I just posted a version of the phytools function phylo.to.map, which can be used to project a tree onto a geographic map. Based on some user feedback, including at the Latin American Macroevolutionary Workshop we just held at the Universidad de los Andes in Bogotá, Colombia, I have added a couple of new features & attributes to the function.
First, the function now automatically removes the underscore character ("_") from within species names. Note that this is only for type="phylogram", not type="direct"; although in the latter case it can easily be done manually.
Second, again for type="phylogram", the lines connecting the tree to locations on a geographic map now (by default) arise from the end of the tip label - rather than from the tip itself.
Finally, third, the function now allows user control of the color of both the dashed lines & points connecting species labels to their geographic locations (for type="phylogram"); and of the both the lines and tip dot colors (for type="direct".
These updates are in the latest non-CRAN phytools build. Here's a quick demo:
> ## simulate some realistic looking data
> foo<-function() paste(c(sample(LETTERS,1),
> ## ok, first the (new) standard plot: