We have combined traditional population genetic approaches with coalescent and graphical modeling techniques to gain insight into how deep-time geological and shallow-time climatic changes have influenced species distributions and the spatial organization of genetic variation. Mexico’s Baja California Peninsula is for us a model landscape in which to study large-scale patterns of spatial genetic structure. Numerous studies have used mtDNA sequences to quantify this structure in vertebrates, extrapolating common signals of deep-time vicariance events to other organisms. Sonoran Desert plants are frost intolerant, however, and, indeed, using sequence and marker data we have found that shallow-time climatic changes may over-write the deeper time patterns of vicariance in both plants (Euphorbia and Pachycereus) and their associated insects (pollinators and herbivores) (Nason et al. 2002; Garrick et al. 2009b; Kuester et al. 2012; Garrick et al. 2013). We have extended our phylogeographic analyses to the obligate pollination mutualism involving figs and fig wasps, both in the Sonoran Desert (Nason et al. in prep) and in Southeast Asia (Yu et al. 2010; Yu & Nason 2012).