Understanding the factors that contribute to the formation of population genetic structure is a central goal of phylogeographic research, but achieving this goal can be complicated by the stochastic variance inherent to genetic processes. Statistical approaches to testing phylogeographic hypotheses accommodate this stochasticity by evaluating competing models of putative historical population structure, often by simulating null distributions of the expected variance. The effectiveness of these tests depends on the biological realism of the models. Information from the fossil record can aid in reconstructing the historical distributions of some taxa.However, for the majority of taxa, which lack sufficient fossils, paleodistributional modeling can provide valuable spatial-geographic data concerning ancestral distributions. Paleodistributional models are generated by projecting ecological niche models, which predict the current distribution of each species, onto a model of past climatic conditions. Here, we generate paleodistributional models describing the suitable habitat during the last glacial maximum for lineages from the mesic forests of the Pacific Northwest of North America, and use these models to generate alternative phylogeographic hypotheses. Coalescent simulations are then used to test these hypotheses to improve our understanding of the historical events that promoted the formation of population genetic structure in this ecosystem. Results from Pacific Northwest mesic forest organisms demonstrate the utility of these combined approaches. Paleodistribution models and population genetic structure are congruent across three amphibian lineages, suggesting that they have responded in a concerted manner to environmental change. Two other species, a willow and a water vole, despite being currently codistributed and having similar population genetic structure, were predicted by the paleodistributional model to have had markedly different distributions during the last glacial maximum. This suggests that congruent phylogeographic patterns can arise from incongruent ancestral distributions. Paleodistributional models introduce a much-needed spatial-geographic perspective to statistical phylogeography. In conjunction with coalescent models of population genetic structure, they have the potential to improve our understanding of the factors that promote population divergence and ultimately produce regional patterns of biodiversity.

Statistical phylogeographic studies contribute to our understanding of the factors that influence population divergence and speciation, and that ultimately generate biogeographical patterns. The use of coalescent modelling for analyses of genetic data provides a framework for statistically testing alternative hypotheses about the timing and pattern of divergence. However, the extent to which such approaches contribute to our understanding of biogeography depends on how well the alternative hypotheses chosen capture relevant aspects of species histories. New modelling techniques, which explicitly incorporate spatio‐geographic data external to the gene trees themselves, provide a means for generating realistic phylogeographic hypotheses, even for taxa without a detailed fossil record. Here we illustrate how two such techniques – species distribution modelling and its historical extension, palaeodistribution modelling – in conjunction with coalescent simulations can be used to generate and test alternative hypotheses. In doing so, we highlight a few key studies that have creatively integrated both historical geographic and genetic data and argue for the wider incorporation of such explicit integrations in biogeographical studies.

Determining what factors affect the structuring of genetic variation is key to deciphering the relative roles of different evolutionary processes in species differentiation. Such information is especially critical to understanding how the frequent shifts and fragmentation of species distributions during the Pleistocene translates into species differences, and why the effect of such rapid climate change on patterns of species diversity varies among taxa. Studies of mitochondrial DNA (mtDNA) have detected significant population structure in many species, including those directly impacted by the glacial cycles. Yet, understanding the ultimate consequence of such structure, as it relates to how species divergence occurs, requires demonstration that such patterns are also shared with genomic patterns of differentiation. Here we present analyses of amplified fragment length polymorphisms (AFLPs) in the montane grasshopper Melanoplus oregonensis to assess the evolutionary significance of past demographic events and associated drift-induced divergence as inferred from mtDNA. As an inhabitant of the sky islands of the northern Rocky Mountains, this species was subject to repeated and frequent shifts in species distribution in response to the many glacial cycles. Nevertheless, significant genetic structuring of M. oregonensis is evident at two different geographic and temporal scales: recent divergence associated with the recolonization of the montane meadows in individual sky islands, as well as older divergence associated with displacements into regional glacial refugia. The genomic analyses indicate that drift-induced divergence, despite the lack of long-standing geographic barriers, has significantly contributed to species divergence during the Pleistocene. Moreover, the finding that divergence associated with past demographic events involves the repartitioning of ancestral variation without significant reductions of genomic diversity has intriguing implications - namely, the further amplification of drift-induced divergence by selection.

Evolutionarily significant units (ESUs) differ in the extent to which they capture, or even consider, adaptive variation, and most such designations are based solely on neutral genetic differences that may not capture variation relevant to species' adaptabilities to changing environmental conditions. While concordant patterns of divergence among data sets (i.e. neutral and potentially non-neutral characters) can strengthen ESU designations, determining whether such criteria are met for highly variable taxa is especially challenging. This study tests whether previously defined ESUs for endangered Panamanian golden frogs (Atelopus varius and Atelopus zeteki) exhibit concordant variation among multiple phenotypic traits and mitochondrial DNA sequences, and the extent to which such divergence corresponds to environmental differences. Multivariate analyses identify phenotypic and genetic differentiation consistent with proposed ESUs and support the status of A. varius and A. zeteki as separate species. Moreover, the significant association detected between ESU co-membership and genetic similarity, which remained strong after removing the effect of geographic distance, also indicates that genetic differences are not simply due to isolation by distance. Two phenotypic characters (body size and the extent of dorsal black patterning) that differ among ESUs also co-vary with environmental differences, suggesting that to the extent that these phenotypic differences are heritable, variation may be associated with adaptive divergence. Lastly, discriminant function analyses show that the frogs can be correctly assigned to ESUs based on simultaneous analysis of multiple characters. The study confirms the merit of conserving the previously proposed golden frog ESUs as well as demonstrates the utility and feasibility of combined analyses of ecological, morphological and genetic variation in evaluating ESUs, especially for highly variable taxa.