Session 3: Comparative method: Tracing character evolution (RDMP)

[Lecture slides]

One hour practical in the Wolfson Bioinformatics Suite

One hour lecture in the seminar room

This session explores the use of phylogenies to infer character evolution. In the first half you will explore the construction and interpretation of evolutionary trees, then second half we will discuss how we can use these techniques to test specific evolutionary hypotheses.

Practical

The practical will introduce the programs MacClade and PAUP. After a short tutorial on using the programs (using the Caminalcules) we will use the program to visualise character evolution, and use it to test specific evolutionary hypotheses.

Learning objectives

At the end of this lab you should be able to:

• describe the parsimony method for reconstructing ancestral character states
• use the program MacClade to explore character evolution
• state evolutionary hypotheses explicitly in terms of patterns of character evolution

Seminar

The seminar discusses the problem of mapping characters on trees, which you will have encountered when playing with the Caminalcules data set. Some problems with estimating ancestral character states are reviewed. We then look at the comparative method, which provides a set of tools for investigating hypotheses about covariation among characters (for example, is there a relationship between the evolution of gregariousness and palatability in butterfly larvae?). A key notion is the need to accomodate the nonindependence of species -- because species are related by an evolutionary tree they are not independent. We briefly consider simple techniques for identifying pairs of independent species, and more efficient quantitative techniques.

Reading (avaible online or in course folder)

Overviews

Harvey, P. H. and M. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford. Chapter 2: Why worry about phylogeny?.

Harvey, P.H. and A Purvis. 1991. Comparative methods for explaining adaptations. Nature, 351: 619-624.

Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature, 401: 877-884. doi:10.1038/44766 [PDF]

Recent developments

Chang, B. S. W. and M. J. Donoghue (2000). Reconstructing ancestral proteins. TREE 15: 109-113. doi:10.1016/S0169-5347(99)01778-4.

Cunningham, C. W., K. E. Omland, and T. H. Oakley (1998) Reconstructing ancestral states: a critical reappraisal. TREE 13: 361-366.doi:10.1016/S0169-5347(98)01382-2

Martin, E. P. (2000). Adaptation and the comparative method. TREE 15: 296-299.doi:10.1016/S0169-5347(00)01880-2