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Nearly 10 years ago I began wittering on Taxacom about the lack of explicit locations in phylogenies. There are identities at nodes (ancestors) but no addresses for those identities, which makes the phylogeny placeless.
IMO, that's created a blind spot in the field of view of many phylogenetics practitioners. Since they can't *see* location in their trees, they don't think about it, or they regard historical biogeography as something too vague to be bothered with. Yet nearly everyone would agree that an evolutionary history must include both the times and places of events, or it isn't a history. Instead, it's just a sketch of possible relationships, divorced from the biogeographical reality in which every living thing, past and present, has or has had an address.
An article in the latest issue of Systematic Biology attempts to address the placelessness of phylogenies by generating space-time diagrams with explicit procedures:
Kidd, D.M. 2010. Geophylogenies and the Map of Life. Systematic Biology 59(6): 741-752.