![]() Most species are found in Asia and Eastern Europe with one North American congener in Alaska and Canada, O. The American pika is one of only 30 Ochotonidae species worldwide. Talus (rocky slopes formed by freeze–thaw processes) provides thermal refuge for the pika, which has a relatively narrow thermal tolerance, and thus relies heavily on the stable thermal microclimate provided by the interstitial spaces of this rocky habitat. This small lagomorph is found in the mountainous regions of western North America where it lives primarily on talus slopes above timberline. The American pika has become a canary-in-the-coal-mine for the effects of anthropogenic climate change in montane habitats, as a result of extensive extirpations from warmer, lower elevation sites over the past two decades. We consider variation across geographic scales shaped by both historical (Pleistocene-era) and contemporary levels of connectivity. Here we examine extant genetic variation within and among American pika ( Ochotona princeps) populations sampled from diverse habitats across the western United States. Therefore, in addition to habitat predictors of persistence, connectivity among habitat patches via gene flow may be critical to maintain genetic diversity and evolutionary potential within species. Although the complex topography and temporal variability of mountain ecosystems may offer refugia across relatively small spatial scales (kilometers), anthropogenic climate change threatens to test the limits of such microhabitat buffering. For widely dispersed alpine mammals that are already constrained by warming ambient air temperatures, the habitat characteristics that correlate with population persistence across mountain ranges will help define those areas where refugia may be found. ![]() The impact of global climate change on species with wide geographic distributions is of particular interest given the greater likelihood that refugia from climate-mediated extirpations may exist for these taxa. Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada. Tajima’s D was positive for all sites ( D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. These effects have been exacerbated for the American pika ( Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations.
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