Trends in Ecology & Evolution
Volume 13, Issue 9, 1 September 1998, Pages 356-359
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Trees within trees: phylogeny and historical associations

https://doi.org/10.1016/S0169-5347(98)01438-4Get rights and content

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 `historical association', 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.

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.

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