The nature of the phylogenetic tree determines how you interpret the
results of the analyses.
A phylogram has branch lengths measured in units of features used to
build the tree, for example base pairs or morphological characters.
A chronogram is calibrated so the branches are in units of time.
If you calculate PD using a cladogram then the value for a location
will be the number of branches. If you use a phylogram then it is
the number of features, while for a chronogram it is the sum of
PE is simply a range weighted PD measure (See Laffan et al. 2016,
), so for a cladogram it is
the sum of range weighted branches.
A phylogenetic analysis would typically use a a phylogram or
chronogram, but the cladogram can still be useful. It is actually
what is used as the alternate tree in the CANAPE analyses. (See
The above is not a definitive answer, but hopefully is useful.
There are also some members on the list who have experience
accessing and/or building phyogenetic trees, so hopefully they can
shed some light for you in that regard.