Extension modules are optional, and only needed for storing or retrieving the respective data types it accommodates. Language mappings should not expect these modules to be present if only core-schema data types are being persisted or retrieved.
A PhyloDB extension module for storing phylogenetic trees and taxonomies has been under development since December 2006 (started by Bill Piel and Hilmar Lapp at the Phyloinformatics Hackathon). The schema overview is a good place to start.
The module is in pre-release status and is only available via Git.
The schema module has undergone considerable extensions at the BioHackathon 2008, and is still subject to changes.