Emmanuel wrote --
2. I understand that the gamma-statistic index of Pybus and Harvey
applies only to ultrametric trees, there is a similar index for
trees that are not ultrametric?
The 'ultrametricity' of the tree gives it a temporal feature (if
done properly, of course), so that methods considering the tempo of
evolution can be used to analyse such trees. If you cannot get
ultrametric dated trees, see the package apTreeshape which has
methods to analyse tree shapes, but the range of inferences will
usually be less than with dated trees.
To rephrase what he said (but probably not change
the meaning), if the intent of the gamma statistic
is to measure the change through time of the speciation
rate (or the difference between the speciation and
extinction rates) then you need some way to
associate a time with each point in the tree.
Lacking an ultrametric tree, you don't have a
non-arbitrary way to do that.
Joe
----
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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