I have been trying out this package recently for some other projects. There are several functions (e.g. PD, PSV, etc) that are very handy for looking at phylogenetic structure of the species in different communities — alpha and beta diversity. I think this will be a good tool for the second module, about phylogenetic diversity and biogeography of mammals.
Here is the webpage for the package: http://picante.r-forge.r-project.org/