Phylogenetics for Dummies I: Optimization (Character Mapping)
The workshop covered the following topics: (A) What is optimization (or mapping)? (B) How are characters optimized? (C) What can be learned from optimization? We include brief instructions for analyzing your data in MacClade (Maddison and Maddison, 1992) [instructions are in brackets]. Note that MacClade is used for comparing trees that you give it, and for evaluating the implications of those trees for character evolution; it cannot generate a tree from character data. The program is also useful for generating data matrices for input into programs that can generate trees from the data.
(A) What is Optimization? Optimization is the process of inferring histories of character state transformations from a phylogeny. Optimization is also called mapping because the character states are "mapped" onto a branching diagram (a cladogram or tree) which depicts a hypothesis of the phylogeny of the taxa. The distributions of character states among the observed taxa and the branching pattern of the cladogram are used to infer the history of the character (which state was transformed into which other state, how many transformations were there and in which lineages did those transformations occur).
(B) How are Characters Optimized? The first step is to get a tree from the literature; the second is to create a data matrix of your characters and then the evolution of that character can be reconstructed in MacClade. Here is a simple example of tooth shape in nine taxa: