A strength of the Bayesian approach we exploit in this paper is the ability to integrate together into a joint model of spatial locations X and aligned molecular sequence data Y~(Y 1 , . . . , Y N ) collected from the N taxa. The joint model affords a natural way to incorporate uncertainty about the unobserved phylogeny F and the character substitution process giving rise to Y. We take a standard statistical phylogenetic approach and assume that a separate CTMC characterized by w generates Y. While we discuss specific choices about this process in the Results sections, we do assume that the sequence and location CTMCs are independent given F, enabling us to write the joint model posterior distribution as Likelihoods Pr X jF, L ð Þ and Pr Yj F, w ð Þ follow directly from Felsenstein's pruning algorithm [15] , efficiently integrating over all possible locations and sequences at the root and internal nodes in F.