Again phytools comes to the rescue….

I thought overlaying a phylogenetic tree onto a map would be easy – little bit of ancestral state reconstruction to place the nodes of the tree onto the map and away we go. Yet I’ve been mucking around for weeks trying to do it. I think the error of the ancestral states have been making my overlay look pretty strange (I’ve been using ML/REML reconstruction methods in package ape).  Feeling annoyed at my self for not being able to solve a relatively simple problem, I went looking for another option and I found this: http://blog.phytools.org/2013/07/new-phylotomap-with-direct-projection.html.  It doesn’t do ancestral states, the graphics are enough to show the spatial dimensions of my phylogeny. Phytools may again be my top R package of the month!