Long story about why, but essentially, very early in my graduate career I was interested in salticids. The distributional information on these species are quite well known. We are really interested in inferring rates of dispersal/vicariance based on the distributions of these species. We also have fossil records from this family (and other salticids) as well as quite extensive sequence data from extant members of the group.
The challenge has been this — all software that I know about for inferring dispersal/vicariance events (e.g., Lagrange, S-DIVA, RASP) don’t take account of known geographic history. This is because such software assumes that we don’t know when these areas split or converged. However, for groups with global distributions, and quite deep histories, we do know about the large-scale movements of continents, and we should be able to incorporate this information into our methods. At this point there is no way that I know of to do this.
Now, this also relates to the issue of the gene-tree/species-tree problem, but in a not-so-obvious way. The multi-species coalescent embeds the gene genealogies within the species phylogeny. This allows us to take account of multiple gene histories and reconstruct the species history. StarBEAST does this, as does BEST. There is a parallel here with the biogeography situation — we are embedding species phylogenies within area histories. The difference is this — area histories can be networks rather than trees.
So, at present there is no way that I know of, either with biogeographies or the multi-species coalescent, to specify the known tree/network of the larger process (i.e., either the larger species tree which contains the gene trees, or the larger area tree that contains the species phylogenies). I don’t think that this is theoretically difficult — its just that no one seems to do it this way.