I was wondering if there is any difference in using a phylogram or chronogram when performing PGLS. Is it one more correct than the other?
A phylogram is a branching diagram (tree) that is assumed to be an estimate of a phylogeny. The branch lengths are proportional to the amount of inferred evolutionary change
A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch spans.
Your choice of phylogram or chronogram depends on your question. Chronograms are ultrametric (i.e. all the path lengths from the root to the tips are equal, and proportional to the time since divergence). Phylograms on the other hand are non-ultrametric, where the branch lengths are proportional to the probability of character changes in the data. If you are investigating evolutionary rates on a time-calibrated phylogeny I would tend to an ultrametric tree (i.e. chronogram).
Take a look at this paper, this should hopefully make things clearer: Article Choice between phylogram and chronogram can have a dramatic ...
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