VI. Testing Temporal Patterns of Character Evolution in R

Primary Contact(s)	Created	Required Software
Rich Glor	9 March 2009	R
Example Datafile	Prerequisites
See Introduction	R for Phylogenetics parts I, II, III, IV, and V

Introduction|I. Getting Started|II. Tree Basics|III. Loading Character Data|IV. Testing Phylogenetic Signal|V. Ancestral Reconstruction|VI. Testing Patterns

Just as it's possible to use R to test phylogenetic signal by manipulating branch lengths, it is also possible to investigate the temporal pattern of sequence evolution with branch length transformations in R. The method known as Delta, which was introduced by Pagel is the most widely-used approach.

1. First let's get an idea of what Delta does to our our trees.

deltaTransform(anolisComparativeTree, 0) -> anolisDelta0
deltaTransform(anolisComparativeTree, 0.5) -> anolisDelta0.5
deltaTransform(anolisComparativeTree, 50) -> anolisDelta50

and plot these trees:

par(mfcol=c(1,4)) 
plot(anolisComparativeData)
plot(anolisDeta0)
plot(anolisDeta0.5)
plot(anolisDeta50)

2. Now let's see what value of Delta best fits our data.

fitDiscrete(anolisComparativeTree, micro, treeTransform="delta")