Understanding how climatic change impacts biological diversity is critical to conservation. Yet despite demonstrated effects of climatic perturbation on geographic ranges and population persistence, surprisingly little is known of the genetic response of species. Even less is known over ecologically long time scales pertinent to understanding the interplay between microevolution and environmental change. Here, we present a study of population variation by directly tracking genetic change and population size in two geographically widespread mammal species (Microtus montanus and Thomomys talpoides) during late-Holocene climatic change. We use ancient DNA to compare two independent estimates of population size (ecological and genetic) and corroborate our results with gene diversity and serial coalescent simulations. Our data and analyses indicate that, with population size decreasing at times of climatic change, some species will exhibit declining gene diversity as expected from simple population genetic models, whereas others will not. While our results could be consistent with selection, independent lines of evidence implicate differences in gene flow, which depends on the life history strategy of species.

We illustrate the use of Faith's 'Phylogenetic Diversity' measure to compare the phylogeographic structure of two bird species with patterns of avian endemism across six mountains in Cameroon and Equatorial Guinea. The Mountain Greenbul and Cameroon Blue-headed Sunbird showed phylogeographic patterns that together defined three biogeographic regions: Bioko, Mt. Cameroon, and the northern mountains of Cameroon. In contrast, the distributions of endemic species were largely a function of geographical distance, with close mountains sharing more endemic species than distant mountains. Moreover, for both species, populations on Mt. Cameroon were distinctive with respect to the ecologically relevant character bill size. Our results, while preliminary, illustrate the utility of a comparative approach for identifying geographical regions that harbour evolutionarily distinct populations and caution against using only the distributional patterns of endemics to prioritize regions for conservation. Results show that patterns of endemism may not be concordant with patterns of phylogenetic diversity nor morphological variation in a character important in fitness. While incorporation of additional species from unrelated taxa will be necessary to draw definitive conclusions about evolutionarily distinct regions, our preliminary results suggest a conservation approach for the Afromontane region of the Gulf of Guinea that would: (i) emphasize protection of both Bioko and Mt. Cameroon, thereby maximizing preservation of within-species phylogenetic and morphologic diversity; (ii) emphasize protection within the northern mountains to further conserve intraspecific phylogenetic diversity and maximize protection of endemic species.

The range of the Uinta ground squirrel, Spermophilus armatus, is centred over one of the most tectonically active regions today, the Yellowstone hotspot. We document the role of Quaternary tectonic and climatic history on the genetic structure of this species by screening museum and extant individuals throughout its range. Phylogeographic, divergence time, and demographic analyses of partial mitochondrial cytochrome b and control region DNA sequences yield insight into the cadence of evolution across three spatiotemporal scales: (i) a relatively deep intraspecific divergence of S. armatus into three lineages coincident with the last major volcanic eruption in the region and maintained by the Snake River Plain; (ii) demographic expansion in two lineages corresponding to the time of last deglaciation of the region; and (iii) a recent (< 50 years) local extinction of the third lineage coincident with climatic change and conversion of habitat for agricultural purposes in eastern Idaho. Beyond these inferences, our study highlights the unique value of museum material to phylogeography, and shows that small mammal recolonization of previously glaciated montane 'islands' differs from northward postglacial expansion observed in areas previously covered by continental ice sheets. Montane 'islands' may harbour high genetic diversity because of admixture and recurrent expansion/extinction.

Assessing the relative role of evolutionary processes on genetic diversity is critical for understanding species response to climatic change. However, many processes, independent of climate, can lead to the same genetic pattern. Because effective population size and gene flow are affected directly by abundance and dispersal, population ecology has the potential to profoundly influence patterns of genetic variation over microevolutionary timescales. Here, we use aDNA data and simulations to explore the influence of population ecology and Holocene climate change on genetic diversity of the Uinta ground squirrel (Spermophilus armatus). We examined phylochronology from three modern and two ancient populations spanning the climate transitions of the last 3000 years. Population genetic analyses based on summary statistics suggest that changes in genetic diversity and structure coincided with the Medieval Warm Period (MWP), c. 1000 years ago. Serial coalescent simulations allowed us to move beyond correlation with climate to statistically compare the likelihoods of alternative population histories given the observed data. The data best fit source-sink models that include large, mid-elevation populations that exchange many migrants and small populations at the elevational extremes. While the MWP is likely to have reduced genetic diversity, our model-testing approach revealed that MWP-driven changes in genetic structure were not better supported for the range of models explored. Our results point to the importance of species ecology in understanding responses to climate, and showcase the use of ancient genetic data and simulation-based inference for unraveling the relative roles of microevolutionary processes.