In the case of biodiversity, diversity is basically the number of different species present. Phylogenetic diversity is the differences between species in terms of their evolutionary history.
A phylogenetic tree is the foundation from which phylogenetic diversity can be estimated. Such a tree ideally represents both time and character differences between species. Character differences can either by in physical properties such as the number of legs, or differences in DNA sequences.
In the Spatial Portal, phylogenetic diversity is based on any available phylogenetic tree and any defined area. The output is the phylogenetic diversity of the species in the tree within the defined area.
More information can be found at Tools | phylogenetic diversity.