Reconstructing the history of an association
Despite the relative lack of interaction among these different disciplines, strikingly similar concepts have arisen independently from them. Parasitologists16, 17recognized the problem of multiple parasite lineages decades before Fitch's[8]analogous distinction between paralogous and orthologous genes[18](Appendix A). Molecular systematists[19]and cladistic biogeographers[20]independently developed similar methods for interpreting the history of gene trees and biogeographic patterns,
`Jungles'
Reconciled trees have nice properties but also some limitations, the most severe being that they do not accommodate horizontal transfer. Other methods, such as Brooks' parsimony analysis (BPA)[4], do incorporate this process, but they do not always produce biologically reasonable reconstructions[33]. Horizontal transfer poses problems that have only recently been appreciated (Appendix C). Charleston[34]has developed a solution to this problem that employs a mathematical structure called a
Prospects
Methods for phylogenetic analysis of historical associations are still being refined, with considerable scope for future development. The analogy between the different categories of association has proved a useful heuristic tool, but detailed analogies between the processes may prove strained. More sophisticated analyses will require careful consideration of the actual processes operating in each association, especially if maximum likelihood methods are to be developed5, 35. Alternatively,
Acknowledgements
We thank Rob Cruickshank, Richard Griffiths, Vince Smith, Chris Simon and two anonymous reviewers for their comments. This work was supported by NERC grant GR3/1A095 to the first author.
References (40)
Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses
J. Mol. Biol.
(1995)- et al.
Lice and cospeciation: a response to Barker
Int. J. Parasitol.
(1996) - et al.
Nothofagus and Pacific biogeography
Cladistics
(1995) Preparing for the flood: evolutionary biology in the age of genomics
Trends Ecol. Evol.
(1996)- et al.
From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem
Mol. Phylog. Evol.
(1997) - et al.
Reconstruction of ancient molecular phylogeny
Mol. Phylog. Evol.
(1996) Jungles: a new solution to the host/parasite phylogeny reconciliation problem
Math. Biosci.
(1998)Parallel phylogenies: reconstructing the history of host–parasite assemblages
Cladistics
(1994)Reconstructing the history of host–parasite associations using generalised parsimony
Cladistics
(1995)Genes, organisms, and areas: the problem of multiple lineages
Syst. Biol.
(1993)