Many organisms have undergone dramatic range shifts in response to Quaternary climate change. Recent studies combining population genetic analyses, paleorecords, and species distribution models (SDMs) provide evidence that isolated pockets of favorable microclimates might have allowed small populations to persist in ‘cryptic refugia’ through the Last Glacial Maximum (LGM). The main objective of this study is to assess the locations of refugia for alder in the vast unglaciated areas with topographic complexity in Alaska and adjacent Canada. We obtained 570 foliar samples from 71 populations of a species complex (n=3 taxa) of Alnus, a common constituent of high-latitude vegetation. These samples were analyzed for RADSeq (restriction-site associated DNA sequencing) to assess genome-wide variation, yielding a high-spatial-resolution dataset. We use these results in conjunction with SDMs-based hindcasts of the probability of species presence during the LGM to infer the locations and dynamics of refugial populations.
For each of the three taxa sampled in the Alnus complex, our RADseq results and paleoSDMs provide evidence for multiple LGM refugia in isolated areas nested in a complex topography. The locations of these refugia differed among these closely related taxa, highlighting individualistic ecological and evolutionary responses to climate change. Alnus viridis subsp. fruticosa persisted in northwestern and eastern refugia, whereas populations of Alnus viridis subsp. sinuata survived the LGM in southwestern and southeastern Alaska. Alnus incana subsp. tenuifolia expanded locally from a distinct southern Alaska refugium. Pollen records from several decades of palynological research suggest glacial refugia of Alnus in southern and northwestern Alaska, without differentiation among these three taxa. Our data from RADseq analysis and paleoSDMs reveal taxon-specific refugia that are far more clear and complex than the pollen records. Moreover, comparing our tentative refugial locations with an Alaskan digital elevation model suggests landscape heterogeneity in unglaciated areas facilitated in situ persistence of multiple isolated populations through the LGM. Overall our results suggest that small populations of Alnus existed in a mosaic of high-latitude LGM refugia and that landscape heterogeneity played an important role in their responses to climate shifts.