The simple Mk model provides a useful foundation for a number of innovative methods. These methods capture evolutionary processes that are more complicated than the original model, including models that vary through time or across clades. Modeling more than one discrete character at a time allows us to test for the correlated evolution of discrete characters.
Taken as a whole, chapters 7 through 9 provide a basis for the analysis of discrete characters on trees. One can test a variety of biologically relevant hypotheses about how these characters have changed along the branches of the tree of life.
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