Lost in a sagebrush sea: comparative genetic assessment of an isolated montane population of .

The montane sky islands of the Great Basin are characterized by unique, isolated habitats and communities that likely are vulnerable to extirpation with environmental change. A subspecies of yellow pine chipmunk, the Humboldt yellow pine chipmunk (), is associated with the whitebark and limber pine forests of the Pine Forest Range (PFR) in Nevada. We sampled and least chipmunks () from the isolated PFR and compared genetic diversity between these populations and more "mainland" populations, including other subspecies of chipmunks. Given the high frequency of hybridization in , we tested for hybridization between and in the PFR. We examined phylogenetic relationships, population divergence and diversity, and screened populations for a common pathogen, , to gain insight into population health. We found of the PFR are closely related to in the Warner Mountains and Sierra Nevada, but maintain substantively lower genetic variation. Microsatellite analyses show PFR are highly genetically differentiated from other populations. In contrast, PFR had higher genetic diversity that was comparable to the other population we sampled. Pathogen screening revealed that carried higher pathogen loads than in the PFR, although the prevalence of infection was similar to other populations. Our assessment of habitat associations suggests that the Humboldt yellow pine chipmunk almost entirely is restricted to the conifer systems of the PFR, while least chipmunks are prevalent in the other forests. Our work highlights the need for continued conservation and research efforts to identify how response to environmental change can be facilitated in isolated species and habitats.